# ent

id: cord-000562-ocp6yodg
type: DISEASE
entity:
  influenza A H1N1 2009 close contacts of cases were traced to provide antiviral prophylaxis within 48 h after exposure and to alert them on signs of disease


id: cord-000562-ocp6yodg
type: DISEASE
entity:
  influenza A H1N1 virus via global airline transportation Calculating the potential for withinflight transmission of influenza A H1N1


id: cord-000562-ocp6yodg
type: DISEASE
entity:
  influenza A H1N1 virus kinetics and symptom dynamics Household transmission of pandemic 2009 influenza A H1N1 virus in Osaka Contacting passengers after exposure to measles on an international flight


id: cord-000280-zyaj90nh
type: DISEASE
entity:
  influenza A H1N1 vaccination OR 4 03 95 IC 2 03 7 98 Washing hands before and between patient contact however was negatively independently associated with willingness


id: cord-000963-pwz6rde0
type: ORG
entity:
  Colombo Epidemiology Unit Ministry of Health Care and Nutrition World Health Organization Human Leptospirosis Guidance


id: cord-000268-480d3yfv
type: PROTEIN
entity:
  nTREM 1 above 2 55 MFI Sensitivity and Lung cancer 13 Staphulococcus aureus 3 Pulmonary embolism 6 Haemophilus influenzae 2 Congestive heart failure 5 Pseudomonas aeruginosa 2


id: cord-000268-480d3yfv
type: DISEASE
entity:
  noninfectious processes like peptic ulcer inflammatory bowel disease viral infections malignant pleural effusions


id: cord-001050-lq9tp20z
type: CHEMICAL
entity:
  penicillin oxacillin kanamycin tobramycin gentamicin erythromycin clindamycin tetracycline ofloxacin fusidic acid rifampicin vancomycin teicoplanin fosfomycin trimethoprimsulfamethoxazole


id: cord-261251-ylvqxpba
type: GGP
entity:
  Kaposi s sarcoma associated herpesvirusrelated primary effusion lymphoma Human herpesvirus 8 associated hemophagocytic lymphohistiocytosis


id: cord-261251-ylvqxpba
type: GGP
entity:
  HHV 8 Fatal hemophagocytic syndrome related to active human herpesvirus 8 Kaposi sarcomaassociated herpesvirus


id: cord-258611-uzzs8w1j
type: DNA
entity:
  human metapneumo virus hMPV human respiratory syncytial virus hRSV and human coronaviruses HKU1 229E


id: cord-258611-uzzs8w1j
type: DISEASE
entity:
  influenza B virus 4 for metapneumo virus 2 for respiratory syncytial virus and 3 for human coronavirus


id: cord-000534-ztc5holk
type: DISEASE
entity:
  influenza A H1N1 pandemic in the USA The transmissibility and control of pandemic influenza A H1N1 virus Dutch New Influenza A H1N1 v Investigation Team Epidemiology


id: cord-000534-ztc5holk
type: DISEASE
entity:
  influenza A H1N1 virus and its age specificity in Japan Pros and cons of estimating the reproduction number


id: cord-004488-r50atew9
type: WORK_OF_ART
entity:
  Understanding the Direction of Bias in Studies of Diagnostic Test Accuracy Evaluation of six commercial point


id: cord-274749-ji91qq9q
type: DISEASE
entity:
  respiratory syncytial virus RSV influenza virus INF types A and B adenovirus AV parainfluenza virus PIV human metapneumovirus HMPV and rhinovirus RV 3 4 5


id: cord-276857-i948aq4b
type: CELL_TYPE
entity:
  viral samples T T T TC29 T G T T ND T C 3 0 T G T T T TC32 T G T T ND T C 3 4 T G T T T T C 3 7 T G T T T T C 3 8 T G T T T T C 3 9 T G T T T T C 4 1 T G T T T T C 4 2 T G T T T T C 4 3 T G T T T T C 4 4 T G T T T TC45 T G T T ND TC46 T G T T ND T C 4 8 T G T T T TC51 T G T T ND T C 5 2 T G T T T TC55 T G T T ND TC59 T G T T


id: cord-276857-i948aq4b
type: GGP
entity:
  TC45 T G T T ND TC46 T G T T ND T C 4 8 T G T T T TC51 T G T T ND T C 5 2 T G T T T TC55 T G T T ND TC59 T G T T


id: cord-276857-i948aq4b
type: CHEMICAL
entity:
  TC32 T G T T ND T C 3 4 T G T T T T C 3 7 T G T T T T C 3 8 T G T T T T C 3 9 T G T T T T C 4 1 T G T T T T C 4 2 T G T T T T C 4 3 T G T T T T C 4 4 T G T T T


id: cord-048489-ajafw966
type: PROTEIN
entity:
  IL 1β IL 2 IL 4 IL 5 IL 6 IL 7 CXCL8 IL 8 IL 10 IL 12 p70 IL 13 IL 17 granulocyte colony stimulating factor G CSF granulocyte monocyte colony stimulating factor GM CSF monocyte chemoattractive protein MCP 1


id: cord-048489-ajafw966
type: WORK_OF_ART
entity:
  French Polynesia Correlation Of Serum Levels Of Macrophage Migration Inhibitory Factor With Disease Severity And Clinical Outcome


id: cord-048489-ajafw966
type: DISEASE
entity:
  capillary fragility skin haemorrhages epistaxis gingival gastrointestinal or urinary tract haemorrhage


id: cord-004198-h8ch3x14
type: ORG
entity:
  EPHA Ethiopian Public Health Association HIV Human Immunodeficiency Virus HSTP Health Sector Transformation Plan


id: cord-004198-h8ch3x14
type: ORG
entity:
  PMTCT Prevention of Mother to Child Transmission SPSS Statistical Package for Social Science UNAIDS Joint United Nations Programme


id: cord-011671-7mki5dp9
type: GGP
entity:
  C I 1 10 2 11 P 0 01 Fig 6 No significant heterogeneity was found among studies I 2 0 P 0 48 The symmetrical funnel


id: cord-252304-lwiulri7
type: PROTEIN
entity:
  ceruloplasmin CP vitamin K dependent protein S complement factor properdin antithrombin III secretory component p85 complement factor C1r C1r complement factor C1s angiotensin factor 2 anti factor VIII serum amyloide P component olfactomedin 4 OLFM4 thrombospondin gelsolin platelet factor 4 PF4 complement factor C1q complement factor B moesin


id: cord-252304-lwiulri7
type: PROTEIN
entity:
  globe Complement factor 1R CI Confidence Interval CP ceruloplasmin DF Dengue Fever DIGE Difference Gel Electrophoresis DV Dengue Virus ELISA Enzyme


id: cord-252304-lwiulri7
type: GGP
entity:
  OLFM4 thrombospondin gelsolin platelet factor 4 PF4 complement factor C1q complement factor B moesin


id: cord-252304-lwiulri7
type: WORK_OF_ART
entity:
  Acute Phase Response Signaling the Complement System and the Coagulation System with Prothrombin Activation


id: cord-278508-h145cxlp
type: DNA
entity:
  European countries 28 29 30 31 In Germany paediatric influenza vaccination for pandemic influenza A H1N1 pdm09


id: cord-008584-4eylgtbc
type: ORG
entity:
  the National Influenza Reference Laboratory National Centre for Microbiology World Health Organization National Influenza Centre


id: cord-284393-s9qp9a4e
type: ORG
entity:
  humans National Health Commission of the People s Republic of China National Health Commission of China Clinical


id: cord-271813-nroflfmc
type: ORG
entity:
  Chongqing Public Health Medical Center Yongchuan Affiliated Hospital of Chongqing Medical University


id: cord-282898-hsqvkm2i
type: ORG
entity:
  the National Committee for Clinical Laboratory Standards Clinical and Laboratory Standards Institute


id: cord-004395-erqmbi2b
type: PROTEIN
entity:
  E or L represent early or late time sampling points respectively the 2 computational tools Pearson s correlation coefficient was used Number of experimental assays compared to computationally guided prediction assay projections To experimentally determine epitopes


id: cord-004395-erqmbi2b
type: DISEASE
entity:
  human immunodeficiency virus across multiple ethnicities CD8 T cell recognition of multiple epitopes within specific gag regions


id: cord-012954-3x3rkor5
type: ORG
entity:
  Department of Infectious Diseases Division of Internal Medicine Academic Medical Center University of Amsterdam Amsterdam


id: cord-274438-tgslabi2
type: DISEASE
entity:
  Influenza A H1N1 or B n 42 Rhinovirus n 99 Bocavirus n 23 Adenovirus n 18 Parainfluenza 1 2 3 or 4 n 36 Coronavirus NL63 229E OC43


id: cord-035280-z0bbz19b
type: PROTEIN
entity:
  human Rickettsia tsutsugamuskh antibody Human ehrlichiosis and anaplasmosis Anaplasma phagocytophilum


id: cord-011601-1u1rlwzp
type: ORG
entity:
  the Associate Director for Science Center for Global Health US Centers for Disease Control and Prevention Atlanta


id: cord-274123-wgigtgl9
type: PROTEIN
entity:
  Moraxella catarrhalis 64 S pneumoniae 42 H influenzae spp 29 and Staphylococcus aureus 22 Table 2 M pneumoniae 9 B pertussis 7


id: cord-274123-wgigtgl9
type: TAXON
entity:
  adenovirus parainfluenza 1 hMPV bocavirus C pneumoniae S pneumoniae H influenzae type b M catarrhalis influenza virus C virus


id: cord-281916-v6u5mr2i
type: DNA
entity:
  ERV3 human endogenous retrovirus 3 Flu influenzae virus HBoV human bocavirus HCoV human coronavirus hMPV human metapneumovirus PCR polymerase chain reaction PIV paraInfluenza virus RhV EV rhino entero virus RNA ribonucleic acid ROC receiver


id: cord-287367-1sdt9zz8
type: TAXON
entity:
  adenovirus coronaviruses HKU1 NL63 229E and OC43 human metapneumovirus human rhinovirus enterovirus parainfluenza virus types


id: cord-287367-1sdt9zz8
type: DISEASE
entity:
  influenza A H1N1 pdm09 matrix gene RNA 1 and H1 RNA influenza A virus RNA influenza B virus RNA rhinovirus RNA RSV


id: cord-272240-s1gnwb2s
type: CELL_LINE
entity:
  radio Trend χ2 14 80 P 0 00 Moreover 12 79 of participants chose consult doctor which was significantly higher in males than in females 16 08 vs 11 10 Regarding the preventive measures 80 76 of participants reported washing hands more often than usual which was significantly higher P 0 05 in females 82 25 than in males 77 59 In addition a total of 68 27 reported ventilating rooms


id: cord-272240-s1gnwb2s
type: ORG
entity:
  Search Better than Structured Instruction for Web Based Health Education Stud Health Technol Inform Widespread


id: cord-272207-jtvf257r
type: ORG
entity:
  State Trait Anxiety Inventory A Test Manual Test Form Center for Health Protection Hong Kong Government


id: cord-004643-uu4uipfy
type: DNA
entity:
  SRX6852761 SRX6852760 SRX6852759 SRX6852758 SRX6852757 SRX6852756 SRX6852755 and SRR10236626 respectively Ethics approval


id: cord-269772-4zrmsw2f
type: ORG
entity:
  the Institute of Epidemiology and Preventive Medicine College of Public Health National Taiwan University


id: cord-269772-4zrmsw2f
type: ORG
entity:
  St Mary s Junior College of Medicine Nursing and Management Central Taiwan University of Science and Technology Taiwan Shoufu University


id: cord-282533-w6kl74c8
type: PROTEIN
entity:
  NL63 Cov HKU1 NL63 229E OC43 human metapneumovirus hMPV RSV human rhinovirus enterovirus Rhino Entero C pneumoniae M pneumoniae


id: cord-282533-w6kl74c8
type: DISEASE
entity:
  FluA H1 FluA 2009H1 FluA H3 and FluB parainfluenza virus types 1 to 4 Para 1 4 coronaviruses 229E HKU1 OC43 and NL63 Cov HKU1 NL63 229E OC43 human metapneumovirus hMPV RSV human rhinovirus enterovirus Rhino Entero C


id: cord-288372-48wao8a0
type: PROTEIN
entity:
  PIV3 6 PIV4 8 7 7 human respiratory syncytial viruses 6 RSV A and 1 RSV B 4 7 6 coronaviruses 4 coronaviruses NL63


id: cord-288372-48wao8a0
type: TAXON
entity:
  human respiratory syncytial virus B human adenovirus human metapneumovirus human coronavirus 229E human coronavirus NL63 human coronavirus OC43 human


id: cord-288372-48wao8a0
type: DISEASE
entity:
  influenza A virus influenza B virus human respiratory syncytial virus A human respiratory syncytial virus B human adenovirus human metapneumovirus human coronavirus 229E human coronavirus NL63 human coronavirus OC43 human parainfluenza virus 1 2 3 4 human rhinovirus A B C human enterovirus and human bocavirus Reactions


id: cord-288372-48wao8a0
type: DISEASE
entity:
  influenza B viruses influenza viruses represented 45 67 150 of viruses detected This influenza detection rate was expected as the enrollment of patients was directed towards patients with ILI


id: cord-272194-h7xnr389
type: DISEASE
entity:
  respiratory syncytial virus infection Respiratory syncytial virus morbidity premorbid factors seasonality


id: cord-275211-1b56a6zc
type: DISEASE
entity:
  influenza A virus infA influenza B virus infB respiratory syncytial virus RSV adenovirus ADV enterovirus EV human metapneumovirus HMPV


id: cord-001512-u3u2k8hj
type: DISEASE
entity:
  influenza A H7N9 virus in Jiangsu Province Global concerns regarding novel influenza A H7N9 virus infections


id: cord-285976-l7voruz7
type: ORG
entity:
  the Department of Epidemiology and Biostatistics School of Public Health Cheeloo College of Medicine Shandong University


id: cord-285976-l7voruz7
type: WORK_OF_ART
entity:
  Improving Estimates of Insecticides Treated Mosquito Net Coverage from Household Surveys Using Geographic Coordinates


id: cord-285976-l7voruz7
type: WORK_OF_ART
entity:
  Demographic and Health Surveys DHS ICF International Incorporating Geographic Information into Demographic and Health Surveys A Field Guide


id: cord-291393-iht5zndl
type: DISEASE
entity:
  viral adenovirus coronaviruses 229E HKU1 NL63 OC43 influenza viruses rhinovirus enterovirus etc or bacterial Bordetella pertussis


id: cord-290432-4dli5emd
type: GGP
entity:
  ARIwC p 0 432 nor any differences within and between age groupings ie 6 months 6 12 months 12 24 months and 24 months p 0 529 Overall 133 164 81 nasal swabs were positive for at least one organism 131 79 9 for any bacteria 59 36 2


id: cord-294062-3esrg1jw
type: DNA
entity:
  illnessFTDFast Track DiagnosticsCtCycle thresholdHi BHaemophilus influenzae type BHi nonBnon type B Haemophilus influenzaeIQRInterquartile


id: cord-288972-dc6xbxha
type: DISEASE
entity:
  influenza A H1N1 virus via global airline transportation World Health Organization Pandemic influenza preparedness


id: cord-293858-dk4snw9r
type: ORG
entity:
  the Research Fund Secretariat Food and Health Bureau the Government of the Hong Kong Special Administrative Region


id: cord-293858-dk4snw9r
type: ORG
entity:
  Hong Kong Australian Institute of Health and Welfare Department of Health of the Australian Government


id: cord-292609-e99y0l5a
type: ORG
entity:
  the Committee of Animal Welfare and Ethics of Veterinary Research Institute Academy of Military Medical Sciences Humane


id: cord-297494-6yxmaihl
type: GGP
entity:
  Sugihiro Hamaguchi 1 9 Shungo Katoh 1 9 Satoshi Kakiuchi 9 Emi Kitashoji 9 Takaharu Shimazaki 9 Masahiro Takaki 9 Additional file 1 Table S1 Proportion of


id: cord-297494-6yxmaihl
type: ORG
entity:
  the Institute of Tropical Medicine Nagasaki University Ebetsu City Hospital Kameda Medical Center Chikamori Hospital


id: cord-297494-6yxmaihl
type: DISEASE
entity:
  diabetes mellitus cerebrovascular disease dementia neuromuscular disease cardiac failure ischaemic heart disease


id: cord-296868-fn4gzsw1
type: ORG
entity:
  influenza World Health Organization Working Group on International and Community Transmission of SARS Public


id: cord-300116-r93w4jm3
type: TAXON
entity:
  rhinovirus respiratory syncytial virus parainfluenza virus adenovirus coronavirus human metapneumovirus


id: cord-300116-r93w4jm3
type: CHEMICAL
entity:
  Streptococcus Prevotella Veillonella Type 2 Streptococcus Haemophilus Neisseria Type 3 Streptococcus Type 4 Moraxella


id: cord-296375-gf0mgz5x
type: DNA
entity:
  Heilongjiang Shanghai Jiangsu Zhejiang Anhui Jiangxi Shandong Henan Hubei Hunan Chongqing and Sichuan


id: cord-296375-gf0mgz5x
type: ORG
entity:
  World Health Organization Cumulative Number of Reported Probable Cases of Severe Acute Respiratory Syndrome SARS World Health Organization Clinical Characteristics of Coronavirus Disease 2019


id: cord-292828-29jbf9ik
type: CHEMICAL
entity:
  Asma N Whiley David M Bialasiewicz Seweryn Lambert Stephen B Ware Robert S Nissen Michael D Sloots Theo P Grimwood Keith title Nasal swab


id: cord-303196-ltmu3ncu
type: ORG
entity:
  Clınicas da Universidade Federal de Pernambuco United Nations Department of Economic and Social Affairs


id: cord-299750-zkrlm3ds
type: GGP
entity:
  CRP C reactive protein LDH lactic dehydrogenase CK creatine kinase AST glutamic oxaloacetic transaminase ALT glutamic


id: cord-299750-zkrlm3ds
type: DISEASE
entity:
  influenza A H1N1 virus in Mexico a retrospective analysis Pandemic Influenza A H1N1 Virus Hospitalizations


id: cord-311382-ioemd0ij
type: ORG
entity:
  Control Influenza Transmission Characterization of Aerosols Generated During Patient Care Activities Influenza


id: cord-298899-lkrmg5qr
type: GPE
entity:
  the Republic of Korea Special Expert Group for Control of the Epidemic of Novel Coronavirus Pneumonia


id: cord-312544-vip4jtlv
type: DISEASE
entity:
  influenza A virus subtype H5N1 detection We thank Jer Ming Chia Martin L Hibberd Christopher W Wong and Jian Jun Liu Genome Institute of Singapore No Na Yeoh Geok Huai Ong and Rafidah Ahmad Johari Veterinary Research Institute Malaysia Fook


id: cord-313529-xm76ae08
type: TAXON
entity:
  virus parainfluenza virus 1 2 3 4 respiratory syncytial virus adenovirus enterovirus human metapneumovirus human coronavirus 229E OC43 NL63 HKU1 Mycoplasma


id: cord-313529-xm76ae08
type: DISEASE
entity:
  influenza A virus influenza B virus parainfluenza virus 1 2 3 4 respiratory syncytial virus adenovirus enterovirus human metapneumovirus human coronavirus 229E OC43 NL63 HKU1 Mycoplasma


id: cord-313529-xm76ae08
type: DISEASE
entity:
  human rhinoviruses paramyxoviruses coronaviruses and bocavirus during acute respiratory tract infections


id: cord-319504-jb455t9p
type: WORK_OF_ART
entity:
  Preventing Transmission of Pandemic Influenza and Other Viral Respiratory Diseases Personal Protective Equipment for Healthcare Personnel Update Non


id: cord-318340-hptjqmrl
type: ORG
entity:
  Ministry of Health Protocol of Surveillance Investigation and Management for Pneumonia of Unknown Etiology Investigation


id: cord-324880-s1oqkqef
type: PROTEIN
entity:
  Streptococcus mitis Streptococcus parasanguinis Streptococcus pneumoniae Streptococcus salivarius Streptococcus infantis Streptococcus suis Neisseria meningitidis Neisseria gonorrhoeae Haemophilus sputorum Haemophilus parainfluenzae Enterococcus cecorum


id: cord-312522-mymgnf8z
type: PROTEIN
entity:
  Mycoplasma tuberculosis 27 28 Neisseria gonorrhoeae Salmonella enterica and methicillin resistant Staphylococcus aureus MRSA 29 Chlamydia trachomatis 30 Francisella tularensis 31 Group B Streptococci 32 Orientia tsutsugamushi scrub typhus and Rickettsia typhi murine typhus 16


id: cord-312522-mymgnf8z
type: ORG
entity:
  UNprepared Executive Order Combating Antibiotic Resistant Bacteria National Action Plan for Combating Antibiotic Resistant


id: cord-334424-z7ygy25e
type: DISEASE
entity:
  influenza viruses rhinoviruses HRVs adenoviruses respiratory syncytial virus RSV and parainfluenza viruses PIVs


id: cord-321235-h3w8827o
type: EVENT
entity:
  Wuhan China Incubation Period and Other Epidemiological Characteristics of Novel Coronavirus Infections with Right Truncation A Statistical Analysis of Publicly Available Case Data


id: cord-321704-jozrgcq3
type: DISEASE
entity:
  Coronavirus HKU1 CoV HKU1 Parainfluenza 1 hPIV 1 hPIV 2 hPIV 4 Influenza A H1N1 the prepandemic strain respiratory syncytial virus A RSV A RSV B CoV


id: cord-320928-flsaa1wx
type: GGP
entity:
  n 21 11 2 P 0 001 Junior HCWs with work experience of 5 years 35 4 had the highest rate of negative perception of knowledge transfer P 0 001 Table 3 HCWs 40 years old PMS 73 4 18 9


id: cord-321848-qys8r6jo
type: DISEASE
entity:
  human adenovirus coronaviruses parainfluenza viruses influenza A virus influenza B virus respiratory syncytial virus A


id: cord-338054-n2r4pzan
type: DISEASE
entity:
  protective behaviors Table 2 The majority of the respondents believed that various groups of people would be highly susceptible to the virus Of the respondents 26 8 believed themselves and 33 6 believed their family members or the general public


id: cord-337028-8fh4pe3i
type: CELL_TYPE
entity:
  human corneal epithelial cells Keratinocyte chemoattractant KC human growth regulated oncogene GRO chemokines


id: cord-328501-mbwgi56x
type: TAXON
entity:
  Mycoplasma pneumoniae Chlamydophila pneumoniae Legionella pneumomophila Streptococcus pneumoniae Neisseria meningitides


id: cord-328501-mbwgi56x
type: ORG
entity:
  Patterns of Illness in Rhinovirus Infections of Military Personnel Relationship of Rhinovirus Infection


id: cord-328501-mbwgi56x
type: DISEASE
entity:
  influenza A H1N1 pdm09 AOR 1 50 95 CI 1 04 2 15 and coxsackie echovirus AOR 1 67 95 CI 1 19 2 36 mono infection


id: cord-328501-mbwgi56x
type: DISEASE
entity:
  influenza A H1N1 pdm09 which was found to be significantly protective was accounted for in the multivariate model Personnel in the recruit camp were


id: cord-341347-nzptmdbe
type: PROTEIN
entity:
  BacBOVP2 the LR recombination system Invitrogen Karlsruhe Germany was used according to the recommendations of the manufacturer Briefly the amplicons were inserted by


id: cord-354690-ywb9krdp
type: ORG
entity:
  the American Association for Public Opinion Research NSW Population Health Survey Review of Weighting Procedures Australian Bureau of Statistics Census of Population and Housing Effects


id: cord-348802-3f8kmw31
type: PROTEIN
entity:
  human rhinovirus hRV respiratory syncytial virus RSV parainfluenza viruses PIVs adenovirus ADV human metapneumovirus hMPV


id: cord-345046-str19r9a
type: PROTEIN
entity:
  lactate dehydrogenase LDH 300 U liter alanine transaminase ALT 50 U Liter and aspartate aminotransferase AST 40 U


id: cord-344770-aoi42xq4
type: WORK_OF_ART
entity:
  Epidemiology and Clinical Presentation of Parainfluenza Type 4 in Children A 3 Year Comparative Study


id: cord-344770-aoi42xq4
type: ORG
entity:
  the Midwest Regional Center of Excellence for Biodefense and Emerging Infectious Disease Research ARC


id: cord-302833-6kntd89t
type: ORG
entity:
  NIOSH National Institute for Occupational Safety and Health OSHA Occupational Safety and Health Administration


id: cord-356349-ey5vnddu
type: ORG
entity:
  de Guadalajara Hospital Civil Fray Antonio Alcalde Emerging Respiratory Infections Response Team Hospital


id: cord-329256-7njgmdd1
type: ORG
entity:
  edn Vienna Austria R Foundation for Statistical Computing Development Core Team A Language and Environment for Statistical Computing Generalizing


id: cord-329256-7njgmdd1
type: ORG
entity:
  Division of Epidemiology University of Utah School of Medicine Salt Lake City USA 2 Department of Pediatrics University of Utah School of Medicine Salt Lake City USA 3 Division of Disease Control and Prevention Utah Department of Health Salt Lake City USA Authors


id: cord-342210-r8vxz5vu
type: ORG
entity:
  the University Hospitals Case Medical Center Institutional Review Board for Human Investigation Cleveland


id: cord-342210-r8vxz5vu
type: GPE
entity:
  the United States Illness Severity and Work Productivity Loss Among Working Adults With Medically Attended Acute Respiratory Illnesses


id: cord-342210-r8vxz5vu
type: ORG
entity:
  British Industrial Biological Research Association BIBRA Safety Evaluation of Cosmetics Ingredients Effects


# bib

id: cord-000001-ug7v899j
author: Madani, Tariq A
date: 2001-07-04
txt: ./txt/cord-000001-ug7v899j.txt
cache: ./cache/cord-000001-ug7v899j.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC35282/
doi: 10.1186/1471-2334-1-6
summary:
  title: Clinical features of culture-proven Mycoplasma pneumoniae infections at King Abdulaziz University Hospital, Jeddah, Saudi Arabia OBJECTIVE: This retrospective chart review describes the epidemiology and clinical features of 40 patients with culture-proven Mycoplasma pneumoniae infections at King Abdulaziz University Hospital, Jeddah, Saudi Arabia. CONCLUSION: our results were similar to published data except for the finding that infections were more common in infants and preschool children and that the mortality rate of pneumonia in patients with comorbidities was high. Mycoplasma pneumoniae is a common cause of upper and lower respiratory tract infections. pneumoniae infections in Saudi Arabia is scarce, [8, 9, 10] we wished to study the epidemiology and clinical features of cultureproven infections caused by this organism at this hospital. pneumoniae culture were obtained from patients with upper or lower respiratory tract infections seen as inpatients or in the outpatient or emergency departments. Role of Mycoplasma pneumoniae in acute respiratory-tract infections in Saudi paediatric patients

title:
  Clinical features of culture-proven Mycoplasma pneumoniae infections at King Abdulaziz University Hospital, Jeddah, Saudi Arabia

abstract:
  OBJECTIVE: This retrospective chart review describes the epidemiology and clinical features of 40 patients with culture-proven Mycoplasma pneumoniae infections at King Abdulaziz University Hospital, Jeddah, Saudi Arabia. METHODS: Patients with positive M. pneumoniae cultures from respiratory specimens from January 1997 through December 1998 were identified through the Microbiology records. Charts of patients were reviewed. RESULTS: 40 patients were identified, 33 (82.5%) of whom required admission. Most infections (92.5%) were community-acquired. The infection affected all age groups but was most common in infants (32.5%) and pre-school children (22.5%). It occurred year-round but was most common in the fall (35%) and spring (30%). More than three-quarters of patients (77.5%) had comorbidities. Twenty-four isolates (60%) were associated with pneumonia, 14 (35%) with upper respiratory tract infections, and 2 (5%) with bronchiolitis. Cough (82.5%), fever (75%), and malaise (58.8%) were the most common symptoms, and crepitations (60%), and wheezes (40%) were the most common signs. Most patients with pneumonia had crepitations (79.2%) but only 25% had bronchial breathing. Immunocompromised patients were more likely than non-immunocompromised patients to present with pneumonia (8/9 versus 16/31, P = 0.05). Of the 24 patients with pneumonia, 14 (58.3%) had uneventful recovery, 4 (16.7%) recovered following some complications, 3 (12.5%) died because of M pneumoniae infection, and 3 (12.5%) died due to underlying comorbidities. The 3 patients who died of M pneumoniae pneumonia had other comorbidities. CONCLUSION: our results were similar to published data except for the finding that infections were more common in infants and preschool children and that the mortality rate of pneumonia in patients with comorbidities was high.


id: cord-000268-480d3yfv
author: Porfyridis, Ilias
date: 2010-09-29
txt: ./txt/cord-000268-480d3yfv.txt
cache: ./cache/cord-000268-480d3yfv.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955686/
doi: 10.1186/1471-2334-10-286
summary:
  title: Diagnostic value of triggering receptor expressed on myeloid cells-1 and C-reactive protein for patients with lung infiltrates: an observational study The aim of the present study was to define whether expression of TREM-1 on cell membranes of neutrophils (nTREM-1), of monocytes (mTREM-1) and serum sTREM-1 may help in the diagnosis of acute bacterial infections for patients admitted with a new pulmonary infiltrate or pleural effusion. In conclusion, the presented results indicate that serum sTREM-1 and expression of TREM-1 on neutrophils and monocytes may serve as markers of CAP in patients with pulmonary infiltrates. Increased levels of soluble triggering receptor expressed on myeloid cells-1 in patients with acute pancreatitis Prognosis of community acquired pneumonia(CAP): value of triggering receptor expressed on myeloid cells-1 (TREM-1) and other mediators of the inflammatory response Diagnostic implications of soluble triggering receptor expressed on myeloid cells-1 in BAL fluid of patients with pulmonary infiltrates in the ICU

title:
  Diagnostic value of triggering receptor expressed on myeloid cells-1 and C-reactive protein for patients with lung infiltrates: an observational study

abstract:
  BACKGROUND: Differential diagnosis of patients with lung infiltrates remains a challenge. Triggering receptor expressed on myeloid cells (TREM)-1 is a neutrophil and monocyte receptor up-regulated during infection. The aim of this study was to evaluate the diagnostic accuracy of TREM-1 and of C-reactive protein (CRP) from patients with lung infiltrates to discern community acquired lung infections. METHODS: 68 patients admitted to a medical ward with acute respiratory illness were enrolled in the study. Neutrophil and monocyte TREM-1 expression were measured by flow cytometry, sTREM-1 by an enzyme immunoassay and C-reactive protein by nephelometry. Clinical pulmonary infection score was recorded. RESULTS: 34 patients were diagnosed with bacterial community acquired pneumonia (group A) and 34 with non-bacterial pulmonary disease (group B). Median serum TREM-1 concentration was 102.09 pg/ml in group A and lower than 15.10 pg/ml (p < 0.0001) in group B. Mean±SE neutrophil TREM-1 expression was 4.67 ± 0.53 MFI in group A and 2.64 ± 0.25 MFI (p = 0.001) in group B. Monocyte TREM-1 expression was 4.2 ± 0.42 MFI in group A and 2.64 ± 0.35 MFI (p = 0.007) in group B and mean±SE CRP was 18.03 ± 2 mg/ml in group A and 7.1 ± 1.54 mg/ml (p < 0.001) in group B. A cut-off of 19.53 pg/ml of sTREM-1 with sensitivity 82.6% and specificity 63% to discriminate between infectious and non-infectious pulmonary infiltrates was found. sTREM-1 at admission greater than 180 pg/ml was accompanied with unfavourable outcome. CONCLUSION: TREM-1 myeloid expression and sTREM-1 are reliable markers of bacterial infection among patients with pulmonary infiltrates; sTREM-1 is a predictor of final outcome.


id: cord-000280-zyaj90nh
author: Wong, Samuel YS
date: 2010-10-29
txt: ./txt/cord-000280-zyaj90nh.txt
cache: ./cache/cord-000280-zyaj90nh.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988052/
doi: 10.1186/1471-2334-10-316
summary:
  CONCLUSIONS: Similar to previous findings conducted in hospital healthcare workers and nurses, we confirmed that the willingness of community nurses to accept influenza A (H1N1) vaccination is low. In a study conducted of Hong Kong healthcare workers in hospitals, it was found that only 25% of nurses were willing to accept influenza A (H1N1) vaccination, compared with 47% of doctors and 29% of allied professionals [13] . Consistent with findings from previous surveys conducted in hospital healthcare workers and nurses [13, 17] , we have shown that the majority of nurses from community nursing services in Hong Kong were not willing to be vaccinated against H1N1 influenza when the vaccine becomes available. Consistent with previous findings which were conducted in healthcare workers and nurses [13, 17] , we confirm that the acceptance rate of pandemic influenza vaccination is low amongst community nurses.

title:
  Willingness to accept H1N1 pandemic influenza vaccine: A cross-sectional study of Hong Kong community nurses

abstract:
  BACKGROUND: The 2009 pandemic of influenza A (H1N1) infection has alerted many governments to make preparedness plan to control the spread of influenza A (H1N1) infection. Vaccination for influenza is one of the most important primary preventative measures to reduce the disease burden. Our study aims to assess the willingness of nurses who work for the community nursing service (CNS) in Hong Kong on their acceptance of influenza A (H1N1) influenza vaccination. METHODS: 401 questionnaires were posted from June 24, 2009 to June 30, 2009 to community nurses with 67% response rate. Results of the 267 respondents on their willingness to accept influenza A (H1N1) vaccine were analyzed. RESULTS: Twenty-seven percent of respondents were willing to accept influenza vaccination if vaccines were available. Having been vaccinated for seasonable influenza in the previous 12 months were significantly independently associated with their willingness to accept influenza A (H1N1) vaccination (OR = 4.03; 95% CI: 2.03-7.98). CONCLUSIONS: Similar to previous findings conducted in hospital healthcare workers and nurses, we confirmed that the willingness of community nurses to accept influenza A (H1N1) vaccination is low. Future studies that evaluate interventions to address nurses' specific concerns or interventions that aim to raise the awareness among nurses on the importance of influenza A (H1N1) vaccination to protect vulnerable patient populations is needed.


id: cord-000332-u3f89kvg
author: Broeck, Wouter Van den
date: 2011-02-02
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048541/
doi: 10.1186/1471-2334-11-37
title:
  The GLEaMviz computational tool, a publicly available software to explore realistic epidemic spreading scenarios at the global scale

abstract:
  BACKGROUND: Computational models play an increasingly important role in the assessment and control of public health crises, as demonstrated during the 2009 H1N1 influenza pandemic. Much research has been done in recent years in the development of sophisticated data-driven models for realistic computer-based simulations of infectious disease spreading. However, only a few computational tools are presently available for assessing scenarios, predicting epidemic evolutions, and managing health emergencies that can benefit a broad audience of users including policy makers and health institutions. RESULTS: We present "GLEaMviz", a publicly available software system that simulates the spread of emerging human-to-human infectious diseases across the world. The GLEaMviz tool comprises three components: the client application, the proxy middleware, and the simulation engine. The latter two components constitute the GLEaMviz server. The simulation engine leverages on the Global Epidemic and Mobility (GLEaM) framework, a stochastic computational scheme that integrates worldwide high-resolution demographic and mobility data to simulate disease spread on the global scale. The GLEaMviz design aims at maximizing flexibility in defining the disease compartmental model and configuring the simulation scenario; it allows the user to set a variety of parameters including: compartment-specific features, transition values, and environmental effects. The output is a dynamic map and a corresponding set of charts that quantitatively describe the geo-temporal evolution of the disease. The software is designed as a client-server system. The multi-platform client, which can be installed on the user's local machine, is used to set up simulations that will be executed on the server, thus avoiding specific requirements for large computational capabilities on the user side. CONCLUSIONS: The user-friendly graphical interface of the GLEaMviz tool, along with its high level of detail and the realism of its embedded modeling approach, opens up the platform to simulate realistic epidemic scenarios. These features make the GLEaMviz computational tool a convenient teaching/training tool as well as a first step toward the development of a computational tool aimed at facilitating the use and exploitation of computational models for the policy making and scenario analysis of infectious disease outbreaks.


id: cord-000349-k0p166fr
title: Severe pneumococcal pneumonia: impact of new quinolones on prognosis
author: Olive, David
date: 2011-03-15
txt: ./txt/cord-000349-k0p166fr.txt
cache: ./cache/cord-000349-k0p166fr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065411/
doi: 10.1186/1471-2334-11-66
summary:
  BACKGROUND: Most guidelines have been proposing, for more than 15 years, a β-lactam combined with either a quinolone or a macrolide as empirical, first-line therapy of severe community acquired pneumonia (CAP) requiring ICU admission. METHODS: Retrospective study of consecutive patients admitted in a 16-bed general intensive care unit (ICU), between January 1996 and January 2009, for severe (Pneumonia Severity Index > or = 4) community-acquired pneumonia due to non penicillin-resistant Streptococcus pneumoniae and treated with a β-lactam combined with a fluoroquinolone. CONCLUSION: Our results suggest that, when combined to a β-lactam, levofloxacin is associated with lower mortality than ofloxacin or ciprofloxacin in severe pneumococcal community-acquired pneumonia. Firstly, we retrospectively collected all consecutive patients aged > 18 years who were admitted into our ICU (16-bed medical and surgical intensive care unit in a 450-bed general hospital) between January 1996 and January 2009 for severe community-acquired pneumonia (CAP) and who received a definite diagnosis of pneumococcal pneumonia.

abstract:
  BACKGROUND: Most guidelines have been proposing, for more than 15 years, a β-lactam combined with either a quinolone or a macrolide as empirical, first-line therapy of severe community acquired pneumonia (CAP) requiring ICU admission. Our goal was to evaluate the outcome of patients with severe CAP, focusing on the impact of new rather than old fluoroquinolones combined with β-lactam in the empirical antimicrobial treatments. METHODS: Retrospective study of consecutive patients admitted in a 16-bed general intensive care unit (ICU), between January 1996 and January 2009, for severe (Pneumonia Severity Index > or = 4) community-acquired pneumonia due to non penicillin-resistant Streptococcus pneumoniae and treated with a β-lactam combined with a fluoroquinolone. RESULTS: We included 70 patients of whom 38 received a β-lactam combined with ofloxacin or ciprofloxacin and 32 combined with levofloxacin. Twenty six patients (37.1%) died in the ICU. Three independent factors associated with decreased survival in ICU were identified: septic shock on ICU admission (AOR = 10.6; 95% CI 2.87-39.3; p = 0.0004), age > 70 yrs. (AOR = 4.88; 95% CI 1.41-16.9; p = 0.01) and initial treatment with a β-lactam combined with ofloxacin or ciprofloxacin (AOR = 4.1; 95% CI 1.13-15.13; p = 0.03). CONCLUSION: Our results suggest that, when combined to a β-lactam, levofloxacin is associated with lower mortality than ofloxacin or ciprofloxacin in severe pneumococcal community-acquired pneumonia.


id: cord-000441-5rm1za8z
author: Curtale, Filippo
date: 2010-03-11
txt: ./txt/cord-000441-5rm1za8z.txt
cache: ./cache/cord-000441-5rm1za8z.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161360/
doi: 10.1186/1471-2334-10-62
summary:
  Pockets of low vaccine coverage individuals (Roma/Sinti communities, high school students) facilitated the reintroduction of serotypes not endemic in Italy and facilitated the measles infection to spread. Two cases among the Italian ethnic population, who developed symptoms on 19 and 20 July, reported contact with Roma/Sinti patients with measles in a hospital waiting area, on 4 and 10 July They confirmed that pockets of low vaccination coverage exist in some areas of the Lazio region, particularly among Roma/Sinti communities and adolescents Thanks to relatively high immunisation rates amongst new born children (90,7%) [10] and the work done by the local health authorities, conducting contact investigation of cases'', vaccination of susceptible school and household contacts, and implementing isolation measures, the outbreaks did not affect the whole region and, in the city of Rome, was mainly limited to a few peripheral districts (Figure 2 ).

title:
  Description of two measles outbreaks in the Lazio Region, Italy (2006-2007). Importance of pockets of low vaccine coverage in sustaining the infection

abstract:
  BACKGROUND: Despite the launch of the national plan for measles elimination, in Italy, immunization coverage remains suboptimal and outbreaks continue to occur. Two measles outbreaks, occurred in Lazio region during 2006-2007, were investigated to identify sources of infection, transmission routes, and assess operational implications for elimination of the disease. METHODS: Data were obtained from several sources, the routine infectious diseases surveillance system, field epidemiological investigations, and molecular genotyping of virus by the national reference laboratory. RESULTS: Overall 449 cases were reported, sustained by two different stereotypes overlapping for few months. Serotype D4 was likely imported from Romania by a Roma/Sinti family and subsequently spread to the rest of the population. Serotype B3 was responsible for the second outbreak which started in a secondary school. Pockets of low vaccine coverage individuals (Roma/Sinti communities, high school students) facilitated the reintroduction of serotypes not endemic in Italy and facilitated the measles infection to spread. CONCLUSIONS: Communities with low vaccine coverage represent a more serious public health threat than do sporadic susceptible individuals. The successful elimination of measles will require additional efforts to immunize low vaccine coverage population groups, including hard-to-reach individuals, adolescents, and young adults. An enhanced surveillance systems, which includes viral genotyping to document chains of transmission, is an essential tool for evaluating strategy to control and eliminate measles


id: cord-000451-te75jsd3
title: Forecasting incidence of hemorrhagic fever with renal syndrome in China using ARIMA model
author: Liu, Qiyong
date: 2011-08-15
txt: ./txt/cord-000451-te75jsd3.txt
cache: ./cache/cord-000451-te75jsd3.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169483/
doi: 10.1186/1471-2334-11-218
summary:
  title: Forecasting incidence of hemorrhagic fever with renal syndrome in China using ARIMA model In this study, we applied a stochastic autoregressive integrated moving average (ARIMA) model with the objective of monitoring and short-term forecasting HFRS incidence in China. This study aimed to develop a univariate time series model for the HFRS incidence; specifically, a stochastic ARIMA model, for short-term forecasting of HFRS incidence (per 100,000 population) in China. Thus, the fitted ARIMA(0,3,1) model can be used to predict the next three years'' HFRS incidence in China. To the best of our knowledge, this is the first study to apply ARIMA model to fit the HFRS incidence in China with as many as 34 observations at year level. A time series model in incidence forecasting of hemorrhagic fever with renal syndrome Forecasting incidence of hemorrhagic fever with renal syndrome in China using ARIMA model

abstract:
  BACKGROUND: China is a country that is most seriously affected by hemorrhagic fever with renal syndrome (HFRS) with 90% of HFRS cases reported globally. At present, HFRS is getting worse with increasing cases and natural foci in China. Therefore, there is an urgent need for monitoring and predicting HFRS incidence to make the control of HFRS more effective. In this study, we applied a stochastic autoregressive integrated moving average (ARIMA) model with the objective of monitoring and short-term forecasting HFRS incidence in China. METHODS: Chinese HFRS data from 1975 to 2008 were used to fit ARIMA model. Akaike Information Criterion (AIC) and Ljung-Box test were used to evaluate the constructed models. Subsequently, the fitted ARIMA model was applied to obtain the fitted HFRS incidence from 1978 to 2008 and contrast with corresponding observed values. To assess the validity of the proposed model, the mean absolute percentage error (MAPE) between the observed and fitted HFRS incidence (1978-2008) was calculated. Finally, the fitted ARIMA model was used to forecast the incidence of HFRS of the years 2009 to 2011. All analyses were performed using SAS9.1 with a significant level of p < 0.05. RESULTS: The goodness-of-fit test of the optimum ARIMA (0,3,1) model showed non-significant autocorrelations in the residuals of the model (Ljung-Box Q statistic = 5.95,P = 0.3113). The fitted values made by ARIMA (0,3,1) model for years 1978-2008 closely followed the observed values for the same years, with a mean absolute percentage error (MAPE) of 12.20%. The forecast values from 2009 to 2011 were 0.69, 0.86, and 1.21per 100,000 population, respectively. CONCLUSION: ARIMA models applied to historical HFRS incidence data are an important tool for HFRS surveillance in China. This study shows that accurate forecasting of the HFRS incidence is possible using an ARIMA model. If predicted values from this study are accurate, China can expect a rise in HFRS incidence.


id: cord-000457-e50a0suk
author: Rhim, Jung-Woo
date: 2011-08-24
txt: ./txt/cord-000457-e50a0suk.txt
cache: ./cache/cord-000457-e50a0suk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176209/
doi: 10.1186/1471-2334-11-225
summary:
  METHODS: We evaluated the epidemiologic characteristics of all the subjects infected with the 2009 H1N1 influenza A virus (2,971 patients, ≤ 15 years of age), and the clinical and laboratory findings of the inpatients (217 patients, 80 had pneumonia) between 1 September 2009 and 31 January 2010 in a single hospital throughout the epidemic. In addition, during the study period we observed a dramatic effect of early treatment with corticosteroids and oseltamivir for patients with severe pneumonia including rapidly progressive pneumonia [9, 10] . We retrospectively evaluated all patients with 2009 H1N1 virus infection during the pandemic (2,971 patients) for epidemiologic characteristics, and for clinical characteristics, we reviewed the medical records and chest radiographic findings of 217 children admitted to The Catholic University of Korea, Daejeon St Mary''s Hospital between 1 September 2009 and 31 January 2010. In pandemic 2009 H1N1 virus infections, children of all ages were evenly affected, and males were predominant in pneumonia patients.

title:
  Epidemiological and clinical characteristics of childhood pandemic 2009 H1N1 virus infection: an observational cohort study

abstract:
  BACKGROUND: There was a pandemic influenza around the world in 2009 including South Korea since last pandemic occurred four decades ago. We aimed to evaluate the epidemiological and clinical characteristics of this infection in childhood. METHODS: We evaluated the epidemiologic characteristics of all the subjects infected with the 2009 H1N1 influenza A virus (2,971 patients, ≤ 15 years of age), and the clinical and laboratory findings of the inpatients (217 patients, 80 had pneumonia) between 1 September 2009 and 31 January 2010 in a single hospital throughout the epidemic. RESULTS: The age distribution of all the subjects was relatively even. Over 90% of cases occurred during a two-month period. Two hundred and five patients (94.5%) received oseltamivir within 48 h of fever onset, and 97% of inpatients defervesced within 48 h of medication. The group with pneumonia included more males than females, and had higher leukocytes counts with lower lymphocyte differentials than the group without pneumonia. The white blood cell count and lymphocyte differential were associated with the severity of pneumonia. Corticosteroid treatment for severe pneumonia patients was highly effective in preventing disease progression. CONCLUSION: Children of all ages affected with even rates of infection, but males were predominant in pneumonia patients. Pneumonia patients showed lymphopenia and its severity was associated with the severity of illness. Our results suggest that the mechanism of lung injury in 2009 H1N1 virus infection may be associated with the host immune response.


id: cord-000534-ztc5holk
title: Transmissibility and temporal changes of 2009 pH1N1 pandemic during summer and fall/winter waves
author: Hsieh, Ying-Hen
date: 2011-12-02
txt: ./txt/cord-000534-ztc5holk.txt
cache: ./cache/cord-000534-ztc5holk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3247203/
doi: 10.1186/1471-2334-11-332
summary:
  BACKGROUND: In order to compare the transmissibility of the 2009 pH1N1 pandemic during successive waves of infections in summer and fall/winter in the Northern Hemisphere, and to assess the temporal changes during the course of the outbreak in relation to the intervention measures implemented, we analyze the epidemiological patterns of the epidemic in Taiwan during July 2009-March 2010. METHODS: We utilize the multi-phase Richards model to fit the weekly cumulative pH1N1 epidemiological data (numbers of confirmed cases and hospitalizations) as well as the daily number of classes suspended under a unique "325" partial school closing policy in Taiwan, in order to pinpoint the turning points of the summer and fall/winter waves, and to estimate the reproduction numbers R for each wave. The estimates for effective reproduction number R obtained from the confirmed case and hospitalization data are in good agreement, with R in the range of 1.04-1.27 for the first summer wave during July-September, and 1.01-1.05 for the second wave in fall/winter, using the generation time estimated by [26] for the spring outbreak in Mexico.

abstract:
  BACKGROUND: In order to compare the transmissibility of the 2009 pH1N1 pandemic during successive waves of infections in summer and fall/winter in the Northern Hemisphere, and to assess the temporal changes during the course of the outbreak in relation to the intervention measures implemented, we analyze the epidemiological patterns of the epidemic in Taiwan during July 2009-March 2010. METHODS: We utilize the multi-phase Richards model to fit the weekly cumulative pH1N1 epidemiological data (numbers of confirmed cases and hospitalizations) as well as the daily number of classes suspended under a unique "325" partial school closing policy in Taiwan, in order to pinpoint the turning points of the summer and fall/winter waves, and to estimate the reproduction numbers R for each wave. RESULTS: Our analysis indicates that the summer wave had slowed down by early September when schools reopened for fall. However, a second fall/winter wave began in late September, approximately 4 weeks after the school reopened, peaking at about 2-3 weeks after the start of the mass immunization campaign in November. R is estimated to be in the range of 1.04-1.27 for the first wave, and between 1.01-1.05 for the second wave. CONCLUSIONS: Transmissibility of the summer wave in Taiwan during July-early September, as measured by R, was lower than that of the earlier spring outbreak in North America and Europe, as well as that of the winter outbreak in Southern Hemisphere. Furthermore, transmissibility during fall/winter in Taiwan was noticeably lower than that of the summer, which is attributable to population-level immunity acquired from the earlier summer wave and also to the intervention measures that were implemented prior to and during the fall/winter wave.


id: cord-000562-ocp6yodg
title: Timeliness of contact tracing among flight passengers for influenza A/H1N1 2009
author: Swaan, Corien M
date: 2011-12-28
txt: ./txt/cord-000562-ocp6yodg.txt
cache: ./cache/cord-000562-ocp6yodg.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3265549/
doi: 10.1186/1471-2334-11-355
summary:
  This study evaluates the timeliness of flight-contact tracing (CT) as performed following national and international CT requests addressed to the Center of Infectious Disease Control (CIb/RIVM), and implemented by the Municipal Health Services of Schiphol Airport. In this study, we assess the time delay in contact tracing of flight passengers for influenza A/H1N1 2009 as performed in the Netherlands during the initial phase of the pandemic. For each contact investigation performed in the period April 29th until June 22nd 2009, the following data were collected: flight arrival date, first day of illness of index patient, date of laboratory diagnosis, date of contact tracing request and the date passenger lists were obtained and contact details were completed (''contacts details identified''). Our study among 17 contact investigations showed an average total delay of 3,9 days between flight arrival and identification of contacts by passenger list, which is too late for effective PEP, and late for alerting on first symptoms of disease.

abstract:
  BACKGROUND: During the initial containment phase of influenza A/H1N1 2009, close contacts of cases were traced to provide antiviral prophylaxis within 48 h after exposure and to alert them on signs of disease for early diagnosis and treatment. Passengers seated on the same row, two rows in front or behind a patient infectious for influenza, during a flight of ≥ 4 h were considered close contacts. This study evaluates the timeliness of flight-contact tracing (CT) as performed following national and international CT requests addressed to the Center of Infectious Disease Control (CIb/RIVM), and implemented by the Municipal Health Services of Schiphol Airport. METHODS: Elapsed days between date of flight arrival and the date passenger lists became available (contact details identified - CI) was used as proxy for timeliness of CT. In a retrospective study, dates of flight arrival, onset of illness, laboratory diagnosis, CT request and identification of contacts details through passenger lists, following CT requests to the RIVM for flights landed at Schiphol Airport were collected and analyzed. RESULTS: 24 requests for CT were identified. Three of these were declined as over 4 days had elapsed since flight arrival. In 17 out of 21 requests, contact details were obtained within 7 days after arrival (81%). The average delay between arrival and CI was 3,9 days (range 2-7), mainly caused by delay in diagnosis of the index patient after arrival (2,6 days). In four flights (19%), contacts were not identified or only after > 7 days. CI involving Dutch airlines was faster than non-Dutch airlines (P < 0,05). Passenger locator cards did not improve timeliness of CI. In only three flights contact details were identified within 2 days after arrival. CONCLUSION: CT for influenza A/H1N1 2009 among flight passengers was not successful for timely provision of prophylaxis. CT had little additional value for alerting passengers for disease symptoms, as this information already was provided during and after the flight. Public health authorities should take into account patient delays in seeking medical advise and laboratory confirmation in relation to maximum time to provide postexposure prophylaxis when deciding to install contact tracing measures. International standardization of CT guidelines is recommended.


id: cord-000619-3bakci02
author: Zhang, Peng-jun
date: 2012-02-01
txt: ./txt/cord-000619-3bakci02.txt
cache: ./cache/cord-000619-3bakci02.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3311613/
doi: 10.1186/1471-2334-12-29
summary:
  title: Clinical features and risk factors for severe and critical pregnant women with 2009 pandemic H1N1 influenza infection in China Data on risk factors associated with death of pregnant women and neonates with pH1N1 infections are limited outside of developed countries. METHODS: Retrospective observational study in 394 severe or critical pregnant women admitted to a hospital with pH1N1 influenza from Sep. 1, 2009 to Dec. 31, 2009. Preterm delivery was a risk factor for neonatal death among pregnant women with pH1N1 influenza infection. However, information is limited concerning the risk factors for maternal and neonatal death when pregnancy is complicated by severe or critical illness related to 2009 pH1N1 influenza. In this report, we described the characteristics of pH1N1 influenza in pregnant women and the risk factors for maternal and neonatal death. The clinical data reported herein is consistent with previous studies that demonstrate that pregnant women with influenza are at an increased risk of serious illness and death.

title:
  Clinical features and risk factors for severe and critical pregnant women with 2009 pandemic H1N1 influenza infection in China

abstract:
  BACKGROUND: 2009 pandemic H1N1 (pH1N1) influenza posed an increased risk of severe illness among pregnant women. Data on risk factors associated with death of pregnant women and neonates with pH1N1 infections are limited outside of developed countries. METHODS: Retrospective observational study in 394 severe or critical pregnant women admitted to a hospital with pH1N1 influenza from Sep. 1, 2009 to Dec. 31, 2009. rRT-PCR testing was used to confirm infection. In-hospital mortality was the primary endpoint of this study. Univariable logistic analysis and multivariate logistic regression analysis were used to investigate the potential factors on admission that might be associated with the maternal and neonatal mortality. RESULTS: 394 pregnant women were included, 286 were infected with pH1N1 in the third trimester. 351 had pneumonia, and 77 died. A PaO(2)/FiO(2 )≤ 200 (odds ratio (OR), 27.16; 95% confidence interval (CI), 2.64-279.70) and higher BMI (i.e. ≥ 30) on admission (OR, 1.26; 95% CI, 1.09 to 1.47) were independent risk factors for maternal death. Of 211 deliveries, 146 neonates survived. Premature delivery (OR, 4.17; 95% CI, 1.19-14.56) was associated neonatal mortality. Among 186 patients who received mechanical ventilation, 83 patients were treated with non-invasive ventilation (NIV) and 38 were successful with NIV. The death rate was lower among patients who initially received NIV than those who were initially intubated (24/83, 28.9% vs 43/87, 49.4%; p = 0.006). Septic shock was an independent risk factor for failure of NIV. CONCLUSIONS: Severe hypoxemia and higher BMI on admission were associated with adverse outcomes for pregnant women. Preterm delivery was a risk factor for neonatal death among pregnant women with pH1N1 influenza infection. NIV may be useful in selected pregnant women without septic shock.


id: cord-000963-pwz6rde0
title: Low serum total nitrite and nitrate levels in severe leptospirosis
author: Kalugalage, Thilini
date: 2013-05-06
txt: ./txt/cord-000963-pwz6rde0.txt
cache: ./cache/cord-000963-pwz6rde0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651868/
doi: 10.1186/1471-2334-13-206
summary:
  We previously demonstrated through a preliminary study that serum nitrite levels are elevated in patients with acute leptospirosis compared to healthy controls [20] . The aim of this study was to determine the relationship between NO x (i.e., total nitrite and nitrate) levels in the blood (as a marker of iNOS activity) and disease severity in leptospirosis. The objectives of our study were to a) determine serum NO x (nitrate and nitrite) levels in patients with confirmed leptospirosis, b) compare serum NO x levels in leptospirosis patients with mild and severe disease, healthy controls and non-leptospirosis fever patients (NLFs), and c) seek a correlation between serum NO x levels and disease severity after correcting for impaired renal clearance. Patients with severe leptospirosis were defined as those presenting with acute fever and clinical symptoms compatible with leptospirosis (confirmed serologically by a positive MAT result) with two or more of the following criteria: jaundice (bilirubin> 51.3 μmol/l), oliguria (urine output < 400 ml/day), serum creatinine> 133 μmol/l or blood urea > 25.5 mmol/l [14] , or the presence of acute organ dysfunction.

abstract:
  BACKGROUND: The relationship between inducible nitric oxide synthatase activity and disease severity in leptospirosis is unclear. Nitric oxide is converted to nitrites and nitrates, thus nitrite and nitrate levels (NO(x)) in serum are considered surrogate markers for nitric oxide. NO(x) are excreted through the kidneys, and elimination is diminished in renal impairment. We assessed the correlation of NO(x) with disease severity in patients with leptospirosis, compared with healthy controls and non-leptospirosis fever patients. METHODS: All patients admitted over a two-month period to the National Hospital, Colombo, Sri Lanka with a clinical picture suggestive of leptospirosis were included. Leptospirosis was confirmed by the microscopic agglutination test (titre≥400). Severe leptospirosis was defined by the presence of two or more of the following criteria: jaundice (bilirubin> 51.3 μmol/l), oliguria (urine output < 400 ml/day), serum creatinine> 133 μmol/l or blood urea > 25.5 mmol/l, or the presence of organ dysfunction. Non-leptospirosis fever patients and healthy volunteers were used as control groups. NO(x) levels were measured using a modified Griess reaction. RESULTS: Forty patients were confirmed as having leptospirosis and 26 of them had severe disease. NO(x) levels were significantly higher in confirmed leptospirosis patients compared to healthy controls, MAT equivocal patients and non-leptospirosis fever patients (p<0.001). NO(x) concentrations were also significantly higher in patients with severe compared to mild leptospirosis (p<0.001). Once NO(x) levels were corrected for renal function, by using the ratio NO(x)/creatinine, NO(x) levels were actually significantly lower in patients with severe disease compared to other patients, and values were similar to those of healthy controls. CONCLUSIONS: We postulate that high NOx levels may be protective against severe leptospirosis, and that finding low NOx levels (when corrected for renal function) in patients with leptospirosis may predict the development of severe disease and organ dysfunction.


id: cord-000996-ef5d81cg
author: Han, Seung Beom
date: 2013-06-17
txt: ./txt/cord-000996-ef5d81cg.txt
cache: ./cache/cord-000996-ef5d81cg.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3685537/
doi: 10.1186/1471-2334-13-273
summary:
  BACKGROUND: This study was performed to compare the clinical characteristics and antibiotic susceptibilities of viridans streptococcal bacteremia (VSB) between febrile neutropenic adults and children with hematologic malignancies. We performed this retrospective study to compare clinical characteristics including the occurrence of severe complications and antibiotic susceptibilities of viridans streptococci between febrile neutropenic adults and children with hematologic malignancies, and to propose appropriate antibacterial treatment strategies for adults and children. Data gathered on patients'' demographics and clinical characteristics consisted of gender, underlying disease with remission status, type of therapy preceding febrile neutropenia, number of days from the beginning of respective therapies to the diagnosis of VSB, use of antibacterial prophylaxis, and occurrence of oral mucositis, respiratory symptoms, gastrointestinal symptoms, severe complications and polymicrobial infection by other bacteria or fungi. In this study, there were no definite differences in clinical and laboratory characteristics, mortality, or occurrence of severe complications between febrile neutropenic adults and children with VSB, despite a significant difference in antibiotic susceptibility to cefepime between the two groups.

title:
  Clinical characteristics and antimicrobial susceptibilities of viridans streptococcal bacteremia during febrile neutropenia in patients with hematologic malignancies: a comparison between adults and children

abstract:
  BACKGROUND: This study was performed to compare the clinical characteristics and antibiotic susceptibilities of viridans streptococcal bacteremia (VSB) between febrile neutropenic adults and children with hematologic malignancies. METHODS: The consecutive medical records of neutropenic patients with hematologic malignancies who were admitted to the Catholic Blood and Marrow Transplantation Center between April 2009 and July 2012, and who were subsequently diagnosed with VSB were reviewed retrospectively. A comparison was made between the clinical and laboratory characteristics of adults and pediatric patients and also between patients with cefepime susceptible or not susceptible VSB. RESULTS: A total of 202 episodes (141 in adults, 61 in children) of VSB were identified. Among them, 26 (12.9%) cases had severe complications including four (2.0%) cases of death attributable to VSB. For antibacterial prophylaxis, most adults received ciprofloxacin (97.1%), but children more frequently received trimethoprim/sulfamethoxazole (86.9%). Oral mucositis (p = 0.005) and abdominal pain (p = 0.001) were found more frequently in adults, and cough was found more frequently in children (p = 0.004). The occurrence rates of severe complications and death attributable to VSB were not significantly different between adults and children. Susceptibility rate to cefepime was significantly higher in adults than children (85.7% vs. 66.1%, p = 0.002). However, in multivariate analysis, cefepime susceptibility had no impact on clinical outcome. CONCLUSIONS: There was no significant difference in clinical outcome between adults and children with VSB despite a difference in cefepime susceptibility. Hence, different antibiotic treatment strategies may not be necessary.


id: cord-001050-lq9tp20z
author: Khanafer, Nagham
date: 2013-08-01
txt: ./txt/cord-001050-lq9tp20z.txt
cache: ./cache/cord-001050-lq9tp20z.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3750359/
doi: 10.1186/1471-2334-13-359
summary:
  title: Severe leukopenia in Staphylococcus aureus-necrotizing, community-acquired pneumonia: risk factors and impact on survival BACKGROUND: Necrotizing pneumonia attributed to Panton-Valentine leukocidin-positive Staphylococcus aureus has mainly been reported in otherwise healthy children and young adults, with a high mortality rate. The objectives of this study were to define the characteristics of patients with severe leukopenia at 48-h hospitalization and to update our data regarding mortality predicting factors in a larger population than we had previously described. Multivariate analysis indicated that the factors associated with severe leukopenia were influenza-like illness (adjusted odds ratio (aOR) 4.45, 95% CI (95% confidence interval) 1.67-11.88, P=0.003), airway bleeding (aOR 4.53, 95% CI 1.85-11.13, P=0.001) and age over 30 years (aOR 2.69, 95% CI 1.08-6.68, P=0.033). Severe community-acquired pneumonia caused by Panton-Valentine leukocidin-positive Staphylococcus aureus: first reported case in the United Kingdom Factors predicting mortality in necrotizing community-acquired pneumonia caused by Staphylococcus aureus containing Panton-Valentine leukocidin

title:
  Severe leukopenia in Staphylococcus aureus-necrotizing, community-acquired pneumonia: risk factors and impact on survival

abstract:
  BACKGROUND: Necrotizing pneumonia attributed to Panton-Valentine leukocidin-positive Staphylococcus aureus has mainly been reported in otherwise healthy children and young adults, with a high mortality rate. Erythroderma, airway bleeding, and leukopenia have been shown to be predictive of mortality. The objectives of this study were to define the characteristics of patients with severe leukopenia at 48-h hospitalization and to update our data regarding mortality predicting factors in a larger population than we had previously described. METHODS: It was designed as a case-case study nested in a cohort study. A total of 148 cases of community-acquired, necrotizing pneumonia were included. The following data were collected: basic demographic information, medical history, signs and symptoms, radiological findings and laboratory results during the first 48 h of hospitalization. The study population was divided into 2 groups: (1) with severe leukopenia (leukocyte count ≤3,000 leukocytes/mL, n=62) and (2) without severe leukopenia (>3,000 leukocytes/mL, n=86). RESULTS: Median age was 22 years, and the male-to-female gender ratio was 1.5. The overall in-hospital mortality rate was 41.2%. Death occurred in 75.8% of severe leukopenia cases with median survival time of 4 days, and in 16.3% of cases with leukocyte count >3,000/mL (P<0.001). Multivariate analysis indicated that the factors associated with severe leukopenia were influenza-like illness (adjusted odds ratio (aOR) 4.45, 95% CI (95% confidence interval) 1.67-11.88, P=0.003), airway bleeding (aOR 4.53, 95% CI 1.85-11.13, P=0.001) and age over 30 years (aOR 2.69, 95% CI 1.08-6.68, P=0.033). A personal history of furuncles appeared to be protective (OR 0.11, 95% CI 0.01-0.96, P=0.046). CONCLUSION: S. aureus-necrotizing pneumonia is still an extremely severe disease in patients with severe leukopenia. Some factors could distinguish these patients, allowing better initial identification to initiate adapted, rapid administration of appropriate therapy.


id: cord-001470-hn288o97
author: Pivette, Mathilde
date: 2014-11-18
txt: ./txt/cord-001470-hn288o97.txt
cache: ./cache/cord-001470-hn288o97.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4240820/
doi: 10.1186/s12879-014-0604-2
summary:
  CONCLUSIONS: Drug sales data analyses appear to be a useful tool for surveillance of gastrointestinal and respiratory disease, and OTC drugs have the potential for early outbreak detection. Published articles were searched for on electronic databases (Pubmed, Embase, Scopus, LILACS, African Index Medicus, Cochrane Library), using combinations of the following key words: ("surveillance" OR outbreak detection OR warning system) AND (overthe-counter OR "prescription drugs" OR pharmacy OR (pharmaceutical OR drug OR medication) sales). Articles excluded based on fulltext review (no drug sales data, no infectious disease, no outbreak detection) N= 85 Figure 1 Flow chart of study selection process in a systematic review of drug sales data analysis for syndromic surveillance of infectious diseases. Nineteen of the 27 studies were descriptive retrospective studies assessing the strength of the correlation between drug sales and reference surveillance data of the corresponding disease or evaluating outbreak-detection performance [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] .

title:
  Drug sales data analysis for outbreak detection of infectious diseases: a systematic literature review

abstract:
  BACKGROUND: This systematic literature review aimed to summarize evidence for the added value of drug sales data analysis for the surveillance of infectious diseases. METHODS: A search for relevant publications was conducted in Pubmed, Embase, Scopus, Cochrane Library, African Index Medicus and Lilacs databases. Retrieved studies were evaluated in terms of objectives, diseases studied, data sources, methodologies and performance for real-time surveillance. Most studies compared drug sales data to reference surveillance data using correlation measurements or indicators of outbreak detection performance (sensitivity, specificity, timeliness of the detection). RESULTS: We screened 3266 articles and included 27 in the review. Most studies focused on acute respiratory and gastroenteritis infections. Nineteen studies retrospectively compared drug sales data to reference clinical data, and significant correlations were observed in 17 of them. Four studies found that over-the-counter drug sales preceded clinical data in terms of incidence increase. Five studies developed and evaluated statistical algorithms for selecting drug groups to monitor specific diseases. Another three studies developed models to predict incidence increase from drug sales. CONCLUSIONS: Drug sales data analyses appear to be a useful tool for surveillance of gastrointestinal and respiratory disease, and OTC drugs have the potential for early outbreak detection. Their utility remains to be investigated for other diseases, in particular those poorly surveyed. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-014-0604-2) contains supplementary material, which is available to authorized users.


id: cord-001512-u3u2k8hj
author: Ding, Hua
date: 2014-12-31
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4304124/
doi: 10.1186/s12879-014-0698-6
title:
  A family cluster of three confirmed cases infected with avian influenza A (H7N9) virus in Zhejiang Province of China

abstract:
  BACKGROUND: A total of 453 laboratory-confirmed cases infected with avian influenza A (H7N9) virus (including 175 deaths) have been reported till October 2,2014, of which 30.68% (139/453) of the cases were identified from Zhejiang Province. We describe the largest reported cluster of virologically confirmed H7N9 cases, comprised by a fatal Index case and two mild secondary cases. METHODS: A retrospective investigation was conducted in January of 2014. Three confirmed cases, their close contacts, and relevant environments samples were tested by real-time reverse transcriptase-polymerase chain reaction (RT-PCR), viral culture, and sequencing. Serum samples were tested by haemagglutination inhibition (HI) assay. RESULTS: The Index case, a 49-year-old farmer with type II diabetes, who lived with his daughter (Case 2, aged 24) and wife (Case 3, aged 43) and his son-in-law (H7N9 negative). The Index case and Case 3 worked daily in a live bird market. Onset of illness in Index case occurred in January 13, 2014 and subsequently, he died of multi-organ failure on January 20. Case 2 presented with mild symptoms on January 20 following frequent unprotected bed-side care of the Index case between January 14 to 19, and exposed to live bird market on January 17. Case 3 became unwell on January 23 after providing bedside care to the Index case on January 17 to 18, and following the contact with Case 2 during January 21 to 22 at the funeral of the Index case. The two secondary cases were discharged on February 2 and 5 separately after early treatment with antiviral medication. Four virus strains were isolated and genome analyses showed 99.6 ~100% genetic homology, with two amino mutations (V192I in NS and V280A in NP). 42% (11/26) of environmental samples collected in January were H7N9 positive. Twenty-five close contacts remained well and were negative for H7N9 infection by RT-PCR and HI assay. CONCLUSIONS: In the present study, the Index case was infected from a live bird market while the two secondary cases were infected by the Index case during unprotected exposure. This family cluster is, therefore, compatible with non-sustained person-to-person transmission of avian influenza A/H7N9. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-014-0698-6) contains supplementary material, which is available to authorized users.


id: cord-001725-pw7coi3v
author: Ballus, Josep
date: 2015-07-30
txt: ./txt/cord-001725-pw7coi3v.txt
cache: ./cache/cord-001725-pw7coi3v.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520265/
doi: 10.1186/s12879-015-1050-5
summary:
  title: Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes We therefore aimed to assess the incidence, epidemiology and microbiology of SSI and its association with outcomes in patients with severe peritonitis in the intensive care unit (ICU). Physicians may consider antibiotic-resistant pathogens, gram-positive cocci and fungi when choosing empiric antibiotic treatment for SSI, although more studies are needed to confirm our results due to the inherent limitations of the microbiological sampling with swabs performed in our research. This study therefore aimed to describe the incidence, epidemiology, microbiology and outcomes of SSI in patients admitted with secondary or tertiary peritonitis to the ICU of a tertiary referral hospital. This study provides data on the incidence and microbiology of SSIs for a large cohort of critically ill patients admitted with secondary or tertiary peritonitis to a surgical ICU.

title:
  Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes

abstract:
  BACKGROUND: Surgical site infection (SSI) remains a significant problem in the postoperative period that can negatively affect clinical outcomes. Microbiology findings are typically similar to other nosocomial infections, with differences dependent on microbiology selection due to antibiotic pressure or the resident flora. However, this is poorly understood in the critical care setting. We therefore aimed to assess the incidence, epidemiology and microbiology of SSI and its association with outcomes in patients with severe peritonitis in the intensive care unit (ICU). METHODS: We prospectively studied 305 consecutive patients admitted to our surgical ICU from 2010 to 2014 with a diagnosis of secondary or tertiary peritonitis. We collected the following data: SSI diagnosis, demographics, Acute Physiology and Chronic Health Evaluation (APACHE) II score, Simplified Acute Physiology Score (SAPS) II score, type of surgery, microbiology, antibiotic treatment and outcomes. Microbiological sampling was done by means of swabs. RESULTS: We identified 269 episodes of SSI in 162 patients (53.1 %) aged 64.4 ± 14.3 years, of which 200 episodes occurred in men (64.6 %). The mean APACHE II and SAPS II scores were 19.7 ± 7.8 and 36.5 ± 16.1 respectively. The mean ICU and hospital stays were 19.8 ± 24.8 and 21.7 ± 30 days respectively. Pseudomonas spp. (n = 52, 19.3 %), Escherichia coli (n = 55, 20.4 %) and Candida spp. (n = 46, 17.1 %) were the most frequently isolated microorganisms, but gram-positive cocci (n = 80, 29.7 %) were also frequent. Microorganisms isolated from SSIs were associated with a higher incidence of antibiotic resistance (64.9 %) in ICU patients, but not with higher in-hospital mortality. However, patients who suffered from SSI had longer ICU admissions (odds ratio = 1.024, 95 % confidence interval 1.010–1.039, P = 0.001). CONCLUSIONS: The incidence of SSI in secondary or tertiary peritonitis requiring ICU admission is very high. Physicians may consider antibiotic-resistant pathogens, gram-positive cocci and fungi when choosing empiric antibiotic treatment for SSI, although more studies are needed to confirm our results due to the inherent limitations of the microbiological sampling with swabs performed in our research. The presence of SSI may be associated with prolonged ICU stays, but without any influence on overall mortality.


id: cord-001746-pbahviaz
author: Garg, Shikha
date: 2015-08-26
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4550040/
doi: 10.1186/s12879-015-1004-y
title:
  Pneumonia among adults hospitalized with laboratory-confirmed seasonal influenza virus infection—United States, 2005–2008

abstract:
  BACKGROUND: Influenza and pneumonia combined are the leading causes of death due to infectious diseases in the United States. We describe factors associated with pneumonia among adults hospitalized with influenza. METHODS: Through the Emerging Infections Program, we identified adults ≥ 18 years, who were hospitalized with laboratory-confirmed influenza during October 2005 through April 2008, and had a chest radiograph (CXR) performed. Pneumonia was defined as the presence of a CXR infiltrate and either an ICD-9-CM code or discharge summary diagnosis of pneumonia. RESULTS: Among 4,765 adults hospitalized with influenza, 1392 (29 %) had pneumonia. In multivariable analysis, factors associated with pneumonia included: age ≥ 75 years, adjusted odds ratio (AOR) 1.27 (95 % confidence interval 1.10–1.46), white race AOR 1.24 (1.03–1.49), nursing home residence AOR 1.37 (1.14–1.66), chronic lung disease AOR 1.37 (1.18–1.59), immunosuppression AOR 1.45 (1.19–1.78), and asthma AOR 0.76 (0.62–0.92). Patients with pneumonia were significantly more likely to require intensive care unit (ICU) admission (27 % vs. 10 %), mechanical ventilation (18 % vs. 5 %), and to die (9 % vs. 2 %). CONCLUSIONS: Pneumonia was present in nearly one-third of adults hospitalized with influenza and was associated with ICU admission and death. Among patients hospitalized with influenza, older patients and those with certain underlying conditions are more likely to have pneumonia. Pneumonia is common among adults hospitalized with influenza and should be evaluated and treated promptly. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-015-1004-y) contains supplementary material, which is available to authorized users.


id: cord-001922-zfpg6dgj
author: Zhang, Xu-Sheng
date: 2016-01-29
txt: ./txt/cord-001922-zfpg6dgj.txt
cache: ./cache/cord-001922-zfpg6dgj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731987/
doi: 10.1186/s12879-016-1373-x
summary:
  The method uses knowledge of which subtype each case is infected with (and whether they were co-infected), contact information and symptom onset date of each case in the influenza outbreak. RESULTS: Analysis of the constructed transmission tree shows that the simultaneous presence of the two influenza viruses increases the infectivity and the transmissibility of A/H1N1 virus but whether it changes the infectivity of A/H3N2 is unclear. In this short report we extend this inference method to construct the transmission tree that includes two influenza A viruses and their co-infection. The likely reason for this difference lies in the fact that pandemic A/H1N1 is a novel virus while A/ H3N2 is an endemic seasonal virus in the study region [12] so some pre-existing immunity against A/H3N2 Fig. 2 Constructed transmission tree of influenza A virus: a The relative frequency of the generation intervals; b The average case reproduction number R t as it varies with time.

title:
  Construction of the influenza A virus transmission tree in a college-based population: co-transmission and interactions between influenza A viruses

abstract:
  BACKGROUND: Co-infection of different influenza A viruses is known to occur but how viruses interact within co-infection remains unknown. An outbreak in a college campus during the 2009 pandemic involved two subtypes of influenza A: persons infected with pandemic A/H1N1; persons infected with seasonal A/H3N2 viruses; and persons infected with both at the same time (co-infection). This provides data to analyse the possible interaction between influenza A viruses within co-infection. METHODS: We extend a statistical inference method designed for outbreaks caused by one virus to that caused by two viruses. The method uses knowledge of which subtype each case is infected with (and whether they were co-infected), contact information and symptom onset date of each case in the influenza outbreak. We then apply it to construct the most likely transmission tree during the outbreak in the college campus. RESULTS: Analysis of the constructed transmission tree shows that the simultaneous presence of the two influenza viruses increases the infectivity and the transmissibility of A/H1N1 virus but whether it changes the infectivity of A/H3N2 is unclear. The estimation also shows that co-transmission of both subtypes from co-infection is low and therefore co-infection cannot be sustained on its own. CONCLUSIONS: This study suggests that influenza A viruses within co-infected patients can interact in some ways rather than transmit independently, and this can enhance the spread of influenza A virus infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-016-1373-x) contains supplementary material, which is available to authorized users.


id: cord-002828-ml6mgyf3
author: Huang, Linna
date: 2018-01-08
txt: ./txt/cord-002828-ml6mgyf3.txt
cache: ./cache/cord-002828-ml6mgyf3.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5759204/
doi: 10.1186/s12879-017-2903-x
summary:
  title: Application of extracorporeal membrane oxygenation in patients with severe acute respiratory distress syndrome induced by avian influenza A (H7N9) viral pneumonia: national data from the Chinese multicentre collaboration Our study is aimed to investigate the current application, efficacy and safety of ECMO in for severe H7N9 pneumonia-associated acute respiratory distress syndrome (ARDS) in the Chinese population. Conclusions: ECMO is effective at improving oxygenation and ventilation of patients with avian influenza A (H7N9) induced severe ARDS. Conclusions: ECMO is effective at improving oxygenation and ventilation of patients with avian influenza A (H7N9) induced severe ARDS. Keywords: Extracorporeal membrane oxygenation (ECMO), Avian influenza A (H7N9), Acute respiratory distress syndrome (ARDS), Complications, Mortality Background Avian influenza A (H7N9) viral pneumonia can manifest with varying degrees of dyspnea and is associated with a mortality of~30% [1] . ECMO is effective at improving oxygenation and ventilation of patients with avian influenza A (H7N9)-induced severe ARDS.

title:
  Application of extracorporeal membrane oxygenation in patients with severe acute respiratory distress syndrome induced by avian influenza A (H7N9) viral pneumonia: national data from the Chinese multicentre collaboration

abstract:
  BACKGROUND: Evidence concerning the efficacy and safety of extracorporeal membrane oxygenation (ECMO) in patients with influenza A (H7N9) has been was limited to case reports. Our study is aimed to investigate the current application, efficacy and safety of ECMO in for severe H7N9 pneumonia-associated acute respiratory distress syndrome (ARDS) in the Chinese population. METHODS: A multicentre retrospective cohort study was conducted at 20 hospitals that admitted patients with avian influenza A (H7N9) viral pneumonia patients’ admission from 9 provinces in China between October 1, 2016, and March 1, 2017. Data from the National Health and Family Planning Commission of China, including general conditions, outcomes and ECMO management, were analysed. Then, successfully weaned and unsuccessfully weaned groups were compared. RESULTS: A total of 35 patients, aged 57 ± 1 years, were analysed; 65.7% of patients were male with 63% mortality. All patients underwent invasive positive pressure ventilation (IPPV), and rescue ventilation strategies were implemented for 23 cases (65.7%) with an average IPPV duration of 5 ± 1 d, PaO(2)/FiO(2) of 78 ± 23 mmHg, tidal volume (VT) of 439 ± 61 ml and plateau pressure (P(plat)) of 29 ± 8 cmH(2)O pre-ECMO. After 48 h on ECMO, PaO(2) improved from 56 ± 21 mmHg to 90 ± 24 mmHg and PaCO(2) declined from 52 ± 24 mmHg to 38 ± 24 mmHg. Haemorrhage, ventilator-associated pneumonia (VAP) and barotrauma occurred in 45.7%, 60% and 8.6% of patients, respectively. Compared with successfully weaned patients (n = 14), the 21 unsuccessfully weaned patients had a longer duration of IPPV pre-ECMO (6 ± 4 d vs. 2 ± 1 d, P < 0.01) as well as a higher P(plat) (25 ± 5 cmH(2)O vs. 21 ± 3 cmH(2)O, P < 0.05) and VT (343 ± 96 ml vs. 246 ± 93 ml, P < 0.05) after 48 h on ECMO support. Furthermore, the unsuccessfully weaned group had a higher mortality (100% vs. 7.1%, P < 0.01) with more haemorrhage (77.3% vs. 28.6%, P < 0.01). CONCLUSIONS: ECMO is effective at improving oxygenation and ventilation of patients with avian influenza A (H7N9) induced severe ARDS. Early initiation of ECMO with appropriate IPPV settings and anticoagulation strategies are necessary to reduce complications.


id: cord-002853-vj8t28hn
author: Joffe, Michael
date: 2018-01-27
txt: ./txt/cord-002853-vj8t28hn.txt
cache: ./cache/cord-002853-vj8t28hn.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5787257/
doi: 10.1186/s12879-018-2962-7
summary:
  BACKGROUND: We report a fatal case of disseminated adenovirus infection in a non-transplant haematology adult patient with chronic lymphocytic leukaemia who had completed combination chemoimmunotherapy a few months before developing respiratory symptoms. CASE PRESENTATION: This case started with an initial bacterial chest infection that responded to treatment, followed by an adenovirus pneumonitis that disseminated to his blood a week later with levels of up to 92 million adenovirus DNA copies/ml. We report here a case of adenovirus pneumonitis which led to a fatal disseminated adenovirus infection in an adult patient with chronic lymphocytic leukaemia (CLL) on chemotherapy. This patient''s chemotherapy regimen included fludarabine which has severe lymphopaenia as a recognised adverse effect, and which has been present in treatment regimens where various other viral reactivations have occurred, including hepatitis B [10] [11] [12] , BK virus [13] , herpes simplex and Epstein-Barr viruses [14] , cytomegalovirus [15] , as well as adenovirus [16] .

title:
  Case report: a fatal case of disseminated adenovirus infection in a non-transplant adult haematology patient

abstract:
  BACKGROUND: We report a fatal case of disseminated adenovirus infection in a non-transplant haematology adult patient with chronic lymphocytic leukaemia who had completed combination chemoimmunotherapy a few months before developing respiratory symptoms. In such non-transplant patients, monitoring for adenovirus in the blood is not routine. However, with adenoviruses, when there is a more peripheral (i.e. non-blood) site of infection such as the chest, serial adenovirus monitoring in blood for the duration of that illness may be warranted. CASE PRESENTATION: This case started with an initial bacterial chest infection that responded to treatment, followed by an adenovirus pneumonitis that disseminated to his blood a week later with levels of up to 92 million adenovirus DNA copies/ml. Despite prompt treatment with cidofovir, his respiratory function continued to deteriorate over the next two weeks and he was moved to intensive care. Intravenous immunoglobulin and ribavirin were subsequently added to his treatment. However, he died soon after this with a final adenovirus load of 20 million copies/ml in his blood. CONCLUSIONS: We recommend that even in non-transplant haematology patients, where such patients present with an acute respiratory adenovirus infection, teams should consider checking the blood for adenovirus to check for signs of disseminated infection. The earlier this can be tested, the earlier treatment can be initiated (if adenovirus positive), which may produce more successful clinical outcomes.


id: cord-003085-7krf1yxz
author: Li, Xi
date: 2018-06-28
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6027797/
doi: 10.1186/s12879-018-3195-5
title:
  Cytomegalovirus infection and outcome in immunocompetent patients in the intensive care unit: a systematic review and meta-analysis

abstract:
  BACKGROUND: Cytomegalovirus (CMV) infection is common in immunocompetent patients in intensive care units (ICUs). However, whether CMV infection or CMV reactivation contributes to mortality of immunocompetent patients remains unclear. METHODS: A literature search was conducted for relevant studies published before May 30, 2016. Studies reporting on CMV infection in immunocompetent patients in ICUs and containing 2 × 2 tables on CMV results and all-cause mortality were included. RESULTS: Eighteen studies involving 2398 immunocompetent patients admitted to ICUs were included in the meta-analysis. The overall rate of CMV infection was 27% (95%CI 22–34%, I(2) = 89%, n = 2398) and the CMV reactivation was 31% (95%CI 24–39%, I(2) = 74%, n = 666). The odds ratio (OR) for all-cause mortality among patients with CMV infection, compared with those without infection, was 2.16 (95%CI 1.70–2.74, I(2) = 10%, n = 2239). Moreover, upon exclusion of studies in which antiviral treatment was possibly or definitely provided to some patients, the association of mortality rate with CMV infection was also statistically significant (OR: 1.69, 95%CI 1.01–2.83, I(2) = 37%, n = 912,). For CMV seropositive patients, the OR for mortality in patients with CMV reactivation as compared with patients without CMV reactivation was 1.72 (95%CI 1.04–2.85, I(2) = 29%, n = 664). Patients with CMV infection required significantly longer mechanical ventilation (mean difference (MD): 9 days (95% CI 5–14, I(2) = 81%, n = 875)) and longer duration of ICU stay (MD: 12 days (95% CI 7–17, I(2) = 70%, n = 949)) than patients without CMV infection. When analysis was limited to detection in blood, CMV infection without antiviral drug treatment or reactivation was not significantly associated with higher mortality (OR: 1.69, 95%CI 0.81–3.54, I(2) = 52%, n = 722; OR: 1.49, I(2) = 63%, n = 469). CONCLUSION: Critically ill patients without immunosuppression admitted to ICUs show a high rate of CMV infection. CMV infection during the natural unaltered course or reactivation in critically ill patients is associated with increased mortality, but have no effect on mortality when CMV in blood. More studies are needed to clarify the impact of CMV infection on clinical outcomes in those patients. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3195-5) contains supplementary material, which is available to authorized users.


id: cord-003372-cpl7zf7f
author: Provoost, Judith
date: 2018-12-14
txt: ./txt/cord-003372-cpl7zf7f.txt
cache: ./cache/cord-003372-cpl7zf7f.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6295085/
doi: 10.1186/s12879-018-3559-x
summary:
  METHODS: This retrospective, single center study (2013–2016, 45 months) addressed the criteria supporting treatment decision among adults with NTM lung disease without systemic immunodeficiency at our institution, with the assigned goal to harmonize the practice. Patients'' characteristics at diagnosis were collected in order to perform analysis on 146 selected variables: demographics; history of predisposing factors; underlying pulmonary diseases; comorbidities; pulmonary function testing; respiratory bacterial or mycological co-infection(s), which definition was similar to NTM criteria, namely positive culture isolation of the same species from at least two separate expectorated sputum samples or a positive culture result from at least one bronchial wash or lavage; immunologic status; nutritional status; clinical features; microbiologic assessment through identification of NTM species on positive NTM cultures and sample culture conversions; radiologic features on high-resolution CT-scans (fibrocavitary disease or nodular/bronchiectasis disease); prior treatment for NTM lung disease, treatment combination and duration; outcome.

title:
  A retrospective study of factors associated with treatment decision for nontuberculous mycobacterial lung disease in adults without altered systemic immunity

abstract:
  BACKGROUND: Nontuberculous mycobacteria (NTM) lung diseases are increasingly recognized as chronic opportunistic infections, occurring in individuals with a wide variety of underlying conditions. In the absence of systemic immunodeficiency, decision of NTM lung disease treatment must relies on a careful risk/benefit assessment, given the requirement of long-term administration of multidrug therapies supported by limited evidence. The primary objective was to identify the factors associated with anti-NTM treatment initiation. Clinical and radiological outcome upon treatment were studied. METHODS: This retrospective, single center study (2013–2016, 45 months) addressed the criteria supporting treatment decision among adults with NTM lung disease without systemic immunodeficiency at our institution, with the assigned goal to harmonize the practice. All patients matched the current international definitions of NTM lung disease according to the American Thoracic Society criteria. Factors associated with anti-NTM treatment were investigated by conditional logistic regression. Clinical and radiological outcomes of treated and untreated NTM-disease cases were examined. Mortality rate was assessed. An expert radiologist conducted a blinded computed tomography (CT)-scan review of the treated and untreated patients. RESULTS: Among 51 cases of NTM lung diseases, 25 (49%) received anti-NTM treatment. In univariate analysis, a body mass index (BMI) < 18 kg/m(2) (odds ratio (OR), 4.2 [95% confidence interval (CI) 1.2–15.2]; p = 0.042), hemoptysis (OR, 11.8 [95% CI 1.35–12.9]; p = 0.026), excavation(s) (OR, 4.8 [95% CI 1.4–16.4], p = 0.012), prior anti-NTM treatment (OR, 5.65 [95% CI 1.06–29.9]; p = 0.042), Aspergillus spp. co-infection (OR, 6.3 [95% CI 1.8–22.2]; p = 0.004) were associated with treatment initiation. In multivariate analysis, Aspergillus spp. co-infection was the only independent determinant of treatment initiation (OR, 5.3 [95% CI 1.1–25.4]; p = 0.036). Twenty-one (81%) patients received ≥3 anti-NTM drugs. Median treatment duration and follow-up were 36.3 (interquartile range [IQR], 13.1–64.4) weeks and 17.1 (IQR, 8.7–27.1) months, respectively. Regarding radiological outcome, 85 CT-scans were reviewed, showing similar rates of regression or stabilization in treated and untreated patients. Overall mortality rate was not different in treated and untreated patients. CONCLUSION: The most relevant variable associated with anti-NTM treatment initiation was Aspergillus spp. co-infection. Radiological regression or stabilization of pulmonary lesions was not different between the treated and untreated patients.


id: cord-003397-fvrd128w
title: Spotted fever rickettsioses causing myocarditis and ARDS: a case from Sri Lanka
author: Herath, H. M. L. Y.
date: 2018-12-29
txt: ./txt/cord-003397-fvrd128w.txt
cache: ./cache/cord-003397-fvrd128w.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311067/
doi: 10.1186/s12879-018-3631-6
summary:
  title: Spotted fever rickettsioses causing myocarditis and ARDS: a case from Sri Lanka We describe a patient with rapidly progressing ARDS and myocarditis secondary to spotted fever caused by Rickettsia conorii. He was confirmed to have spotted fever rickettsial infection with rising titre of indirect immunofluorescence antibodies to Ricketssia conorii and made a complete recovery with appropriate antibiotic therapy and supportive care. Emergence of spotted fever group of rickettsial infections in the hilly central province of Sri Lanka was first observed in early nineties [1] . The following case report highlights myocarditis and acute respiratory distress syndrome (ARDS) as complications in a severely ill patient with spotted fever group of rickettsioses where timely diagnosis and intervention saved the life. This case demonstrates a rather rare presentation of spotted fever rickettsial infection where patient deteriorated within short time leading to shock and ARDS. Cutaneous manifestations of spotted fever rickettsial infections in the Central Province of Sri Lanka: a descriptive study

abstract:
  BACKGROUND: Spotted fever group of rickettsial infections are emerging in Sri Lanka. We describe a patient with rapidly progressing ARDS and myocarditis secondary to spotted fever caused by Rickettsia conorii. ARDS and myocarditis are rare complications of Rickettsia conorii infections and only a few cases are reported to date. CASE PRESENTATION: A 53 years old manual worker presented with fever for 5 days and a skin rash. He was in circulatory failure on admission and developed severe hypoxaemia with gross changes in chest radiograph by next day requiring assisted ventilation. He had myocarditis causing left ventricular failure and acute respiratory distress syndrome. He was confirmed to have spotted fever rickettsial infection with rising titre of indirect immunofluorescence antibodies to Ricketssia conorii and made a complete recovery with appropriate antibiotic therapy and supportive care. CONCLUSION: Rickettsial infections can present with diverse manifestations. Even the patients with severe organ involvements such as myocarditis and ARDS can be completely cured if timely identified and treated.


id: cord-003425-c5jdp5jv
title: Human adenovirus type 7 infection causes a more severe disease than type 3
author: Fu, Yangxi
date: 2019-01-09
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327436/
doi: 10.1186/s12879-018-3651-2
abstract:
  BACKGROUND: Human adenovirus type 3 (HAdV-3) and 7 (HAdV-7) cause significant morbidity and develop severe complications and long-term pulmonary sequelae in children. However, epidemiologic reports have suggested that nearly all highly severe or fatal adenoviral diseases in children are associated with HAdV-7 rather than HAdV-3. Here, we conduct in-depth investigations to confirm and extend these findings through a comprehensive series of assays in vitro and in vivo as well as clinical correlates. METHODS: A total of 8248 nasopharyngeal aspirate (NPA) samples were collected from hospitalized children with acute respiratory infections in Children’s Hospital of Chongqing Medical University from June 2009 to May 2015. Among 289 samples that tested positive for HAdVs, clinical data of 258 cases of HAdV-3 (127) and HAdV-7 (131) infections were analyzed. All HAdV-positive samples were classified by sequencing the hexon and fiber genes, and compared with clinical data and virological assays. We also performed in vitro assays of virus quantification, viral growth kinetics, competitive fitness, cytotoxicity and C3a assay of the two strains. Mouse adenovirus model was used to evaluate acute inflammatory responses. RESULTS: Clinical characteristics revealed that HAdV-7 infection caused more severe pneumonia, toxic encephalopathy, respiratory failure, longer mean hospitalization, significantly lower white blood cell (WBC) and platelet counts, compared to those of HAdV-3. In cell culture, HAdV-7 replicated at a higher level than HAdV-3, and viral fitness showed significant differences as well. HAdV-7 also exhibited higher C3a production and cytotoxic effects, and HAdV-7-infected mice showed aggravated pathology and higher pulmonary virus loads, compared to HAdV-3-infected mice. Macrophages in BALF remained markedly high during infection, with concomitant increase in pro-inflammatory cytokines (TNF-α, IL-1β, IFN-γ, and IL-6), compared HAdV-3 infection. CONCLUSIONS: These results document that HAdV-7 replicates more robustly than HAdV-3, and promotes an exacerbated cytokine response, causing a more severe airway inflammation. The findings merit further mechanistic studies that offer the pediatricians an informed decision to proceed with early diagnosis and treatment of HAdV-7 infection.


id: cord-003460-legakasx
title: APACHE-II score for anti-tuberculosis tolerance in critically ill patients: a retrospective study
author: Qiu, Junke
date: 2019-02-04
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360662/
doi: 10.1186/s12879-019-3751-7
abstract:
  BACKGROUND: To investigate the status of anti-tuberculosis treatment in critically ill patients, and to explore the value of APACHE-II score in guiding anti-tuberculosis treatment. METHODS: This analysis included critically ill patients with tuberculosis. The utility of APACHE-II score for predicting drug withdrawal was evaluated using receiver operating characteristic (ROC) curve analysis. RESULTS: Among 320 patients enrolled (58 ± 22 years; 256 males), 147 (45.9%) had drugs withdrawn. The drug withdrawal group had higher APACHE-II score (median [interquartile range]: 21 [3–52] vs. 17 [4–42] points), higher CD4%, lower hemoglobin level, higher rates of chronic obstructive pulmonary disease (COPD) and chronic renal failure, and lower rate of extrapulmonary tuberculosis (P < 0.05). Logistic regression identified APACHE-II score > 18 (odds ratio [95% confidence interval]: 2.099 [1.321–3.334], P < 0.01), COPD (1.913 [1.028–3.561], P < 0.05) and hemoglobin level (0.987 [0.977–0.997], P < 0.05) as independent factors associated with drug withdrawal. At an optimal cutoff of 18.5, the sensitivity, specificity, positive predictive value and negative predictive value of APACHE-II score for predicting drug withdrawal was 59.2, 61.8, 56.9 and 64.1%, respectively. CONCLUSIONS: APACHE-II score > 18 points might predict patient tolerance of anti-tuberculosis treatment.


id: cord-003466-599x0euj
author: Nickol, Michaela E.
date: 2019-02-06
txt: ./txt/cord-003466-599x0euj.txt
cache: ./cache/cord-003466-599x0euj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364422/
doi: 10.1186/s12879-019-3750-8
summary:
  MAIN TEXT: The 1918 H1N1 pandemic virus spread across Europe, North America, and Asia over a 12-month period resulting in an estimated 500 million infections and 50–100 million deaths worldwide, of which ~ 50% of these occurred within the fall of 1918 (Emerg Infect Dis 12:15-22, 2006, Bull Hist Med 76:105-115, 2002). Influenza viruses have posed a continual threat to global public health since at least as early as the Middle Ages, resulting in an estimated 3-5 million cases of severe illness and 291,243-645,832 deaths annually worldwide, according to a recent estimate [1] . To be considered a pandemic, an influenza virus must: i) spread globally from a distinct location with high rates of infectivity resulting in increased mortality; and ii) the hemagglutinin (HA) cannot be related to influenza strains circulating prior to the outbreak nor have resulted from mutation [14, 15] .

title:
  A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919

abstract:
  BACKGROUND: In the spring of 1918, the “War to End All Wars”, which would ultimately claim more than 37 million lives, had entered into its final year and would change the global political and economic landscape forever. At the same time, a new global threat was emerging and would become one of the most devastating global health crises in recorded history. MAIN TEXT: The 1918 H1N1 pandemic virus spread across Europe, North America, and Asia over a 12-month period resulting in an estimated 500 million infections and 50–100 million deaths worldwide, of which ~ 50% of these occurred within the fall of 1918 (Emerg Infect Dis 12:15-22, 2006, Bull Hist Med 76:105-115, 2002). However, the molecular factors that contributed to the emergence of, and subsequent public health catastrophe associated with, the 1918 pandemic virus remained largely unknown until 2005, when the characterization of the reconstructed pandemic virus was announced heralding a new era of advanced molecular investigations (Science 310:77-80, 2005). In the century following the emergence of the 1918 pandemic virus we have landed on the Moon, developed the electronic computer (and a global internet), and have eradicated smallpox. In contrast, we have a largely remedial knowledge and understanding of one of the greatest scourges in recorded history. CONCLUSION: Here, we reflect on the 1918 influenza pandemic, including its emergence and subsequent rapid global spread. In addition, we discuss the pathophysiology associated with the 1918 virus and its predilection for the young and healthy, the rise of influenza therapeutic research following the pandemic, and, finally, our level of preparedness for future pandemics.


id: cord-003526-ykisq8nz
author: Kallel, Hatem
date: 2019-03-15
txt: ./txt/cord-003526-ykisq8nz.txt
cache: ./cache/cord-003526-ykisq8nz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420753/
doi: 10.1186/s12879-019-3887-5
summary:
  title: Capillary leak-syndrome triggered by Maripa virus in French Guiana: case report and implication for pathogenesis BACKGROUND: We report hereby a severe case of Hantavirus Pulmonary Syndrome" (HPS) induced by Maripa virus in French Guiana and describe the mechanism of severity of the human disease. CONCLUSIONS: The severity of HPS caused by the virus Maripa in French Guiana can be explained by the tropism of hantavirus for the microvascular endothelial cell leading to a CLS. We report here a human case of acute Maripa virus related pulmonary syndrome managed in the ICU of French Guiana with a clear evidence of associated capillary leak syndrome responsible for the severity of the disease. Two patients with severe capillary leak syndrome caused by a Puumala hantavirus infection were successfully treated with a bradykinin receptor antagonist [11, 12] . Hantavirus pulmonary syndrome caused by Maripa virus in French Guiana

title:
  Capillary leak-syndrome triggered by Maripa virus in French Guiana: case report and implication for pathogenesis

abstract:
  BACKGROUND: We report hereby a severe case of Hantavirus Pulmonary Syndrome” (HPS) induced by Maripa virus in French Guiana and describe the mechanism of severity of the human disease. CASE PRESENTATION: A 47-year- old patient started presenting a prodromic period with fever, dyspnea, cough and head ache. This clinical presentation was followed by a rapid respiratory, hemodynamic and renal failure leading to admission in the ICU. Biological exams revealed an increased haematocrit level with a paradoxical low protein level. Echocardiographic and hemodynamic monitoring showed a normal left ventricular function with low filling pressures, an elevated extravascular lung water index and pulmonary vascular permeability index. These findings were compatible with a capillary leak-syndrome (CLS). CONCLUSIONS: The severity of HPS caused by the virus Maripa in French Guiana can be explained by the tropism of hantavirus for the microvascular endothelial cell leading to a CLS.


id: cord-003533-8m0vyxq8
title: An outbreak of leptospirosis with predominant cardiac involvement: a case series
author: Jayathilaka, P. G. N. S.
date: 2019-03-18
txt: ./txt/cord-003533-8m0vyxq8.txt
cache: ./cache/cord-003533-8m0vyxq8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423826/
doi: 10.1186/s12879-019-3905-7
summary:
  We present a case series of severe leptospirosis with cardiac involvement observed during a period of one month at Colombo-North Teaching Hospital, Sri Lanka. CASE PRESENTATION: We report here five patients with severe leptospirosis complicated with cardiac involvement, admitted to a single medical ward, Colombo-North Teaching Hospital, Sri Lanka during a one-month period. In this case series, we describe a series of male patients with severe leptospirosis with cardiac involvement, presented to a single medical ward during a period of one month. By day eleven of illness he was completely recovered clinically and full blood count, liver function tests, renal function tests and ECG were normal. Patient was discharged from the ward on day 7 of illness with complete recovery and normal full blood count, renal and liver function tests. Despite adequate fluid resuscitation patient developed shock with low urine output on the same day of admission.

abstract:
  BACKGROUND: Severe leptospirosis is known to cause multi organ dysfunction including cardiac involvement. In the clinical setting with limited resources, high degree of suspicion is needed to diagnose cardiac involvement including myocarditis. Although myocarditis is not reported as a common complication due to lack of diagnostic facilities, there are evidence to support myocarditis is more prevalent in post mortem studies of patients died due to leptospirosis. We present a case series of severe leptospirosis with cardiac involvement observed during a period of one month at Colombo-North Teaching Hospital, Sri Lanka. CASE PRESENTATION: We report here five patients with severe leptospirosis complicated with cardiac involvement, admitted to a single medical ward, Colombo-North Teaching Hospital, Sri Lanka during a one-month period. Out of six suspected leptospirosis patients admitted during that period, five in a raw developed severe leptospirosis with cardiac involvement. In this case series, four patients were confirmed serologically or quantitative PCR and one patient had possible leptospirosis. All patients developed shock during their course of illness. Two patients developed rapid atrial fibrillation. One patient had dynamic T wave changes in ECG and the other two had sinus tachycardia. Two patients had evidence of myocarditis in 2D echocardiogram, whereas other two patients had nonspecific findings and one patient had normal 2D echocardiogram. All five patients had elevated cardiac troponin I titre and it was normalized with the recovery. All five patients developed acute kidney injury. Four patients needed inotropic/vasopressor support to maintain mean arterial pressure and one patient recovered from shock with fluid resuscitation. All patients were recovered from their illness and repeat 2D echocardiograms after recovery did not show residual complications. One patient had serologically proven dengue co-infection with leptospirosis. CONCLUSIONS: Myocarditis and cardiac involvement in leptospirosis may be overlooked due to non-specific clinical findings and co-existing multi-organ dysfunction. Atypical presentation of this case series may be due to micro-geographic variation and unusual outbreak of leptospirosis. Co-infection of dengue with leptospirosis should be considered in managing patients especially in endemic areas.


id: cord-003803-1t4xyayf
author: He, Hangyong
date: 2019-07-29
txt: ./txt/cord-003803-1t4xyayf.txt
cache: ./cache/cord-003803-1t4xyayf.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6664529/
doi: 10.1186/s12879-019-4306-7
summary:
  title: Successful management of refractory respiratory failure caused by avian influenza H7N9 and secondary organizing pneumonia: a case report and literature review Human infected with avian influenza A H7N9 virus were first confirmed on March 30th, 2013 in China [1, 2] , with high incidence of severe respiratory failure, high intensive care unit (ICU) admission and mortality. However, refractory severe respiratory failure caused by OP secondary to avian influenza H7N9 virus infection was first reported in this case. In these cases reported, OP onset mostly at the second to third week in the course of influenza, and occurred after the releasing of primary virus infection; And the OP is complicated with respiratory failure, and no evidence of other pathogen was found; And the main findings on HRCT for this kind of OP were GGO and consolidation.

title:
  Successful management of refractory respiratory failure caused by avian influenza H7N9 and secondary organizing pneumonia: a case report and literature review

abstract:
  BACKGROUD: Organizing pneumonia (OP) is a rare complication of influenza infection that has substantial morbidity. We report the first case of OP associated with avian influenza H7N9 infection that had significant improvement with corticosteroid treatment. CASE PRESENTATION: A 35-year-old male admitted to intensive care unit because of respiratory failure. He was diagnosed as severe pneumonia caused by avian influenza H7N9 viral infection. After initial clinical improvement supported by extracorporeal membrane oxygenation (ECMO), the patient’s condition worsened with persistent fever, refractory hypoxemia. Chest x-rays and computed tomographies showed areas of consolidation and ground glass opacification. Although OP was suspected and 1 mg/kg methylprednisolone was used, the patient’s condition didn’t improved considerably. An open lung biopsy was performed, and histopathological examination of the specimen was compatible with OP. The patient was treated with methylprednisolone 1.5 mg/kg for 5 days. ECMO was weaned on day 15, and he was discharged on day 71 with good lung recovery. CONCLUSIONS: To the best of our knowledge, this was the first case of successful management of refractory severe respiratory failure caused by avian influenza H7N9 infection complicated with OP. Refractory hypoxia with clinical manifestation and radiological findings compatible with OP, a differential diagnosis should be considered among patients at the second or third week of influenza H7N9 infection, especially in patients with clinical condition deteriorated after the primary influenza pneumonia was controlled. And a steroid dose of methylprednisolone 1.5 mg/kg may be suggested for treatment of OP associated with avian influenza H7N9 infection.


id: cord-003856-05u4t67u
author: Mao, Ying
date: 2019-09-02
txt: ./txt/cord-003856-05u4t67u.txt
cache: ./cache/cord-003856-05u4t67u.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6721277/
doi: 10.1186/s12879-019-4400-x
summary:
  In China, eight IIDs are listed as notifiable infectious diseases, including cholera, poliomyelitis, dysentery, typhoid and paratyphoid (TAP), viral Hepatitis A, viral Hepatitis E, hand-foot-mouth disease (HFMD) and other infectious diarrhoeal diseases (OIDDs). Plots and maps were constructed to visualize the spatio-temporal distribution of IIDs. RESULTS: Regarding temporal analysis, the incidence of HFMD and Hepatitis E showed a distinct increasing trend, while the incidence of TAP, dysentery, and Hepatitis A presented decreasing trends over the last decade. CONCLUSIONS: Based on our temporal and spatial analysis of IIDs, we identified the high-risk periods and clusters of regions for the diseases. Eight IIDs are listed in the law, including cholera, poliomyelitis, dysentery, typhoid and paratyphoid (TAP), viral Hepatitis A, viral Hepatitis E, hand-foot-mouth disease (HFMD) and other infectious intestinal diseases (OIIDs). Figure 1 shows the results of the decomposition analysis for all IIDs. Regarding the seasonal variation, the incidence rates of HFMD and dysentery were high in summer.

title:
  A descriptive analysis of the Spatio-temporal distribution of intestinal infectious diseases in China

abstract:
  BACKGROUND: Intestinal infectious diseases (IIDs) have caused numerous deaths worldwide, particularly among children. In China, eight IIDs are listed as notifiable infectious diseases, including cholera, poliomyelitis, dysentery, typhoid and paratyphoid (TAP), viral Hepatitis A, viral Hepatitis E, hand-foot-mouth disease (HFMD) and other infectious diarrhoeal diseases (OIDDs). The aim of the study is to analyse the spatio-temporal distribution of IIDs from 2006 to 2016. METHODS: Data on the incidence of IIDs from 2006 to 2016 were collected from the public health science data centre issued by the Chinese Center for Disease Control and Prevention. This study applied seasonal decomposition analysis, spatial autocorrelation analysis and space-time scan analysis. Plots and maps were constructed to visualize the spatio-temporal distribution of IIDs. RESULTS: Regarding temporal analysis, the incidence of HFMD and Hepatitis E showed a distinct increasing trend, while the incidence of TAP, dysentery, and Hepatitis A presented decreasing trends over the last decade. The incidence of OIID remained steady. Summer is the season with the greatest number of cases of different IIDs. Regarding the spatial distribution, approximately all p values for the global Moran’s I from 2006 to 2016 were less than 0.05, indicating that the incidences of the epidemics were unevenly distributed throughout the country. The high-risk areas for HFMD and OIDD were located in the Beijing-Tianjin-Tangshan (BTT) region and south China. The high-risk areas for TAP were located in some parts of southwest China. A higher incidence rates for dysentery and Hepatitis A were observed in the BTT region and some west provincial units. The high-risk areas for Hepatitis E were the BTT region and the Yangtze River Delta area. CONCLUSIONS: Based on our temporal and spatial analysis of IIDs, we identified the high-risk periods and clusters of regions for the diseases. HFMD and OIDD exhibited high incidence rates, which reflected the negligence of Class C diseases by the government. At the same time, the incidence rate of Hepatitis E gradually surpassed Hepatitis A. The authorities should pay more attention to Class C diseases and Hepatitis E. Regardless of the various distribution patterns of IIDs, disease-specific, location-specific, and disease-combined interventions should be established. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-019-4400-x) contains supplementary material, which is available to authorized users.


id: cord-004110-xc8vv9x8
author: Eslahi, Aida Vafae
date: 2020-01-07
txt: ./txt/cord-004110-xc8vv9x8.txt
cache: ./cache/cord-004110-xc8vv9x8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6947998/
doi: 10.1186/s12879-020-4759-8
summary:
  Herein, a meta-analysis was contrived to assess the prevalence of Toxocara/Toxascaris in carnivore and human hosts in different regions of Iran from April 1969 to June 2019. CONCLUSION: Our meta-analysis results illustrate a considerable prevalence rate of Toxocara/Toxascaris, particularly in cats and dogs of northern parts of Iran. A combination of the following search terms were employed in our literature searches as follows: ("Toxocariasis" OR "Toxocara infection" OR "Toxocara canis" OR "Toxocara cati" OR "Toxascaris leonina") AND ("Carnivora" OR "Human") AND ("Prevalence" OR "Epidemiology") AND ("Iran"). in various carnivores and human populations in Iran; (D) Studies that detected Toxocara infection using at least one of the parasitological, serological and molecular methods; (e) exact total sample size, positive samples and the respective prevalence rates were available. The weighted prevalence of Toxocara/ Toxascaris in Iran dogs by study method Additional file 5: Figure S5 .

title:
  Prevalence of Toxocara and Toxascaris infection among human and animals in Iran with meta-analysis approach

abstract:
  BACKGROUND: Toxocariasis is a worldwide zoonotic parasitic disease caused by species of Toxocara and Toxascaris, common in dogs and cats. Herein, a meta-analysis was contrived to assess the prevalence of Toxocara/Toxascaris in carnivore and human hosts in different regions of Iran from April 1969 to June 2019. METHODS: The available online articles of English (PubMed, Science Direct, Scopus, and Ovid) and Persian (SID, Iran Medex, Magiran, and Iran Doc) databases and also the articles that presented in held parasitology congresses of Iran were involved. RESULTS: The weighted prevalence of Toxocara/Toxascaris in dogs (Canis familiaris) and cats (Felis catus) was 24.2% (95% CI: 18.0–31.0%) and 32.6% (95% CI: 22.6–43.4%), respectively. Also, pooled prevalence in jackal (Canis aureus) and red fox (Vulpes vulpes) was 23.3% (95% CI: 7.7–43.2%) and 69.4% (95% CI: 60.3–77.8%), correspondingly. Weighted mean prevalence of human cases with overall 28 records was 9.3% (95% CI: 6.3–13.1%). The weighted prevalence of Toxocara canis, Toxocara cati, and Toxascaris leonina was represented as 13.8% (95% CI: 9.8–18.3%), 28.5% (95% CI: 20–37.7%) and 14.3% (95% CI: 8.1–22.0%), respectively. CONCLUSION: Our meta-analysis results illustrate a considerable prevalence rate of Toxocara/Toxascaris, particularly in cats and dogs of northern parts of Iran. The presence of suitable animal hosts, optimum climate and close contact of humans and animals would have been the reason for higher seroprevalence rates of human cases in our region. Given the significance clinical outcomes of human Toxocara/Toxascaris, necessary measures should be taken.


id: cord-004198-h8ch3x14
author: Ebuy, Hiluf
date: 2020-01-21
txt: ./txt/cord-004198-h8ch3x14.txt
cache: ./cache/cord-004198-h8ch3x14.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6975065/
doi: 10.1186/s12879-020-4790-9
summary:
  title: HIV testing, test results and factors influencing among infants born to HIV positive mothers in public hospitals of Mekelle City, North Ethiopia: a cross-sectional study While world health organization recommends HIV exposed infants to be tested between 4 to 6 weeks of age, in developing countries like Ethiopia, access to timely infant testing is still very limited. The study is intended to assess timely infant testing, testing for HIV at the 18th month, test results and factors influencing HIV positivity among infants born to HIV positive mothers in public hospitals of Mekelle, Ethiopia. Timely infant testing, counselling on feeding options and adherence should be intensified, and prevention of mother-to-child transmission program in rural settings need to be strengthened. Thus, the present study is intended to assess timely infant testing, testing for HIV at the 18th month, test results and factors influencing overall HIV positivity and HIV positivity at 18 months among infants born to HIV positive mothers in public hospitals of Mekelle city, North Ethiopia.

title:
  HIV testing, test results and factors influencing among infants born to HIV positive mothers in public hospitals of Mekelle City, North Ethiopia: a cross-sectional study

abstract:
  BACKGROUND: Timely infant testing for HIV is critical to ensure optimal treatment outcomes among exposed infants. While world health organization recommends HIV exposed infants to be tested between 4 to 6 weeks of age, in developing countries like Ethiopia, access to timely infant testing is still very limited. The study is intended to assess timely infant testing, testing for HIV at the 18th month, test results and factors influencing HIV positivity among infants born to HIV positive mothers in public hospitals of Mekelle, Ethiopia. METHODS: A cross-sectional study design was employed on 558 HIV exposed infants, using consecutive sampling technique. A checklist was used to extract 4 years (January 2014–December 2017) secondary data, collected from January–April 2018. Data were analyzed using SPSS version 20, and binary logistic regression model was used to examine the association of independent variables with the outcome variables. RESULTS: Timely infant testing for HIV accounted for 346(62.0%). Mothers who attended antenatal care (AOR: 2.77; 95% CI: 1.17, 6.55) and who were counselled on feeding options (AOR: 2.01; 95% CI: 1.11, 3.65) were strongly associated with timely infant testing. Poor maternal adherence status was associated with infants’ HIV positivity at the 18th month of antibody test (AOR: 15.93; 95% CI: 2.21, 94.66). Being rural resident (AOR: 4.0; 95% CI: 1.23, 13.04), being low birth weight (AOR: 5.64; 95% CI: 2.00, 16.71) and not receiving ARV prophylaxis (AOR: 4.70; 95% CI: 1.15, 19.11) were positively associated with the overall HIV positivity. CONCLUSIONS: A considerable proportion of exposed infants did not undergo timely testing for HIV. Antenatal care follow-up and counselling on feeding options were associated with timely infant testing. Mother’s poor adherence status was associated with infant’s HIV positivity at the 18th month of antibody testing. Being rural resident, being low birth weight, and not receiving ARV prophylaxis were the factors that enhance the overall HIV positivity. Timely infant testing, counselling on feeding options and adherence should be intensified, and prevention of mother-to-child transmission program in rural settings need to be strengthened.


id: cord-004239-cu6atqvr
author: Morikane, Keita
date: 2020-01-29
txt: ./txt/cord-004239-cu6atqvr.txt
cache: ./cache/cord-004239-cu6atqvr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6988210/
doi: 10.1186/s12879-020-4805-6
summary:
  title: Clinical and microbiological effect of pulsed xenon ultraviolet disinfection to reduce multidrug-resistant organisms in the intensive care unit in a Japanese hospital: a before-after study This study aimed to evaluate the effectiveness of disinfection by portable pulsed xenon ultraviolet (PX-UV) devices in controlling transmission of MDROs in a non-US healthcare setting. Ultraviolet light disinfection has recently been used as an adjunct to terminal cleaning, and many studies have shown its effectiveness in reducing environmental contamination [3] [4] [5] and healthcare-associated transmission of these pathogens [6] [7] [8] [9] [10] [11] [12] . There are a number of studies which have demonstrated the effect of ultraviolet light disinfection in reducing environmental microbiological contamination [3] [4] [5] and healthcare-acquired infections by MRSA [6, 7] , VRE [7, 8] and Clostridioides difficile [7] [8] [9] [10] [11] [12] .

title:
  Clinical and microbiological effect of pulsed xenon ultraviolet disinfection to reduce multidrug-resistant organisms in the intensive care unit in a Japanese hospital: a before-after study

abstract:
  BACKGROUND: No-touch environmental disinfection using ultraviolet devices has been highlighted in the past several years to control the transmission of multidrug-resistant organisms (MDROs). However, its effectiveness in non-US healthcare settings is yet to be examined. This study aimed to evaluate the effectiveness of disinfection by portable pulsed xenon ultraviolet (PX-UV) devices in controlling transmission of MDROs in a non-US healthcare setting. METHODS: All patients admitted in the intensive care unit in a 629-bed tertiary referral hospital in Japan from August 2016 to February 2019 were enrolled. During the study period, PX-UV disinfection was added to manual terminal cleaning after every patient transfer/discharge. For microbiological evaluation, surfaces were selected for sampling by contact plates before/after manual cleaning and after PX-UV. After overnight incubation, colonies on the plates were counted. RESULTS: The incidence of newly acquired methicillin-resistant Staphylococcus aureus (MRSA) declined significantly (13.8 to 9.9 per 10,000 patient days, incidence rate ratio 0.71, p = 0.002), as well as that of newly acquired drug-resistant Acinetobacter (48.5 to 18.1, 0.37, p < 0.001). The percent reduction of the microbiological burden by manual cleaning was 81%, but a further 59% reduction was achieved by PX-UV. CONCLUSIONS: PX-UV is effective in further reducing the microbial burden and controlling MDROs in a non-US healthcare setting.


id: cord-004316-mnqn1t3q
author: Zhao, Xia
date: 2020-02-10
txt: ./txt/cord-004316-mnqn1t3q.txt
cache: ./cache/cord-004316-mnqn1t3q.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7011547/
doi: 10.1186/s12879-020-4840-3
summary:
  title: Epidemiological and clinical characteristics of healthcare-associated infection in elderly patients in a large Chinese tertiary hospital: a 3-year surveillance study BACKGROUND: We analyzed the results of a 3-year surveillance study on the epidemiological and clinical characteristics of healthcare associated-infections (HAIs) in elderly inpatients in a large tertiary hospital in China. Here we describe and analyze the results of a 3-year real-time surveillance study on the incidence of HAIs and the epidemiological and clinical characteristics of elderly inpatients in a large tertiary hospital in China. The incidence of ventilator-associated pneumonia (VAP) in elderly patients was lower than in non-elderly patients, catheter-associated urinary tract infections (CAUTIs) were significantly more common in elderly patients, and central line-associated bloodstream infection (CLABSI) rates were similar in both groups (Tables 2 and 3 ).

title:
  Epidemiological and clinical characteristics of healthcare-associated infection in elderly patients in a large Chinese tertiary hospital: a 3-year surveillance study

abstract:
  BACKGROUND: We analyzed the results of a 3-year surveillance study on the epidemiological and clinical characteristics of healthcare associated-infections (HAIs) in elderly inpatients in a large tertiary hospital in China. METHODS: Real-time surveillance was performed from January 1, 2015 to December 31, 2017. All HAIs were identified by infection control practitioners and doctors. Inpatient data were collected with an automatic surveillance system. RESULTS: A total of 134,637 inpatients including 60,332 (44.8%) elderly ≥60 years were included. The overall incidence of HAI was 2.0%. The incidence of HAI in elderly patients was significantly higher than that in non-elderly patients (2.6% vs. 1.5%, χ(2) = 202.421, P < 0.01) and increased with age. The top five sites of HAIs in the elderly were the lower respiratory tract, urinary tract, blood stream, antibiotic-associated diarrhea, and surgical site. The five most common pathogens detected in elderly HAI patients were Candida albicans, Klebsiella pneumonia, Acinetobacter baumannii, Escherichia coli, and Pseudomonas aeruginosa. The incidence of ventilator-associated pneumonia in the elderly was lower than in the non-elderly, catheter-associated urinary tract infections were more common in elderly patients, and the rate of central line-associated bloodstream infection was similar between groups. The numbers of male patients and patients with comorbidities and special medical procedures (e.g., intensive care unit admission, cerebrovascular disease, brain neoplasms, hypertension, hyperlipidemia, diabetes mellitus, coronary artery disease, chronic obstructive pulmonary disease, malignant tumor, malignant hematonosis, and osteoarthropathy) were significantly higher in the elderly group, but the number of patients who underwent surgery was lower. CONCLUSION: We observed a significantly higher overall incidence of HAI in elderly inpatients ≥60 compared to non-elderly inpatients < 60 years, but the trend was different for device-associated HAIs, which was attributed to the higher rates of comorbidities and special medical procedures in the elderly group. The main HAI sites in elderly inpatients were the lower respiratory tract, urinary tract, and bloodstream, and the main pathogens were gram-negative bacilli and Candida albicans.


id: cord-004394-0h2wvv40
author: Li, Fengqin
date: 2020-02-22
txt: ./txt/cord-004394-0h2wvv40.txt
cache: ./cache/cord-004394-0h2wvv40.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7036182/
doi: 10.1186/s12879-020-4892-4
summary:
  title: Vancomycin-resistant Enterococcus faecium pneumonia in a uremic patient on hemodialysis: a case report and review of the literature CONCLUSIONS: Physicians should consider multi-drug resistant organisms such as VRE in uremic patients with pneumonia that fails to resolve with broad-spectrum antibiotics, especially in the cases with aspiration induced by epilepsy, immunocompromised conditions, and repeated or prolonged hospitalizations. In this case report, we aimed to present a uremic patient with VRE-fm pneumonia, possibly related to epileptic seizures, being treated successfully with linezolid. Previous case reports of enterococcal pneumonia were based on clinical findings and infiltrate on chest X ray or CT in combination with the isolation of enterococci in cultures from a transtracheal aspirate, protected brush (PS), bronchoalveolar lavage (BAL), sputum or lung tissue. Physicians should consider multi-drug resistant organisms such as VRE in uremic patients with pneumonia that fails to resolve with broad-spectrum antibiotics, especially in the cases with aspiration induced by epilepsy, immunocompromised conditions, and repeated or prolonged hospitalizations.

title:
  Vancomycin-resistant Enterococcus faecium pneumonia in a uremic patient on hemodialysis: a case report and review of the literature

abstract:
  BACKGROUND: Even though enterococci can cause serious infections in multiple sites, they are a rare cause of pneumonia. We reported a uremic patient with vancomycin-resistant E. faecium (VRE-fm) pneumonia, possibly related to epileptic seizures. CASE PRESENTATION: A 57-year old man with uremia on hemodialysis was admitted to the hospital with complaint of recurrent epileptic seizures, followed by a two-week history of recurrent fever and cough with purulent sputum. Chest CT demonstrated multiple exudation of both lungs. He was diagnosed as community acquired pneumonia. Despite antibiotic combination therapy, abnormal chest shadows aggravated. Sputum and blood cultures were initially negative, but later blood culture grew VRE-fm. We suspected aspiration of gastrointestinal content induced by epilepsy as the most likely mechanism. The patient was successfully treated with a four-week course of linezolid according to the antibiotic susceptibility testing. CONCLUSIONS: Physicians should consider multi-drug resistant organisms such as VRE in uremic patients with pneumonia that fails to resolve with broad-spectrum antibiotics, especially in the cases with aspiration induced by epilepsy, immunocompromised conditions, and repeated or prolonged hospitalizations.


id: cord-004395-erqmbi2b
author: Bugembe, Daniel Lule
date: 2020-02-22
txt: ./txt/cord-004395-erqmbi2b.txt
cache: ./cache/cord-004395-erqmbi2b.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7036183/
doi: 10.1186/s12879-020-4876-4
summary:
  METHODS: We tested the performance of the NetMHCpan4.0 computational neural network in re-identifying 93 T-cell epitopes that had been previously independently mapped using the whole proteome IFN-γ ELISPOT assays in 6 HLA class I typed Ugandan individuals infected with HIV-1 subtypes A1 and D. Using experimental epitope mapping data generated from 757 peptides tested on cells of 6 early HIV-1 infected individuals at paired time points, we show that NetMHCpan4.0 can be useful for markedly reducing pooled peptide experiments as demonstrated by the 95% experimental and computational concordance. Experimental data of peptides previously mapped for HIV-1 epitope recognition of 6 individuals for a separate study (Table 1) at 2 time points each was used for comparison with the computationally predicted binders. In this analysis we showed that the computational method NetMHCpan4.0 predicted 95% of previously experimentally mapped HIV-1 epitopes in 6 HIV-1 infected individuals expressing a total of 22 different HLA class I alleles.

title:
  Computational MHC-I epitope predictor identifies 95% of experimentally mapped HIV-1 clade A and D epitopes in a Ugandan cohort

abstract:
  BACKGROUND: Identifying immunogens that induce HIV-1-specific immune responses is a lengthy process that can benefit from computational methods, which predict T-cell epitopes for various HLA types. METHODS: We tested the performance of the NetMHCpan4.0 computational neural network in re-identifying 93 T-cell epitopes that had been previously independently mapped using the whole proteome IFN-γ ELISPOT assays in 6 HLA class I typed Ugandan individuals infected with HIV-1 subtypes A1 and D. To provide a benchmark we compared the predictions for NetMHCpan4.0 to MHCflurry1.2.0 and NetCTL1.2. RESULTS: NetMHCpan4.0 performed best correctly predicting 88 of the 93 experimentally mapped epitopes for a set length of 9-mer and matched HLA class I alleles. Receiver Operator Characteristic (ROC) analysis gave an area under the curve (AUC) of 0.928. Setting NetMHCpan4.0 to predict 11-14mer length did not improve the prediction (37–79 of 93 peptides) with an inverse correlation between the number of predictions and length set. Late time point peptides were significantly stronger binders than early peptides (Wilcoxon signed rank test: p = 0.0000005). MHCflurry1.2.0 similarly predicted all but 2 of the peptides that NetMHCpan4.0 predicted and NetCTL1.2 predicted only 14 of the 93 experimental peptides. CONCLUSION: NetMHCpan4.0 class I epitope predictions covered 95% of the epitope responses identified in six HIV-1 infected individuals, and would have reduced the number of experimental confirmatory tests by > 80%. Algorithmic epitope prediction in conjunction with HLA allele frequency information can cost-effectively assist immunogen design through minimizing the experimental effort.


id: cord-004397-ypli7wtu
author: Ma, Zhan-Ying
date: 2020-02-22
txt: ./txt/cord-004397-ypli7wtu.txt
cache: ./cache/cord-004397-ypli7wtu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7036252/
doi: 10.1186/s12879-020-4900-8
summary:
  title: Suspension microarray-based comparison of oropharyngeal swab and bronchoalveolar lavage fluid for pathogen identification in young children hospitalized with respiratory tract infection The primary purpose of this study was to compare the detection rates of OPS and paired BALF in detecting key respiratory pathogens using suspension microarray. In the present study, we used the suspension microarray, a multipathogen detection platform, to simultaneously detect viral and bacterial respiratory pathogens in matched OPS and BALF specimens from pediatric patients for comparison of the sensitivities between the two sample types. To compare the OPS and paired BALF for pathogens detection in young children with RTI, we tested the two sample types using suspension microarray. In the present study, we used suspension array to simultaneously detect multiple viral and bacterial pathogens in paired BALF and OPS specimens from symptomatic patients hospitalized with respiratory illness. We used suspension-array to compare BALF and paired OPS specimens for detecting multiple pathogens in children hospitalized with respiratory illness.

title:
  Suspension microarray-based comparison of oropharyngeal swab and bronchoalveolar lavage fluid for pathogen identification in young children hospitalized with respiratory tract infection

abstract:
  BACKGROUND: Respiratory tract infection (RTI) in young children is a leading cause of morbidity and hospitalization worldwide. There are few studies assessing the performance for bronchoalveolar lavage fluid (BALF) versus oropharyngeal swab (OPS) specimens in microbiological findings for children with RTI. The primary purpose of this study was to compare the detection rates of OPS and paired BALF in detecting key respiratory pathogens using suspension microarray. METHODS: We collected paired OPS and BALF specimens from 76 hospitalized children with respiratory illness. The samples were tested simultaneously for 8 respiratory viruses and 5 bacteria by suspension microarray. RESULTS: Of 76 paired specimens, 62 patients (81.6%) had at least one pathogen. BALF and OPS identified respiratory pathogen infections in 57 (75%) and 49 (64.5%) patients, respectively (P > 0.05). The etiology analysis revealed that viruses were responsible for 53.7% of the patients, whereas bacteria accounted for 32.9% and Mycoplasma pneumoniae for 13.4%. The leading 5 pathogens identified were respiratory syncytial virus, Streptococcus pneumoniaee, Haemophilus influenzae, Mycoplasma pneumoniae and adenovirus, and they accounted for 74.2% of etiological fraction. For detection of any pathogen, the overall detection rate of BALF (81%) was marginally higher than that (69%) of OPS (p = 0.046). The differences in the frequency distribution and sensitivity for most pathogens detected by two sampling methods were not statistically significant. CONCLUSIONS: In this study, BALF and OPS had similar microbiological yields. Our results indicated the clinical value of OPS testing in pediatric patients with respiratory illness.


id: cord-004471-1r714dmm
author: Seo, Jun-Won
date: 2020-03-12
txt: ./txt/cord-004471-1r714dmm.txt
cache: ./cache/cord-004471-1r714dmm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7066777/
doi: 10.1186/s12879-020-4940-0
summary:
  title: Scalp eschar and neck lymphadenopathy after tick bite (SENLAT) caused by Bartonella henselae in Korea: a case report BACKGROUND: Tick-borne lymphadenopathy (TIBOLA) is an infectious disease, mainly caused by species from the spotted fever group rickettsiae and is characterized by enlarged lymph nodes following a tick bite. Tick-borne lymphadenopathy (TIBOLA) is an infectious disease, mainly caused by species from the spotted fever group rickettsiae (e.g. Rickettsia slovaca, Rickettsia raoultii) and is characterized by enlarged lymph nodes following a tick bite. hensealse was < 1:20 at both first visit and Fig. 1 A photograph of the eschar on the scalp and right cervical area of a 58-year-old male patient with a confirmed diagnosis of Bartonella henselae, and a cytology report from fine needle aspiration of an enlarged cervical lymph node. henselae from pus aspirates and lymph node biopsy specimens of patients with cat scratch disease have been reported [21] , and very low levels of sensitivity in serologic and PCR tests have been found against B.

title:
  Scalp eschar and neck lymphadenopathy after tick bite (SENLAT) caused by Bartonella henselae in Korea: a case report

abstract:
  BACKGROUND: Tick-borne lymphadenopathy (TIBOLA) is an infectious disease, mainly caused by species from the spotted fever group rickettsiae and is characterized by enlarged lymph nodes following a tick bite. Among cases of TIBOLA, a case of scalp eschar and neck lymphadenopathy after tick bite (SENLAT) is diagnosed when an eschar is present on the scalp, accompanied by peripheral lymphadenopathy (LAP). Only a few cases of SENLAT caused by Bartonella henselae have been reported. CASE PRESENTATION: A 58-year-old male sought medical advice while suffering from high fever and diarrhea. Three weeks before the visit, he had been hunting a water deer, and upon bringing the deer home discovered a tick on his scalp area. Symptoms occurred one week after hunting, and a lump was palpated on the right neck area 6 days after the onset of symptoms. Physical examination upon presentation confirmed an eschar-like lesion on the right scalp area, and cervical palpation revealed that the lymph nodes on the right side were non-painful and enlarged at 2.5 × 1.5 cm. Fine needle aspiration of the enlarged lymph nodes was performed, and results of nested PCR for the Bartonella internal transcribed spacer (ITS) confirmed B. henselae as the causative agent. CONCLUSION: With an isolated case of SENLAT and a confirmation of B. henselae in Korea, it is pertinent to raise awareness to physicians in other Asian countries that B. henselae could be a causative agent for SENLAT.


id: cord-004488-r50atew9
author: Chong, Zhuo Lin
date: 2020-03-12
txt: ./txt/cord-004488-r50atew9.txt
cache: ./cache/cord-004488-r50atew9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069157/
doi: 10.1186/s12879-020-4911-5
summary:
  This study evaluated the accuracy and utility of ViroTrack Dengue Acute a new biosensors-based dengue NS1 RDT, SD Bioline Dengue Duo NS1/IgM/IgG combo a commercially available RDT, and SD Dengue NS1 Ag enzyme-linked immunosorbent assay (ELISA), for the diagnosis of acute dengue infection. In this evaluation study, we aimed to estimate the diagnostic accuracy and utility of a newly developed biosensors-based dengue NS1 assay, and one each of commercially available NS1 ELISA and NS1/IgM/IgG RDT. The true positive (TP), false negative (FN), false positive (FP), and true negative (TN) of each index test and various combinations of the components of combo test as compared to the reference standard were used to calculate various diagnostic accuracy parameters and their 95% confidence intervals (95%CI) using standard formulas [24, 25] Subgroup analyses by exposure (serotype, day of illness or DOI, dengue infection status) and outcome (lab-confirmed vs presumptive dengue) were also performed to compare sensitivity estimates.

title:
  Diagnostic accuracy and utility of three dengue diagnostic tests for the diagnosis of acute dengue infection in Malaysia

abstract:
  BACKGROUND: Dengue is an emerging infectious disease that infects up to 390 million people yearly. The growing demand of dengue diagnostics especially in low-resource settings gave rise to many rapid diagnostic tests (RDT). This study evaluated the accuracy and utility of ViroTrack Dengue Acute - a new biosensors-based dengue NS1 RDT, SD Bioline Dengue Duo NS1/IgM/IgG combo - a commercially available RDT, and SD Dengue NS1 Ag enzyme-linked immunosorbent assay (ELISA), for the diagnosis of acute dengue infection. METHODS: This prospective cross-sectional study consecutively recruited 494 patients with suspected dengue from a health clinic in Malaysia. Both RDTs were performed onsite. The evaluated ELISA and reference tests were performed in a virology laboratory. The reference tests comprised of a reverse transcription-polymerase chain reaction and three ELISAs for the detection of dengue NS1 antigen, IgM and IgG antibodies, respectively. The diagnostic performance of evaluated tests was computed using STATA version 12. RESULTS: The sensitivity and specificity of ViroTrack were 62.3% (95%CI 55.6–68.7) and 95.0% (95%CI 91.7–97.3), versus 66.5% (95%CI 60.0–72.6) and 95.4% (95%CI 92.1–97.6) for SD NS1 ELISA, and 52.4% (95%CI 45.7–59.1) and 97.7% (95%CI 95.1–99.2) for NS1 component of SD Bioline, respectively. The combination of the latter with its IgM and IgG components were able to increase test sensitivity to 82.4% (95%CI 76.8–87.1) with corresponding decrease in specificity to 87.4% (95%CI 82.8–91.2). Although a positive test on any of the NS1 assays would increase the probability of dengue to above 90% in a patient, a negative result would only reduce this probability to 23.0–29.3%. In contrast, this probability of false negative diagnosis would be further reduced to 14.7% (95%CI 11.4–18.6) if SD Bioline NS1/IgM/IgG combo was negative. CONCLUSIONS: The performance of ViroTrack Dengue Acute was comparable to SD Dengue NS1 Ag ELISA. Addition of serology components to SD Bioline Dengue Duo significantly improved its sensitivity and reduced its false negative rate such that it missed the fewest dengue patients, making it a better point-of-care diagnostic tool. New RDT like ViroTrack Dengue Acute may be a potential alternative to existing RDT if its combination with serology components is proven better in future studies.


id: cord-004643-uu4uipfy
author: Hasan, Mohammad Rubayet
date: 2020-03-20
txt: ./txt/cord-004643-uu4uipfy.txt
cache: ./cache/cord-004643-uu4uipfy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7083060/
doi: 10.1186/s12879-020-04966-z
summary:
  Here, we present a fatal case of HLH secondary to cytomegalovirus (CMV) infection complicated by both anti-viral drug resistance and sepsis from multiple MDROs including pandrug-resistant superbug bacteria. Whole genome sequencing (WGS) of the MDR bacteria and metagenomic analysis of his blood sample revealed an unusual accumulation of a wide range of antimicrobial resistance mechanisms in a single patient, including antiviral resistance to ganciclovir, and resistance mechanisms to all currently available antibiotics. Ganciclovir resistance was confirmed by the presence of the A594V mutation in UL97 [6] What was unique in our patient compared to other reported CMV-associated HLH cases was the overwhelming infection with MDROs. On hospital admission, the patient was found to be colonized with multiple MDROs including VRE, and carbapenamase-producing Enterobacteriaceae, which may have been acquired during his previous hospital course in India.

title:
  Unusual accumulation of a wide array of antimicrobial resistance mechanisms in a patient with cytomegalovirus-associated hemophagocytic lymphohistiocytosis: a case report

abstract:
  BACKGROUND: Infections with multidrug-resistant organisms (MDRO) pose a serious threat to patients with dysregulated immunity such as in hemophagocytic lymphohistiocytosis (HLH), but such infections have rarely been comprehensively characterized. Here, we present a fatal case of HLH secondary to cytomegalovirus (CMV) infection complicated by both anti-viral drug resistance and sepsis from multiple MDROs including pandrug-resistant superbug bacteria. CASE PRESENTATION: A previously healthy, six-year-old boy presented with a 45-day history of fever prior to a diagnosis of hemophagocytic lymphohistiocytosis and hemorrhagic colitis, both associated with CMV. On hospital admission, the patient was found to be colonized with multiple, multidrug-resistant (MDR) bacteria including vancomycin-resistant enterococci (VRE) and carbapenamase-producing organisms (CPO). He eventually developed respiratory, urine and bloodstream infections with highly drug-resistant, including pandrug-resistant bacteria, which could not be controlled by antibiotic treatment. Antiviral therapy also failed to contain his CMV infection and the patient succumbed to overwhelming bacterial and viral infection. Whole genome sequencing (WGS) of the MDR bacteria and metagenomic analysis of his blood sample revealed an unusual accumulation of a wide range of antimicrobial resistance mechanisms in a single patient, including antiviral resistance to ganciclovir, and resistance mechanisms to all currently available antibiotics. CONCLUSIONS: The case highlights both the risk of acquiring MDR superbugs and the severity of these infections in HLH patients.


id: cord-008584-4eylgtbc
title: Evaluating the impact of the weather conditions on the influenza propagation
author: Singh, David E.
date: 2020-04-05
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7132999/
doi: 10.1186/s12879-020-04977-w
abstract:
  BACKGROUND: Predicting the details of how an epidemic evolves is highly valuable as health institutions need to better plan towards limiting the infection propagation effects and optimizing their prediction and response capabilities. Simulation is a cost- and time-effective way of predicting the evolution of the infection as the joint influence of many different factors: interaction patterns, personal characteristics, travel patterns, meteorological conditions, previous vaccination, etc. The work presented in this paper extends EpiGraph, our influenza epidemic simulator, by introducing a meteorological model as a modular component that interacts with the rest of EpiGraph’s modules to refine our previous simulation results. Our goal is to estimate the effects of changes in temperature and relative humidity on the patterns of epidemic influenza based on data provided by the Spanish Influenza Sentinel Surveillance System (SISSS) and the Spanish Meteorological Agency (AEMET). METHODS: Our meteorological model is based on the regression model developed by AB and JS, and it is tuned with influenza surveillance data obtained from SISSS. After pre-processing this data to clean it and reconstruct missing samples, we obtain new values for the reproduction number of each urban region in Spain, every 10 minutes during 2011. We simulate the propagation of the influenza by setting the date of the epidemic onset and the initial influenza-illness rates for each urban region. RESULTS: We show that the simulation results have the same propagation shape as the weekly influenza rates as recorded by SISSS. We perform experiments for a realistic scenario based on actual meteorological data from 2010-2011, and for synthetic values assumed under simplified predicted climate change conditions. Results show that a diminishing relative humidity of 10% produces an increment of about 1.6% in the final infection rate. The effect of temperature changes on the infection spread is also noticeable, with a decrease of 1.1% per extra degree.Conclusions: Using a tool like ours could help predict the shape of developing epidemics and its peaks, and would permit to quickly run scenarios to determine the evolution of the epidemic under different conditions. We make EpiGraph source code and epidemic data publicly available.


id: cord-009210-qhul89z2
title: Diagnosis of severe scrub typhus infection by next-generation sequencing:a case report
author: Chen, Jie
date: 2020-04-07
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7137524/
doi: 10.1186/s12879-020-04991-y
abstract:
  BACKGROUND: Scrub typhus is an acute febrile illness, which was caused by Orientia tsutsugamushi and transmitted through the bite of chiggers. The diagnosis of scrub typhus could be missed diagnosis due to the absence of the pathognomonic eschar. CASE PRESENTATION: A 76-year-old man was hospitalized with fever and kidney injury and was diagnosed of hemorrhagic fever with renal syndrome first. However, the situation of the illness deteriorated into refractory septic shock and multiple organ dysfunction rapidly,although the treatment of anti-sepsis was used in 3rd-5th day. Orientia tsutsugamushi was determined to be the causative pathogen by Next-generation sequencing of his plasma sample in 6th day. Then, the patient was treated with doxycycline and azithromycin and recovered quickly. CONCLUSIONS: Next-generation sequencing was a new diagnostic technology and could identify scrub typhus in accurately and fast without the pathognomonic eschar.


id: cord-009606-xz23twqx
author: Vorobieva S. Jensen, V.
date: 2020-04-15
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161136/
doi: 10.1186/s12879-020-04998-5
title:
  Epidemiological and molecular characterization of Streptococcus pneumoniae carriage strains in pre-school children in Arkhangelsk, northern European Russia, prior to the introduction of conjugate pneumococcal vaccines

abstract:
  BACKGROUND: The 13-valent Pneumococcal Conjugate Vaccine (PCV-13) was introduced in the National Immunization Programme (NIP) schedule in Russia in March 2014. Previously, the 7-valent Pneumococcal Conjugate Vaccine (PCV-7) was marketed in Russia in 2009 but has never been offered for mass vaccination. A carriage study was performed among children in Arkhangelsk in 2006. The objective was to determine the prevalence of carriage, serotype distribution, antimicrobial susceptibility and the molecular structure of Streptococcus pneumoniae strains before marketing and introduction of PCV-13. METHODS: A cross-sectional study was conducted on a cluster-randomized sample of children and a self-administrated questionnaire for parents/guardians. Nasopharyngeal samples were collected from 438 children younger than 7 years attending nurseries and kindergartens in the Arkhangelsk region, Russia. Detailed demographic data, as well as information about the child’s health, traveling, exposure to antimicrobials within the last 3 months and anthropometric measurements were collected for all study subjects. Variables extracted from the questionnaire were analysed using statistic regression models to estimate the risk of carriage. All pneumococcal isolates were examined with susceptibility testing, serotyping and multilocus sequence typing. RESULTS: The overall prevalence of asymptomatic carriage was high and peaking at 36 months with a rate of 57%. PCV-13 covered 67.3% of the detected strains. High rates of non-susceptibility to penicillin, macrolides and multidrug resistance were associated with specific vaccine serotypes, pandemic clones, and local sequence types. Nine percent of isolates represented three globally disseminated disease-associated pandemic clones; penicillin- and macrolide-resistant clones Norway(NT)-42 and Poland(6B)-20, as well as penicillin- and macrolide-susceptible clone Netherlands(3)-31. A high level of antimicrobial consumption was noted by the study. According to the parent’s reports, 89.5% of the children used at least one antimicrobial regime since birth. None of the hypothesised predictors of S. pneumoniae carriage were statistically significant in univariable and multivariable logistic models. CONCLUSIONS: The study identified a high coverage of the PCV-13-vaccine, but serotype replacement and expansion of globally disseminated disease-associated clones with non-vaccine serotypes may be expected. Further surveillance of antimicrobial resistance and serotype distribution is therefore required.


id: cord-011601-1u1rlwzp
title: Measles outbreak amplified in a pediatric ward: Lyantonde District, Uganda, August 2017
author: Biribawa, Claire
date: 2020-06-05
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7274507/
doi: 10.1186/s12879-020-05120-5
abstract:
  BACKGROUND: Measles is a highly infectious viral disease. In August 2017, Lyantonde District, Uganda reported a measles outbreak to Uganda Ministry of Health. We investigated the outbreak to assess the scope, factors facilitating transmission, and recommend control measures. METHODS: We defined a probable case as sudden onset of fever and generalized rash in a resident of Lyantonde, Lwengo, or Rakai Districts from 1 June-30 September 2017, plus ≥1 of the following: coryza, conjunctivitis, or cough. A confirmed case was a probable case with serum positivity of measles-specific IgM. We conducted a neighborhood- and age-matched case-control study to identified exposure factors, and used conditional logistic regression to analyze the data. We estimated vaccine effectiveness and vaccination coverage. RESULTS: We identified 81 cases (75 probable, 6 confirmed); 4 patients (4.9%) died. In the case-control study, 47% of case-patients and 2.3% of controls were hospitalized at Lyantonde Hospital pediatric department for non-measles conditions 7–21 days before case-patient’s onset (OR(adj) = 34, 95%CI: 5.1–225). Estimated vaccine effectiveness was 95% (95%CI: 75–99%) and vaccination coverage was 76% (95%CI: 68–82%). During the outbreak, an “isolation” ward was established inside the general pediatric ward where there was mixing of both measles and non-measles patients. CONCLUSIONS: This outbreak was amplified by nosocomial transmission and facilitated by low vaccination coverage. We recommended moving the isolation ward outside of the building, supplemental vaccination, and vaccinating pediatric patients during measles outbreaks.


id: cord-011671-7mki5dp9
author: Fawaz, Sarah
date: 2020-06-20
txt: ./txt/cord-011671-7mki5dp9.txt
cache: ./cache/cord-011671-7mki5dp9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7305614/
doi: 10.1186/s12879-020-05149-6
summary:
  title: Comparing clinical outcomes of piperacillin-tazobactam administration and dosage strategies in critically ill adult patients: a systematic review and meta-analysis The aim was to conduct a systematic review to identify and highlight studies comparing clinical outcomes of piperacillin tazobactam dosing regimens, continuous/prolonged infusion vs intermittent infusion in critically ill patients. Continuous/prolonged resulted in significantly: higher clinical cure rates (Odds Ratio 1.56, 95% Confidence Interval 1.28–1.90, P = 0 .0001), lower mortality rates (Odds Ratio 0.68, 95% Confidence Interval 0.55–0.84, P = 0 .0003), higher microbiological success rates (Odds Ratio 1.52, 95% Confidence Interval 1.10–2.11, P = 0.01) and decreasing the length of hospital stay (Mean Difference − 1.27, 95% Confidence Interval − 2.45—0.08, P = 0.04) in critically ill patients. CONCLUSION: Results from this study show that there is a significant level of evidence that clinical outcome in critically ill patients is improved in patients receiving piperacillin-tazobactam via continuous/prolonged infusion. A full review of published studies was implemented addressing and comparing clinical outcome of IV piperacillintazobactam dosing regimens administered to infected critically ill patients.

title:
  Comparing clinical outcomes of piperacillin-tazobactam administration and dosage strategies in critically ill adult patients: a systematic review and meta-analysis

abstract:
  BACKGROUND: Recently, continuous administration of piperacillin-tazobactam has been proposed as a valuable alternative to traditional intermittent administration especially in critically ill patients. However, antibiotic dosing remains a challenge for clinicians as antibiotic dosing regimens are usually determined in non-critically ill hospitalized adult patients. The aim was to conduct a systematic review to identify and highlight studies comparing clinical outcomes of piperacillin tazobactam dosing regimens, continuous/prolonged infusion vs intermittent infusion in critically ill patients. Meta-analyses were performed to assess the overall effect of dosing regimen on clinical efficacy. METHODS: Studies were identified systematically through searches of PubMed and Science Direct, in compliance with PRISMA guidelines. Following the systematic literature review, meta-analyses were performed using Review Manager. RESULTS: Twenty-three studies were included in the analysis involving 3828 critically ill adult participants in total (continuous/prolonged infusion = 2197 and intermittent infusion = 1631) from geographically diverse regions. Continuous/prolonged resulted in significantly: higher clinical cure rates (Odds Ratio 1.56, 95% Confidence Interval 1.28–1.90, P = 0 .0001), lower mortality rates (Odds Ratio 0.68, 95% Confidence Interval 0.55–0.84, P = 0 .0003), higher microbiological success rates (Odds Ratio 1.52, 95% Confidence Interval 1.10–2.11, P = 0.01) and decreasing the length of hospital stay (Mean Difference − 1.27, 95% Confidence Interval − 2.45—0.08, P = 0.04) in critically ill patients. CONCLUSION: Results from this study show that there is a significant level of evidence that clinical outcome in critically ill patients is improved in patients receiving piperacillin-tazobactam via continuous/prolonged infusion. However, more rigorous scientific studies in critically ill patients are warranted to reach a sufficient level of evidence and promote further implementation of C/PI as a dosing strategy.


id: cord-012875-joz31gie
title: Simulating transmission of ESKAPE pathogens plus C. difficile in relevant clinical scenarios
author: Weber, Katharina L.
date: 2020-06-12
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7477864/
doi: 10.1186/s12879-020-05121-4
abstract:
  BACKGROUND: The prevalence of healthcare-acquired infections (HAI) and rising levels of antimicrobial resistance places significant economic and public health burdens on modern healthcare systems. A group of highly drug resistant pathogens known as the ESKAPE pathogens, along with C. difficile, are the leading causes of HAIs. Interactions between patients, healthcare workers, and environmental conditions impact disease transmission. Studying pathogen transfer under varying contact scenarios in a controlled manner is critical for understanding transmission and disinfectant strategies. In lieu of human subject research, this method has the potential to contribute to modeling the routes of pathogen transmission in healthcare settings. METHODS: To overcome these challenges, we have developed a method that utilizes a synthetic skin surrogate to model both direct (skin-to-skin) and indirect (skin-to fomite-to skin) pathogen transfer between infected patients and healthy healthcare workers. This surrogate material includes a background microbiome community simulating typical human skin flora to more accurately mimic the effects of natural flora during transmission events. RESULTS: We demonstrate the ability to modulate individual bacterial concentrations within this microbial community to mimic bacterial concentrations previously reported on the hands of human subjects. We also explore the effect of various decontamination approaches on pathogen transfer between human subjects, such as the use of handwashing or surface disinfectants. Using this method, we identify a potential outlier, S. aureus, that may persist and retain viability in specific transfer conditions better than the overall microbial community during decontamination events. CONCLUSIONS: Our work describes the development of an in vitro method that uses a synthetic skin surrogate with a defined background microbiota to simulate skin-to-skin and skin-to fomite-to skin contact scenarios. These results illustrate the value of simulating a holistic microbial community for transfer studies by elucidating differences in different pathogen transmission rates and resistance to common decontamination practices. We believe this method will contribute to improvements in pathogen transmission modeling in healthcare settings and increase our ability to assess the risk associated with HAIs, although additional research is required to establish the degree of correlation of pathogen transmission by skin or synthetic alternatives.


id: cord-012954-3x3rkor5
author: Honkpehedji, Yabo Josiane
date: 2020-09-29
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7523491/
doi: 10.1186/s12879-020-05445-1
title:
  Prospective, observational study to assess the performance of CAA measurement as a diagnostic tool for the detection of Schistosoma haematobium infections in pregnant women and their child in Lambaréné, Gabon: study protocol of the freeBILy clinical trial in Gabon

abstract:
  BACKGROUND: Schistosoma antigen detection in urine is a valuable diagnostic approach for schistosomiasis control programmes because of the higher sensitivity compared to parasitological methods and preferred sampling of urine over stool. Highly accurate diagnostics are important in low Schistosoma transmission areas. Pregnant women and young children could particularly benefit from antigen testing as praziquantel (PZQ) can be given to only confirmed Schistosoma cases. This prevents the unborn baby from unnecessary exposure to PZQ. We present here the protocol of a diagnostic study that forms part of the freeBILy project. The aim is to evaluate the accuracy of circulating anodic antigen (CAA) detection for diagnosis of Schistosoma haematobium infections in pregnant women and to validate CAA as an endpoint measure for anti-Schistosoma drug efficacy. The study will also investigate Schistosoma infections in infants. METHODS: A set of three interlinked prospective, observational studies is conducted in Gabon. The upconverting phosphor lateral flow (UCP-LF) CAA test is the index diagnostic test that will be evaluated. The core trial, sub-study A, comprehensively evaluates the accuracy of the UCP-LF CAA urine test against a set of other Schistosoma diagnostics in a cross-sectional trial design. Women positive for S. haematobium will proceed with sub-study B and will be randomised to receive PZQ treatment immediately or after delivery followed by weekly sample collection. This approach includes comparative monitoring of CAA levels following PZQ intake and will also contribute further data for safety of PZQ administration during pregnancy. Sub-study C is a longitudinal study to determine the incidence of S. haematobium infection as well as the age for first infection in life-time. DISCUSSION: The freeBILy trial in Gabon will generate a comprehensive set of data on the accuracy of the UCP-LF CAA test for the detection of S. haematobium infection in pregnant women and newborn babies and for the use of CAA as a marker to determine PZQ efficacy. Furthermore, incidence of Schistosoma infection in infants will be reported. Using the ultrasensitive diagnostics, this information will be highly relevant for Schistosoma prevalence monitoring by national control programs as well as for the development of medicaments and vaccines. TRIAL REGISTRATION: The registration number of this study is NCT03779347 (clinicaltrials.gov, date of registration: 19 December 2018).


id: cord-025155-ow3r3469
author: Lokida, Dewi
date: 2020-05-24
txt: ./txt/cord-025155-ow3r3469.txt
cache: ./cache/cord-025155-ow3r3469.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245627/
doi: 10.1186/s12879-020-05057-9
summary:
  title: Underdiagnoses of Rickettsia in patients hospitalized with acute fever in Indonesia: observational study results METHODS: Acute and convalescent blood from 975 hospitalized non-dengue patients was tested for Rickettsia IgM and IgG by ELISA. For the 103/975 (10.6%) non-dengue patients diagnosed with acute rickettsial infection, presenting symptoms included nausea (72%), headache (69%), vomiting (43%), lethargy (33%), anorexia (32%), arthralgia (30%), myalgia (28%), chills (28%), epigastric pain (28%), and rash (17%). Clinicians should include rickettsioses in their differential diagnosis of fever to guide empiric management; laboratories should support evaluation for rickettsial etiologies; and public policy should be implemented to reduce burden of disease. To characterize the epidemiology of rickettsioses in Indonesia, we performed Rickettsia diagnostic panels on blood from subjects in the Acute Fever Requiring Hospitalization (AFIRE) study [13] . Patients found to have rickettsial infection by reference laboratory testing were identified from INA-RESPOND''s [14] AFIRE observational cohort study conducted in Indonesia from 2013 to 2016.

title:
  Underdiagnoses of Rickettsia in patients hospitalized with acute fever in Indonesia: observational study results

abstract:
  BACKGROUND: Reports of human rickettsial infection in Indonesia are limited. This study sought to characterize the epidemiology of human rickettsioses amongst patients hospitalized with fever at 8 tertiary hospitals in Indonesia. METHODS: Acute and convalescent blood from 975 hospitalized non-dengue patients was tested for Rickettsia IgM and IgG by ELISA. Specimens from cases with seroconversion or increasing IgM and/or IgG titers were tested for Rickettsia IgM and IgG by IFA and Rickettsia genomes using primers for Rickettsia (R.) sp, R. typhi, and Orientia tsutsugamushi. Testing was performed retrospectively on stored specimens; results did not inform patient management. RESULTS: R. typhi, R. rickettsii, and O. tsutsugamushi IgG antibodies were identified in 269/872 (30.8%), 36/634 (5.7%), and 19/504 (3.8%) of samples, respectively. For the 103/975 (10.6%) non-dengue patients diagnosed with acute rickettsial infection, presenting symptoms included nausea (72%), headache (69%), vomiting (43%), lethargy (33%), anorexia (32%), arthralgia (30%), myalgia (28%), chills (28%), epigastric pain (28%), and rash (17%). No acute rickettsioses cases were suspected during hospitalization. Discharge diagnoses included typhoid fever (44), dengue fever (20), respiratory infections (7), leptospirosis (6), unknown fever (6), sepsis (5), hepatobiliary infections (3), UTI (3), and others (9). Fatalities occurred in 7 (6.8%) patients, mostly with co-morbidities. CONCLUSIONS: Rickettsial infections are consistently misdiagnosed, often as leptospirosis, dengue, or Salmonella typhi infection. Clinicians should include rickettsioses in their differential diagnosis of fever to guide empiric management; laboratories should support evaluation for rickettsial etiologies; and public policy should be implemented to reduce burden of disease.


id: cord-025163-iyh0d6mj
author: Ding, Lin
date: 2020-05-24
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245847/
doi: 10.1186/s12879-020-05085-5
title:
  Early diagnosis and appropriate respiratory support for Mycoplasma pneumoniae pneumonia associated acute respiratory distress syndrome in young and adult patients: a case series from two centers

abstract:
  BACKGROUND: Mycoplasma pneumoniae (M. pneumoniae) is one of the most common causes of community acquired pneumonia (CAP). Establishing an early diagnosis of M. pneumoniae pneumonia in patients with acute respiratory distress syndrome (ARDS) may have important therapeutic implications. METHODS: We describe diagnosis and management of M. pneumoniae pneumonia induced ARDS in a case series of adults and youth hospitalized with radiographically confirmed CAP prospectively enrolled in an observational cohort study in two university teaching hospitals, from November 2017 to October 2019. RESULTS: In all 10 patients, early and rapid diagnosis for severe M. pneumoniae pneumonia with ARDS was achieved with polymerase chain reaction (PCR) or metagenomic next-generation sequencing (mNGS) testing of samples from the lower respiratory tract or pleural effusion. The average PaO(2)/FiO(2) of all patients was 180 mmHg. Of the 10 cases, 4 cases had moderate ARDS (100 mmHg ≤ PaO(2)/FiO(2) < 200 mmHg) and 3 cases had severe ARDS (PaO(2)/FiO(2) < 100 mmHg). High flow nasal cannula (HFNC) was applied in all patients, though only two patients were sufficiently supported with HFNC. Invasive mechanical ventilation (IMV) was required in 5 patients. High resistance (median 15 L/cmH(2)O/s) and low compliance (median 38 ml/cmH(2)O) was observed in 4 cases. In these 4 cases, recruitment maneuvers (RM) were applied, with 1 patient demonstrating no response to RM. Prone positioning were applied in 4 cases. Two cases needed ECMO support with median support duration of 5.5 days. No patient in our case series received corticosteroid therapy. All patients were survived and were discharged from hospital. CONCLUSIONS: Early and rapid diagnosis of severe M. pneumoniae pneumonia with ARDS can be achieved with PCR/mNGS tests in samples from the lower respiratory tract or pleural effusion. In our case series, half of M. pneumoniae pneumonia induced ARDS cases were adequately supported with HFNC or NIV, while half of cases required intubation. RM and prone position were effective in 30% of intubated cases, and 20% needed ECMO support. When early anti-mycoplasmal antibiotics were given together with sufficient respiratory support, the survival rate was high with no need for corticosteroid use.


id: cord-028945-p3hhd5ed
author: Şahar, Esra Atalay
date: 2020-07-10
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7348124/
doi: 10.1186/s12879-020-05220-2
title:
  Development of a hexavalent recombinant protein vaccine adjuvanted with Montanide ISA 50 V and determination of its protective efficacy against acute toxoplasmosis

abstract:
  BACKGROUND: Toxoplasma gondii is an obligate intracellular parasite that can infect almost all warm-blooded animals, avian species and humans. Toxoplasmosis is asymptomatic in healthy individuals, whereas it may lead to death in immune suppressed or deficient patients. A vaccine against T. gondii is required to prevent consequences of the infection. The aim of this study is to generate a multivalent recombinant protein vaccine against T. gondii. METHODS: 49 previously discovered antigenic proteins of T gondii were evaluated by their expression level in E. coli and by comprehensive bioinformatics analyses to determine antigenic epitopes. Based on these analyses, six vaccine candidate proteins were selected to generate a hexavalent recombinant protein vaccine adjuvanted with Montanide ISA 50 V. Humoral and cellular immune responses were determined by flow cytometry and ELISA. Vaccinated mice were challenged with T. gondii Ankara strain tachyzoites. RESULTS: In mice vaccinated with hexavalent vaccine, strong total IgG (P < 0.0001) and IgG2a (P < 0.001) responses were induced compared to controls, the ratio of CD4(+) and CD8(+) T lymphocytes secreting IFN-γ increased, and significantly higher extracellular IFN-γ secretion was achieved compared to the controls (P < 0.001). The survival time of the vaccinated mice increased to 8.38 ± 2.13 days which was significantly higher than controls (P < 0.01). CONCLUSIONS: Altogether, these results show that the hexavalent vaccine which is developed for the first time against T. gondii induced strong and balanced Th1 and Th2 immune responses as well as conferred significant protection against challenge with lethal toxoplasmosis in murine model.


id: cord-029423-o24dthlk
author: Iwuji, Collins C.
date: 2020-07-20
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7370264/
doi: 10.1186/s12879-020-05240-y
title:
  A phase IV randomised, open-label pilot study to evaluate switching from protease-inhibitor based regimen to Bictegravir/Emtricitabine/Tenofovir Alafenamide single tablet regimen in Integrase inhibitor-naïve, virologically suppressed HIV-1 infected adults harbouring drug resistance mutations (PIBIK study): study protocol for a randomised trial

abstract:
  BACKGROUND: Currently recommended boosted protease-inhibitor (bPI) regimens may be associated with increased risk of cardiovascular or chronic kidney diseases; in addition, boosted regimens are particularly associated with drug-drug interactions. Since both cardiovascular and renal disease, and polypharmacy, are common in ageing people with HIV, there is a need for alternative efficacious regimens. bPI-based regimens are often the treatment of choice for individuals with pre-treatment or treatment-acquired resistance but it is plausible that carefully selected HIV-positive individuals with drug resistance, who are virologically suppressed on their current bPI regimen, could maintain virological efficacy when switched to bictegravir, emtricitabine and tenofovir alafenamide (B/F/TAF) fixed dose combination (FDC). METHODS/DESIGN: A phase IV, investigator-initiated, multicentre, open label pilot, randomised two-arm study to assess the safety and efficacy of switching from bPI regimen to B/F/TAF single tablet regimen in integrase inhibitor-naïve, virologically suppressed adults with HIV-1 infection harbouring drug resistance mutations. Eligible individuals will either continue on their bPI regimen or switch to B/F/TAF FDC. After 24 weeks, all participants in the bPI arm will be switched to B/F/TAF and followed for a further 24 weeks and all participants will be followed for 48 weeks. The primary efficacy endpoint is the proportion of participants with HIV-1 RNA < 50 copies/mL at week 24 using pure virologic response whilst the secondary efficacy endpoint is the proportion of participants with HIV-1 RNA < 50 copies/mL at Week 48. Other secondary outcome measures include between arm comparisons of drug resistance at virological failure, safety and tolerability and patient-reported outcome measures. DISCUSSION: We aim to provide preliminary evidence of the efficacy of switching to B/F/TAF in patients with virological suppression on a bPI-based regimen who harbour select drug resistance mutations. TRIAL REGISTRATION: ISRCTN 44453201, registered 19 June 2019 and EudraCT 2018–004732-30.


id: cord-030134-drw6nqge
author: Weerasooriya, Nilusha
date: 2020-08-06
txt: ./txt/cord-030134-drw6nqge.txt
cache: ./cache/cord-030134-drw6nqge.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7407432/
doi: 10.1186/s12879-020-05315-w
summary:
  title: Staphylococcal endocarditis in a quadricuspid aortic valve following uncomplicated dengue infection: a case report Increased incidence of concurrent bacteremia in patients with dengue infection is a recognized complication. Quadricuspid aortic valve (QAV) is a rare congenital anomaly and few cases of infective endocarditis have been reported in QAV. CASE PRESENTATION: A 32-year-old Sri Lankan male presented to the National Hospital of Sri Lanka with recurrence of fever and acute left hemiplegia following an uncomplicated recovery of dengue fever. A few case series have recognized an increased incidence of concurrent bacteremia in patients with dengue infection [1, 2] . We report a patient presenting with endocarditis of previously undiagnosed QAV, soon after recovering from dengue fever. This patient''s recovery from dengue fever was complicated with MRSA endocarditis of aortic valve with septic embolization to the brain and spleen. There are two reported cases of linezolid induced rhabdomyolysis [5, 8] .

title:
  Staphylococcal endocarditis in a quadricuspid aortic valve following uncomplicated dengue infection: a case report

abstract:
  BACKGROUND: Dengue fever is endemic and a leading health problem in Sri Lanka. Increased incidence of concurrent bacteremia in patients with dengue infection is a recognized complication. However, Staphylococcal endocarditis following dengue fever is uncommon. Quadricuspid aortic valve (QAV) is a rare congenital anomaly and few cases of infective endocarditis have been reported in QAV. CASE PRESENTATION: A 32-year-old Sri Lankan male presented to the National Hospital of Sri Lanka with recurrence of fever and acute left hemiplegia following an uncomplicated recovery of dengue fever. He was diagnosed to have Staphylococcal infective endocarditis of quadricuspid aortic valve, with septic emboli to brain and spleen. He was managed with intravenous vancomycin initially, however, due to inadequate response, intravenous linezolid was added. He developed rhabdomyolysis with very high creatine phosphokinase leading to acute kidney injury, which settled with the cessation of linezolid. The patient succumbed to his illness despite aggressive antimicrobial therapy and maximum supportive care while being assessed for aortic valve replacement. CONCLUSIONS: This case illustrates three clinical issues that a clinician should be aware of. Firstly, the possibility of a serious secondary bacterial infection as a cause for recurrence of fever following dengue infection. Secondly, this case highlights the importance of identifying QAV as a cause for complicated infective endocarditis of increased severity. The report also denotes the value of being vigilant of linezolid induced rhabdomyolysis which had a causal relationship with the commencement of the drug and its cessation.


id: cord-031710-1xl2isee
author: Andrei, Stefan
date: 2020-09-10
txt: ./txt/cord-031710-1xl2isee.txt
cache: ./cache/cord-031710-1xl2isee.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7482381/
doi: 10.1186/s12879-020-05378-9
summary:
  title: Successful treatment of pulmonary haemorrhage and acute respiratory distress syndrome caused by fulminant Stenotrophomonas maltophilia respiratory infection in a patient with acute lymphoblastic leukaemia – case report CASE PRESENTATION: We present the rare case of successful outcome in a 61-year-old female who developed alveolar haemorrhage and acute respiratory distress syndrome 8 days after a chemotherapy session for her acute lymphoblastic leukaemia, in the context of secondary bone marrow aplasia. We report the case of successfully treated severe Stenotrophomonas maltophilia respiratory infection complicated with pulmonary haemorrhage in a chemotherapyinduced pancytopenia patient diagnosed with acute lymphoblastic leukaemia. To our knowledge, this is the first reported case of pulmonary haemorrhage and ARDS caused by a fulminant Stenotrophomonas maltophilia respiratory infection in Eastern Europe, and it seems to be a rare case of positive outcome in a patient with haematological malignancy.

title:
  Successful treatment of pulmonary haemorrhage and acute respiratory distress syndrome caused by fulminant Stenotrophomonas maltophilia respiratory infection in a patient with acute lymphoblastic leukaemia – case report

abstract:
  BACKGROUND: Stenotrophomonas maltophilia-induced pulmonary haemorrhage is considered a fatal infection among haematological patients. The outcome can be explained by the patients’ immunity status and late diagnosis and treatment. CASE PRESENTATION: We present the rare case of successful outcome in a 61-year-old female who developed alveolar haemorrhage and acute respiratory distress syndrome 8 days after a chemotherapy session for her acute lymphoblastic leukaemia, in the context of secondary bone marrow aplasia. Stenotrophomonas maltophilia was isolated in sputum culture. The patient benefitted from early empirical treatment with colistin followed by trimethoprim/sulfamethoxazole, according to the antibiogram. Despite a severe initial clinical presentation in need of mechanical ventilation, neuromuscular blocking agents infusion, and ventilation in prone position, the patient had a favourable outcome and was discharged from intensive care after 26 days. CONCLUSIONS: Stenotrophomonas maltophilia severe pneumonia complicated with pulmonary haemorrhage is not always fatal in haematological patients. Empirical treatment of multidrug-resistant Stenotrophomonas maltophilia in an immunocompromised haematological patient presenting with hemoptysis should be taken into consideration.


id: cord-032382-5tp9i9vh
author: Hackert, Volker H.
date: 2020-09-21
txt: ./txt/cord-032382-5tp9i9vh.txt
cache: ./cache/cord-032382-5tp9i9vh.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7503428/
doi: 10.1186/s12879-020-05400-0
summary:
  CONCLUSION: Whereas signs and symptoms of disease do not appear to predict acute Q fever, they may help rule it out in favour of other respiratory conditions, prompting a delayed or non-prescribing approach instead of early empiric doxycycline in primary care patients with non-severe presentations. Specifically, we assessed whether signs and symptoms could accurately identify acute Q fever in suspect cases prior to laboratory confirmation, or help rule out the diagnosis in favour of other respiratory infections where, depending on national guidelines, treatment with amoxicillin as a first-line antibiotic or a delayed or non-prescribing approach would be considered more appropriate. We performed a retrospective case-control study assessing the association of acute Q fever case status with signs and symptoms of disease in a sample of questionnaire respondents from the cohort of all individuals tested for acute Q fever by GP''s or hospital-based medical specialists in the period from March 2009 through April 2010 (n = 1218).

title:
  Signs and symptoms do not predict, but may help rule out acute Q fever in favour of other respiratory tract infections, and reduce antibiotics overuse in primary care

abstract:
  BACKGROUND: From early 2009, the Dutch region of South Limburg experienced a massive outbreak of Q fever, overlapping with the influenza A(H1N1)pdm09 pandemic during the second half of the year and affecting approximately 2.9% of a 300,000 population. Acute Q fever shares clinical features with other respiratory conditions. Most symptomatic acute infections are characterized by mild symptoms, or an isolated febrile syndrome. Pneumonia was present in a majority of hospitalized patients during the Dutch 2007–2010 Q fever epidemic. Early empiric doxycycline, guided by signs and symptoms and patient history, should not be delayed awaiting laboratory confirmation, as it may shorten disease and prevent progression to focalized persistent Q fever. We assessed signs’ and symptoms’ association with acute Q fever to guide early empiric treatment in primary care patients. METHODS: In response to the outbreak, regional primary care physicians and hospital-based medical specialists tested a total of 1218 subjects for Q fever. Testing activity was bimodal, a first “wave” lasting from March to December 2009, followed by a second “wave” which lasted into 2010 and coincided with peak pandemic influenza activity. We approached all 253 notified acute Q fever cases and a random sample of 457 Q fever negative individuals for signs and symptoms of disease. Using data from 140/229(61.1%) Q fever positive and 194/391(49.6%) Q fever negative respondents from wave 1, we built symptom-based models predictive of Q-fever outcome, validated against subsets of data from wave 1 and wave 2. RESULTS: Our models had poor to moderate AUC scores (0.68 to 0.72%), with low positive (4.6–8.3%), but high negative predictive values (91.7–99.5%). Male sex, fever, and pneumonia were strong positive predictors, while cough was a strong negative predictor of acute Q fever in these models. CONCLUSION: Whereas signs and symptoms of disease do not appear to predict acute Q fever, they may help rule it out in favour of other respiratory conditions, prompting a delayed or non-prescribing approach instead of early empiric doxycycline in primary care patients with non-severe presentations. Signs and symptoms thus may help reduce the overuse of antibiotics in primary care during and following outbreaks of Q fever.


id: cord-033833-woref5g8
author: Fragoso-Saavedra, Sergio
date: 2020-10-16
txt: ./txt/cord-033833-woref5g8.txt
cache: ./cache/cord-033833-woref5g8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7563903/
doi: 10.1186/s12879-020-05485-7
summary:
  title: A parallel-group, multicenter randomized, double-blinded, placebo-controlled, phase 2/3, clinical trial to test the efficacy of pyridostigmine bromide at low doses to reduce mortality or invasive mechanical ventilation in adults with severe SARS-CoV-2 infection: the Pyridostigmine In Severe COvid-19 (PISCO) trial protocol METHODS: A parallel-group, multicenter, randomized, double-blinded, placebo-controlled, phase 2/3 clinical trial to test the efficacy of pyridostigmine bromide 60 mg/day P.O. to reduce the need for invasive mechanical ventilation and mortality in hospitalized patients with severe COVID-19. Exclusion criteria include one or more of the following: allergy to pyridostigmine; pregnancy or breastfeeding status; concomitant autoimmune disease; diagnosed immunodeficiencies (including HIV infection); need for mechanical ventilation, admission to the ICU, or meeting criteria for septic shock before providing signed, informed consent; inability to receive orally or enterally administered drugs; use of immunosuppressants or immune-modulators (including chemotherapy and corticosteroids) in the preceding 28-day period unless recommended by the treatment medical team as part of the therapeutic approach for SARS-CoV-2 infection; and participation in clinical trials of any kind in the previous 28 days.

title:
  A parallel-group, multicenter randomized, double-blinded, placebo-controlled, phase 2/3, clinical trial to test the efficacy of pyridostigmine bromide at low doses to reduce mortality or invasive mechanical ventilation in adults with severe SARS-CoV-2 infection: the Pyridostigmine In Severe COvid-19 (PISCO) trial protocol

abstract:
  BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the causative agent of coronavirus disease 2019 (COVID-19), may lead to severe systemic inflammatory response, pulmonary damage, and even acute respiratory distress syndrome (ARDS). This in turn may result in respiratory failure and in death. Experimentally, acetylcholine (ACh) modulates the acute inflammatory response, a neuro-immune mechanism known as the inflammatory reflex. Recent clinical evidence suggest that electrical and chemical stimulation of the inflammatory reflex may reduce the burden of inflammation in chronic inflammatory diseases. Pyridostigmine (PDG), an ACh-esterase inhibitor (i-ACh-e), increases the half-life of endogenous ACh, therefore mimicking the inflammatory reflex. This clinical trial is aimed at evaluating if add-on of PDG leads to a decrease of invasive mechanical ventilation and death among patients with severe COVID-19. METHODS: A parallel-group, multicenter, randomized, double-blinded, placebo-controlled, phase 2/3 clinical trial to test the efficacy of pyridostigmine bromide 60 mg/day P.O. to reduce the need for invasive mechanical ventilation and mortality in hospitalized patients with severe COVID-19. DISCUSSION: This study will provide preliminary evidence of whether or not -by decreasing systemic inflammation- add-on PDG can improve clinical outcomes in patients with severe COVID-19. TRIAL REGISTRATION: ClinicalTrials.gov NCT04343963 (registered on April 14, 2020).


id: cord-035280-z0bbz19b
author: Lee, Seung Hun
date: 2020-11-11
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7656494/
doi: 10.1186/s12879-020-05522-5
title:
  First identification of Anaplasma phagocytophilum in both a biting tick Ixodes nipponensis and a patient in Korea: a case report

abstract:
  BACKGROUND: Human granulocytic anaplasmosis (HGA) is a tick-borne infectious disease caused by Anaplasma phagocytophilum. To date, there have been no reported cases of A. phagocytophilum infection found in both the biting tick and the patient following a tick bite. CASE PRESENTATION: An 81-year-old woman presented with fever following a tick bite, with the tick still intact on her body. The patient was diagnosed with HGA. The tick was identified as Ixodes nipponensis by morphological and molecular biological detection methods targeting the 16S rRNA gene. The patient’s blood was cultured after inoculation into the human promyelocytic leukemia cell line HL-60. A. phagocytophilum growth was confirmed via culture and isolation. A. phagocytophilum was identified in both the tick and the patient’s blood by Anaplasma-specific groEL- and ankA-based nested polymerase chain reaction followed by sequencing. Moreover, a four-fold elevation in antibodies was observed in the patient’s blood. CONCLUSION: We report a case of a patient diagnosed with HGA following admission for fever due to a tick bite. A. phagocytophilum was identified in both the tick and the patient, and A. phagocytophilum was successfully cultured. The present study suggests the need to investigate the possible incrimination of I. nipponensis as a vector for HGA in Korea. SUPPLEMENTARY INFORMATION: Supplementary information accompanies this paper at 10.1186/s12879-020-05522-5.


id: cord-048467-1dus0u4m
title: Can "presumed consent" justify the duty to treat infectious diseases? An analysis
author: Civaner, Murat
date: 2008-03-06
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2311313/
doi: 10.1186/1471-2334-8-29
abstract:
  BACKGROUND: AIDS, SARS, and the recent epidemics of the avian-flu have all served to remind us the debate over the limits of the moral duty to care. It is important to first consider the question of whether or not the "duty to treat" might be subject to contextual constraints. The purpose of this study was to investigate the opinions and beliefs held by both physicians and dentists regarding the occupational risks of infectious diseases, and to analyze the argument that the notion of "presumed consent" on the part of professionals may be grounds for supporting the duty to treat. METHODS: For this cross-sectional survey, the study population was selected from among physicians and dentists in Ankara. All of the 373 participants were given a self-administered questionnaire. RESULTS: In total, 79.6% of the participants said that they either had some degree of knowledge about the risks when they chose their profession or that they learned of the risks later during their education and training. Of the participants, 5.2% said that they would not have chosen this profession if they had been informed of the risks. It was found that 57% of the participants believed that there is a standard level of risk, and 52% of the participants stated that certain diseases would exceed the level of acceptable risk unless specific protective measures were implemented. CONCLUSION: If we use the presumed consent argument to establish the duty of the HCW to provide care, we are confronted with problems ranging over the difficulty of choosing a profession autonomously, the constant level of uncertainty present in the medical profession, the near-impossibility of being able to evaluate retrospectively whether every individual was informed, and the seemingly inescapable problem that this practice would legitimize, and perhaps even foster, discrimination against patients with certain diseases. Our findings suggest that another problem can be added to the list: one-fifth of the participants in this study either lacked adequate knowledge of the occupational risks when they chose the medical profession or were not sufficiently informed of these risks during their faculty education and training. Furthermore, in terms of the moral duty to provide care, it seems that most HCWs are more concerned about the availability of protective measures than about whether they had been informed of a particular risk beforehand. For all these reasons, the presumed consent argument is not persuasive enough, and cannot be used to justify the duty to provide care. It is therefore more useful to emphasize justifications other than presumed consent when defining the duty of HCWs to provide care, such as the social contract between society and the medical profession and the fact that HCWs have a greater ability to provide medical aid.


id: cord-048489-ajafw966
author: Bozza, Fernando A
date: 2008-06-25
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2474613/
doi: 10.1186/1471-2334-8-86
title:
  Multiplex cytokine profile from dengue patients: MIP-1beta and IFN-gamma as predictive factors for severity

abstract:
  BACKGROUND: Dengue virus pathogenesis is not yet fully understood and the identification of patients at high risk for developing severe disease forms is still a great challenge in dengue patient care. During the present study, we evaluated prospectively the potential of cytokines present in plasma from patients with dengue in stratifying disease severity. METHODS: Seventeen-cytokine multiplex fluorescent microbead immunoassay was used for the simultaneous detection in 59 dengue patients. GLM models using bimodal or Gaussian family were determined in order to associate cytokines with clinical manifestations and laboratory diagnosis. RESULTS: IL-1β, IFN-γ, IL-4, IL-6, IL-13, IL-7 and GM-CSF were significantly increased in patients with severe clinical manifestations (severe dengue) when compared to mild disease forms (mild dengue). In contrast, increased MIP-1β levels were observed in patients with mild dengue. MIP-1β was also associated with CD56+NK cell circulating rates. IL-1β, IL-8, TNF-α and MCP-1 were associated with marked thrombocytopenia. Increased MCP-1 and GM-CSF levels correlated with hypotension. Moreover, MIP-1β and IFN-γ were independently associated with both dengue severity and disease outcome. CONCLUSION: Our data demonstrated that the use of a multiple cytokine assay platform was suitable for identifying distinct cytokine profiles associated with the dengue clinical manifestations and severity. MIP-β is indicated for the first time as a good prognostic marker in contrast to IFN-γ that was associated with disease severity.


id: cord-252304-lwiulri7
author: Fragnoud, Romain
date: 2015-11-14
url: https://doi.org/10.1186/s12879-015-1271-7
doi: 10.1186/s12879-015-1271-7
title:
  Differential proteomic analysis of virus-enriched fractions obtained from plasma pools of patients with dengue fever or severe dengue

abstract:
  BACKGROUND: Dengue is the most widespread mosquito-borne viral disease of public health concern. In some patients, endothelial cell and platelet dysfunction lead to life-threatening hemorrhagic dengue fever or dengue shock syndrome. Prognostication of disease severity is urgently required to improve patient management. The pathogenesis of severe dengue has not been fully elucidated, and the role of host proteins associated with viral particles has received little exploration. METHODS: The proteomes of virion-enriched fractions purified from plasma pools of patients with dengue fever or severe dengue were compared. Virions were purified by ultracentrifugation combined with a water-insoluble polyelectrolyte-based technique. Following in-gel hydrolysis, peptides were analyzed by nano-liquid chromatography coupled to ion trap mass spectrometry and identified using data libraries. RESULTS: Both dengue fever and severe dengue viral-enriched fractions contained identifiable viral envelope proteins and host cellular proteins. Canonical pathway analysis revealed the identified host proteins are mainly involved in the coagulation cascade, complement pathway or acute phase response signaling pathway. Some host proteins were over- or under-represented in plasma from patients with severe dengue compared to patients with dengue fever. ELISAs were used to validate differential expression of a selection of identified host proteins in individual plasma samples of patients with dengue fever compared to patients with severe dengue. Among 22 host proteins tested, two could differentiate between dengue fever and severe dengue in two independent cohorts (olfactomedin-4: area under the curve (AUC), 0.958; and platelet factor-4: AUC, 0.836). CONCLUSION: A novel technique of virion-enrichment from plasma has allowed to identify two host proteins that have prognostic value for classifying patients with acute dengue who are more likely to develop a severe dengue. The impact of these host proteins on pathogenicity and disease outcome are discussed. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-015-1271-7) contains supplementary material, which is available to authorized users.


id: cord-253171-l56qcbat
author: Rao, Huaxiang
date: 2017-08-21
txt: ./txt/cord-253171-l56qcbat.txt
cache: ./cache/cord-253171-l56qcbat.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28826399/
doi: 10.1186/s12879-017-2643-y
summary:
  title: Using the Kulldorff''s scan statistical analysis to detect spatio-temporal clusters of tuberculosis in Qinghai Province, China, 2009–2016 The Kulldorff''s retrospective space-time scan statistics, calculated by using the discrete Poisson probability model, was used to identify the temporal, spatial, and spatio-temporal clusters of TB at the county level in Qinghai. In this study, our aim was to use the Kulldorff''s scan statistical analysis to explore the spatial, temporal, and space-time dynamics of TB at the county level in Qinghai. Our study analyzed the spatial, temporal, and space-time clusters of TB incidents at the county level in Qinghai, from 2009 to 2016, using the Kulldorff''s retrospective scan statistic methods. The spatial and temporal clusters were statistically significant every year, and the spacetime scanning result indicated eight high-risk areas for TB incidents which were predominantly located in the southwest Qinghai.

title:
  Using the Kulldorff’s scan statistical analysis to detect spatio-temporal clusters of tuberculosis in Qinghai Province, China, 2009–2016

abstract:
  BACKGROUND: Although the incidence of tuberculosis (TB) in most parts of China are well under control now, in less developed areas such as Qinghai, TB still remains a major public health problem. This study aims to reveal the spatio-temporal patterns of TB in the Qinghai province, which could be helpful in the planning and implementing key preventative measures. METHODS: We extracted data of reported TB cases in the Qinghai province from the China Information System for Disease Control and Prevention (CISDCP) during January 2009 to December 2016. The Kulldorff’s retrospective space-time scan statistics, calculated by using the discrete Poisson probability model, was used to identify the temporal, spatial, and spatio-temporal clusters of TB at the county level in Qinghai. RESULTS: A total of 48,274 TB cases were reported from 2009 to 2016 in Qinghai. Results of the Kulldorff’s scan revealed that the TB cases in Qinghai were significantly clustered in spatial, temporal, and spatio-temporal distribution. The most likely spatio-temporal cluster (LLR = 2547.64, RR = 4.21, P < 0.001) was mainly concentrated in the southwest of Qinghai, covering seven counties and clustered in the time frame from September 2014 to December 2016. CONCLUSION: This study identified eight significant space-time clusters of TB in Qinghai from 2009 to 2016, which could be helpful in prioritizing resource assignment in high-risk areas for TB control and elimination in the future. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-017-2643-y) contains supplementary material, which is available to authorized users.


id: cord-256094-f85xc5uu
author: Milinovich, Gabriel J
date: 2014-12-31
txt: ./txt/cord-256094-f85xc5uu.txt
cache: ./cache/cord-256094-f85xc5uu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25551277/
doi: 10.1186/s12879-014-0690-1
summary:
  This study aims to systematically investigate the potential for developing surveillance and early warning systems using internet search data, for a wide range of infectious diseases. This study, however, did not aim to develop actionable surveillance systems, produce predictive models of infectious disease based on internet-based data or to identify the best search terms for use in these models. Briefly, the time series analysed were monthly case numbers for the 64 infectious diseases monitored by the Australian Government''s National Notifiable Disease Surveillance System (NNDSS) and Google Trends monthly search metrics for related internet search terms. To our knowledge, assessments of the use of internet-based surveillance have only been performed for five of the 17 diseases that were demonstrated to have a significant association with internet search terms (influenza [4] , dengue [9, 27] , chickenpox [11, 12] , hepatitis B [14] and cryptosporidiosis [13] the authors of the final study were, however, not able to detect signals from internet search queries).

title:
  Using internet search queries for infectious disease surveillance: screening diseases for suitability

abstract:
  BACKGROUND: Internet-based surveillance systems provide a novel approach to monitoring infectious diseases. Surveillance systems built on internet data are economically, logistically and epidemiologically appealing and have shown significant promise. The potential for these systems has increased with increased internet availability and shifts in health-related information seeking behaviour. This approach to monitoring infectious diseases has, however, only been applied to single or small groups of select diseases. This study aims to systematically investigate the potential for developing surveillance and early warning systems using internet search data, for a wide range of infectious diseases. METHODS: Official notifications for 64 infectious diseases in Australia were downloaded and correlated with frequencies for 164 internet search terms for the period 2009–13 using Spearman’s rank correlations. Time series cross correlations were performed to assess the potential for search terms to be used in construction of early warning systems. RESULTS: Notifications for 17 infectious diseases (26.6%) were found to be significantly correlated with a selected search term. The use of internet metrics as a means of surveillance has not previously been described for 12 (70.6%) of these diseases. The majority of diseases identified were vaccine-preventable, vector-borne or sexually transmissible; cross correlations, however, indicated that vector-borne and vaccine preventable diseases are best suited for development of early warning systems. CONCLUSIONS: The findings of this study suggest that internet-based surveillance systems have broader applicability to monitoring infectious diseases than has previously been recognised. Furthermore, internet-based surveillance systems have a potential role in forecasting emerging infectious disease events, especially for vaccine-preventable and vector-borne diseases. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-014-0690-1) contains supplementary material, which is available to authorized users.


id: cord-258611-uzzs8w1j
title: No MERS-CoV but positive influenza viruses in returning Hajj pilgrims, China, 2013–2015
author: Ma, Xuezheng
date: 2017-11-10
txt: ./txt/cord-258611-uzzs8w1j.txt
cache: ./cache/cord-258611-uzzs8w1j.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29126397/
doi: 10.1186/s12879-017-2791-0
summary:
  BACKGROUND: There is global health concern that the mass movement of pilgrims to and from Mecca annually could contribute to the international spread of Middle East Respiratory Syndrome Coronavirus (MERS-CoV). DISCUSSION AND CONCLUSION: The MERS-CoV and respiratory viruses detection results at points of entry in China from 2013 to 2015 indicated that there were no MERS-CoV infection but a 5.7% positive influenza viruses in returning Chinese pilgrims. As of November 2015, there had been 1618 laboratoryconfirmed cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection reported to the World Health Organization, and at least 579 cases had died [1, 2] . Two hypotheses were tested: (1) There is a significant difference in the positive and negative rates of influenza virus detection between Hajj pilgrims with symptoms and those without. In this study, we did not detect any cases of MERS-CoV infection but respiratory virus infections including influenza A and B, hMPV, hRSV, and human coronavirus were detected among Hajj pilgrims returning to China.

abstract:
  BACKGROUND: There is global health concern that the mass movement of pilgrims to and from Mecca annually could contribute to the international spread of Middle East Respiratory Syndrome Coronavirus (MERS-CoV). In China, about 11,000 Muslim pilgrims participate in the Hajj gathering in Mecca annually. This is the first report of MERS-CoV and respiratory virus molecular screening of returning pilgrims at points of entry in China from 2013 to 2015. METHODS AND RESULTS: A total of 847 returning Hajj pilgrims participated in this study. The test results indicated that of the travelers, 34 tested positive for influenza A virus, 14 for influenza B virus, 4 for metapneumo virus, 2 for respiratory syncytial virus, and 3 for human coronavirus. There was a significant difference in the rates of positive and negative influenza virus tests between Hajj pilgrims with symptoms and those without. The detection rates of influenza virus were not significantly different among the three years studied, at 5.3, 6.0 and 6.3% for 2013, 2014 and 2015, respectively. DISCUSSION AND CONCLUSION: The MERS-CoV and respiratory viruses detection results at points of entry in China from 2013 to 2015 indicated that there were no MERS-CoV infection but a 5.7% positive influenza viruses in returning Chinese pilgrims.


id: cord-259667-x51jorbm
author: Chughtai, Abrar Ahmad
date: 2019-06-03
txt: ./txt/cord-259667-x51jorbm.txt
cache: ./cache/cord-259667-x51jorbm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31159777/
doi: 10.1186/s12879-019-4109-x
summary:
  title: Contamination by respiratory viruses on outer surface of medical masks used by hospital healthcare workers BACKGROUND: Medical masks are commonly used in health care settings to protect healthcare workers (HCWs) from respiratory and other infections. Used samples of medical masks were tested for presence of respiratory viruses in upper sections of the medical masks, in line with the pilot studies. Currently there is no standard duration for the time period that facemasks and respirators can safely One study showed that influenza virus may survive on mask surface and maintained infectivity for at least 8 h [25] . High virus positivity on masks samples worn by HCWs who examined > 25 patients, may be due to more frequent clinical contact with infective cases and transfer of more pathogens from patients to mask surface. The study shows that the prolonged use of medical masks (> 6 h) and frequent clinical contact in healthcare setting increase the risk to health workers through contaminated PPE.

title:
  Contamination by respiratory viruses on outer surface of medical masks used by hospital healthcare workers

abstract:
  BACKGROUND: Medical masks are commonly used in health care settings to protect healthcare workers (HCWs) from respiratory and other infections. Airborne respiratory pathogens may settle on the surface of used masks layers, resulting in contamination. The main aim of this study was to study the presence of viruses on the surface of medical masks. METHODS: Two pilot studies in laboratory and clinical settings were carried out to determine the areas of masks likely to contain maximum viral particles. A laboratory study using a mannequin and fluorescent spray showed maximum particles concentrated on upper right, middle and left sections of the medical masks. These findings were confirmed through a small clinical study. The main study was then conducted in high-risk wards of three selected hospitals in Beijing China. Participants (n = 148) were asked to wear medical masks for a shift (6–8 h) or as long as they could tolerate. Used samples of medical masks were tested for presence of respiratory viruses in upper sections of the medical masks, in line with the pilot studies. RESULTS: Overall virus positivity rate was 10.1% (15/148). Commonly isolated viruses from masks samples were adenovirus (n = 7), bocavirus (n = 2), respiratory syncytial virus (n = 2) and influenza virus (n = 2). Virus positivity was significantly higher in masks samples worn for > 6 h (14.1%, 14/99 versus 1.2%, 1/49, OR 7.9, 95% CI 1.01–61.99) and in samples used by participants who examined > 25 patients per day (16.9%, 12/71 versus 3.9%, 3/77, OR 5.02, 95% CI 1.35–18.60). Most of the participants (83.8%, 124/148) reported at least one problem associated with mask use. Commonly reported problems were pressure on face (16.9%, 25/148), breathing difficulty (12.2%, 18/148), discomfort (9.5% 14/148), trouble communicating with the patient (7.4%, 11/148) and headache (6.1%, 9/148). CONCLUSION: Respiratory pathogens on the outer surface of the used medical masks may result in self-contamination. The risk is higher with longer duration of mask use (> 6 h) and with higher rates of clinical contact. Protocols on duration of mask use should specify a maximum time of continuous use, and should consider guidance in high contact settings. Viruses were isolated from the upper sections of around 10% samples, but other sections of masks may also be contaminated. HCWs should be aware of these risks in order to protect themselves and people around them.


id: cord-260550-ld9eieik
author: Ng, Man Wai
date: 2007-06-01
txt: ./txt/cord-260550-ld9eieik.txt
cache: ./cache/cord-260550-ld9eieik.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17540042/
doi: 10.1186/1471-2334-7-50
summary:
  title: The association of RANTES polymorphism with severe acute respiratory syndrome in Hong Kong and Beijing Chinese In this study, we investigated the single nucleotide polymorphisms (SNPs) of inflammatory chemokine genes, i.e. RANTES, IP-10 and monokine induced by gamma interferon gene (Mig) in two Chinese cohorts from Hong Kong and Beijing and found that the RANTES -28 G allele was associated with disease susceptibility and severity of SARS. Among them, 20 patients were classified as severe group, which were identified by their admissions to intensive care units or deaths from SARS (mean ± SD age = 39.45 ± 12.8, 11 male and 9 female). After correction by Bonferroni method, the significant P value should be less than 0.007 This study showed that RANTES -28 G allele was a risk factor that associated with severe clinical outcomes in both Hong Kong and Beijing Chinese SARS patients.

title:
  The association of RANTES polymorphism with severe acute respiratory syndrome in Hong Kong and Beijing Chinese

abstract:
  BACKGROUND: Chemokines play important roles in inflammation and antiviral action. We examined whether polymorphisms of RANTES, IP-10 and Mig affect the susceptibility to and outcome of severe acute respiratory syndrome (SARS). METHODS: We tested the polymorphisms of RANTES, IP-10 and Mig for their associations with SARS in 495 Hong Kong Chinese SARS patients and 578 controls. Then we tried to confirm the results in 356 Beijing Chinese SARS patients and 367 controls. RESULTS: RANTES -28 G allele was associated with SARS susceptibility in Hong Kong Chinese (P < 0.0001, OR = 2.80, 95%CI:2.11–3.71). Individuals with RANTES -28 CG and GG genotypes had a 3.28-fold (95%CI:2.32–4.64) and 3.06-fold (95%CI:1.47–6.39) increased risk of developing SARS respectively (P < 0.0001). This -28 G allele conferred risk of death in a gene-dosage dependent manner (P = 0.014) with CG and GG individuals having a 2.12-fold (95% CI: 1.11–4.06) and 4.01-fold (95% CI: 1.30–12.4) increased risk. For the replication of RANTES data in Beijing Chinese, the -28 G allele was not associated with susceptibility to SARS. However, -28 CG (OR = 4.27, 95%CI:1.64–11.1) and GG (OR = 3.34, 95%CI:0.37–30.7) were associated with admission to intensive care units or death due to SARS (P = 0.011). CONCLUSION: RANTES -28 G allele plays a role in the pathogenesis of SARS.


id: cord-261251-ylvqxpba
title: Debate around infection-dependent hemophagocytic syndrome in paediatrics
author: Ansuini, Valentina
date: 2013-01-16
txt: ./txt/cord-261251-ylvqxpba.txt
cache: ./cache/cord-261251-ylvqxpba.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/23324497/
doi: 10.1186/1471-2334-13-15
summary:
  BACKGROUND: Hemophagocytic syndrome (HPS) is clinically defined as a combination of fever, liver dysfunction, coagulation abnormalities, pancytopenia, progressive macrophage proliferation throughout the reticuloendothelial system, and cytokine over-production, and may be primary or secondary to infectious, auto-immune, and tumoral diseases. In the case of severe EBV-related HPS, the introduction of immuno-chemotherapy and, if necessary, allogenic stem cell transplantation has radically changed the history and prognosis of the disease: in such cases, the optimal treatment strategy can be centred on immunosuppressive medications that inhibit overactive T and NK cell responses (i.e. corticosteroids, cyclosporine A, intravenous immunoglobulin, anti-thymocyte globulins, etoposide, rituximab, and plasma or blood exchange transfusions) [38, 39] . Clinicopathological study of severe chronic active Epstein-Barr virus infection that developed in association with lymphoproliferative disorder and/or hemophagocytic syndrome Quantitative analysis of cell-free Epstein-Barr virus genome copy number in patients with EBV-associated hemophagocytic lymphohistiocytosis Penicilliosis-associated hemophagocytic syndrome in a human immunodeficiency virus-infected child: the first case report in children

abstract:
  BACKGROUND: Hemophagocytic syndrome (HPS) is clinically defined as a combination of fever, liver dysfunction, coagulation abnormalities, pancytopenia, progressive macrophage proliferation throughout the reticuloendothelial system, and cytokine over-production, and may be primary or secondary to infectious, auto-immune, and tumoral diseases. The most consistent association is with viral infections but, as it is still debated whether any micro-organisms are involved in its pathogenesis, we critically appraised the literature concerning HPS and its relationship with infections. DISCUSSION: Infection-dependent HPS has been widely observed, but there are no data concerning its incidence in children. A better understanding of the pathophysiology of HPS may clarify the interactions between the immune system and the variously implicated potential infectious agents. Epstein-Barr virus (EBV) infection has been prominently associated with HPS, with clonal proliferation and the hyperactivation of EBV-infected T cells. However, a number of other viral, bacterial, fungal, and parasitic infections have been reported in association with HPS. In the case of low-risk HPS, corticosteroids and/or intravenous immunoglobulin or cyclosporine A may be sufficient to control the biological process, but etoposide is recommended as a means of reversing infection-dependent lymphohistiocytic dysregulation in high-risk cases. SUMMARY: HPS is a potential complication of various infections. A polymerase chain reaction search for infectious agents including EBV, cytomegalovirus and Leishmania is recommended in clinical settings characterised by non-remitting fever, organomegaly, cytopenia and hyperferritinemia.


id: cord-261756-4lybl57r
author: Dubert, Marie
date: 2020-02-24
txt: ./txt/cord-261756-4lybl57r.txt
cache: ./cache/cord-261756-4lybl57r.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32093612/
doi: 10.1186/s12879-020-4877-3
summary:
  METHODS: Patients, who survived 6 months or more following lung transplantation that took place between 2009 and 2014, were classified into three groups: a viral infection group (VIG) (without any respiratory bacteria), a bacterial infection group (BIG) (with or without any respiratory viruses), and a control group (CG) (no documented infection). In order to include patients at a steady state, we studied only the late respiratory infections, i.e. to censure the first 6 months after the lung transplantation, a period during which postoperative complications are frequent and usually intertwined. Concerning AR, the impact of late respiratory viral and/ or bacterial infections on the graft function was significantly different with three times more AR within 6 months for both the VIG and BIG compared to the CG.

title:
  Late viral or bacterial respiratory infections in lung transplanted patients: impact on respiratory function

abstract:
  BACKGROUND: Respiratory infections are a major threat for lung recipients. We aimed to compare with a monocentric study the impact of late viral and bacterial respiratory infections on the graft function. METHODS: Patients, who survived 6 months or more following lung transplantation that took place between 2009 and 2014, were classified into three groups: a viral infection group (VIG) (without any respiratory bacteria), a bacterial infection group (BIG) (with or without any respiratory viruses), and a control group (CG) (no documented infection). Chronic lung allograft dysfunction (CLAD) and acute rejection were analysed 6 months after the inclusion in the study. RESULTS: Among 99 included lung recipients, 57 (58%) had at least one positive virological respiratory sample during the study period. Patients were classified as follows: 38 in the VIG, 25 in the BIG (among which 19 co-infections with a virus) and 36 in the CG. The BIG presented a higher initial deterioration in lung function (p = 0.05) than the VIG. But 6 months after the infection, only the VIG presented a median decrease of forced expiratory volume in 1 s; − 35 mL (IQR; − 340; + 80) in the VIG, + 140 mL (+ 60;+ 330) in the BIG and + 10 (− 84;+ 160) in the CG, p < 0.01. Acute rejection was more frequent in the VIG (n = 12 (32%)), than the BIG (n = 6 (24%)) and CG (n = 3 (8%)), p < 0.05, despite presenting no more CLAD (p = 0.21). CONCLUSIONS: Despite a less severe initial presentation, single viral respiratory infections seem to lead to a greater deterioration in lung function, and to more acute rejection, than bacterial infections.


id: cord-262646-64ldtrjf
author: Chuang, Pei-Hung
date: 2010-05-27
txt: ./txt/cord-262646-64ldtrjf.txt
cache: ./cache/cord-262646-64ldtrjf.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-10-136
doi: 10.1186/1471-2334-10-136
summary:
  This study proposes a dynamic statistical model to estimate the daily number of new cases and the daily cumulative number of infected cases, which was then applied to historic dengue fever data. Our results show that when an infectious disease required a time-consuming process for diagnosis, such as the dengue fever using the previously mentioned protocol, the actual daily number of infected cases and cumulative positive cases are potentially underestimated. The Figure 3 and Table 1 for cumulative cases showed that a gamma distribution is a more appropriate assumption for the onset-todiagnosis time when estimating the probability of being a positive case using the dengue fever example; nonetheless, the difference between the gamma and the nonparametric method is again only slight except towards the end stage of the epidemic after January 1. This study has proposed a statistical method that more accurately estimates the real-time daily new cases and daily cumulative number of infected cases using a dengue fever epidemic as an example.

title:
  A dynamic estimation of the daily cumulative cases during infectious disease surveillance: application to dengue fever

abstract:
  BACKGROUND: In infectious disease surveillance, when the laboratory confirmation of the cases is time-consuming, there is often a time lag between the number of suspect cases and the number of confirmed cases. This study proposes a dynamic statistical model to estimate the daily number of new cases and the daily cumulative number of infected cases, which was then applied to historic dengue fever data. METHODS: The duration between the date of disease onset and date of laboratory confirmation was assumed to follow a gamma distribution or a nonparametric distribution. A conditional probability of a case being a real case among the unconfirmed cases on a given date was then calculated. This probability along with the observed confirmed cases was integrated to estimate the daily number of new cases and the cumulative number of infected cases. RESULTS: The distribution of the onset-to-confirmation time for the positive cases was different from that of the negative cases. The daily new cases and cumulative epidemic curves estimated by the proposed method have a lower absolute relative bias than the values estimated solely based on the available daily-confirmed cases. CONCLUSION: The proposed method provides a more accurate real-time estimation of the daily new cases and daily cumulative number of infected cases. The model makes use of the most recent "moving window" of information relative to suspect cases and dynamically updates the parameters. The proposed method will be useful for the real-time evaluation of a disease outbreak when case classification requires a time-consuming laboratory process to identify a confirmed case.


id: cord-267090-jc1k3fki
author: Gardner, Emma G.
date: 2019-02-04
txt: ./txt/cord-267090-jc1k3fki.txt
cache: ./cache/cord-267090-jc1k3fki.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30717685/
doi: 10.1186/s12879-019-3729-5
summary:
  METHODS: A case-crossover design was used to identify associations between primary MERS cases and preceding weather conditions within the 2-week incubation period in Saudi Arabia using univariable conditional logistic regression. Data from meteorological stations closest to the largest city in each province were used to calculate the daily mean, minimum, and maximum temperature ((ο)C), relative humidity (%), wind speed (m/s), and visibility (m). Middle East respiratory syndrome coronavirus (MERS--CoV) is an emerging zoonotic agent that was first isolated in 2012 from a patient hospitalized in Saudi Arabia [1] , and has since infected over 2200 people with a 36% case fatality ratio [2] . By comparing weather conditions immediately before MERS cases to weather conditions at other times, this study aimed to identify environmental factors that are associated with primary human MERS in Saudi Arabia. The risk of primary human cases of MERS was associated with a decrease in temperature and humidity, and an increase in ground visibility.

title:
  A case-crossover analysis of the impact of weather on primary cases of Middle East respiratory syndrome

abstract:
  BACKGROUND: Middle East respiratory syndrome coronavirus (MERS-CoV) is endemic in dromedary camels in the Arabian Peninsula, and zoonotic transmission to people is a sporadic event. In the absence of epidemiological data on the reservoir species, patterns of zoonotic transmission have largely been approximated from primary human cases. This study aimed to identify meteorological factors that may increase the risk of primary MERS infections in humans. METHODS: A case-crossover design was used to identify associations between primary MERS cases and preceding weather conditions within the 2-week incubation period in Saudi Arabia using univariable conditional logistic regression. Cases with symptom onset between January 2015 – December 2017 were obtained from a publicly available line list of human MERS cases maintained by the World Health Organization. The complete case dataset (N = 1191) was reduced to approximate the cases most likely to represent spillover transmission from camels (N = 446). Data from meteorological stations closest to the largest city in each province were used to calculate the daily mean, minimum, and maximum temperature ((ο)C), relative humidity (%), wind speed (m/s), and visibility (m). Weather variables were categorized according to strata; temperature and humidity into tertiles, and visibility and wind speed into halves. RESULTS: Lowest temperature (Odds Ratio = 1.27; 95% Confidence Interval = 1.04–1.56) and humidity (OR = 1.35; 95% CI = 1.10–1.65) were associated with increased cases 8–10 days later. High visibility was associated with an increased number of cases 7 days later (OR = 1.26; 95% CI = 1.01–1.57), while wind speed also showed statistically significant associations with cases 5–6 days later. CONCLUSIONS: Results suggest that primary MERS human cases in Saudi Arabia are more likely to occur when conditions are relatively cold and dry. This is similar to seasonal patterns that have been described for other respiratory diseases in temperate climates. It was hypothesized that low visibility would be positively associated with primary cases of MERS, however the opposite relationship was seen. This may reflect behavioural changes in different weather conditions. This analysis provides key initial evidence of an environmental component contributing to the development of primary MERS-CoV infections.


id: cord-269772-4zrmsw2f
author: Liu, Ming-Der
date: 2015-06-24
txt: ./txt/cord-269772-4zrmsw2f.txt
cache: ./cache/cord-269772-4zrmsw2f.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26104109/
doi: 10.1186/s12879-015-0987-8
summary:
  Thus, understanding all possible factors associated with risk awareness, attitudes, and practice of prevention measures (RAP), as well as differences in risk perception of outbreaks due to LPAI versus HPAI viruses between the live-poultry market workers (LPMWs) and community residents (CRs) are all important for providing further education and implementing public health policies on preventing AI infection. Therefore, the data of the reported "acceptance of avian influenza vaccine between live-poultry market workers and community residents" were thus compared only after the 2nd survey in Table 4 respondents with higher risk perception (concerning human AI infections in Taiwan) before HPAI outbreaks had not only more awareness about the AI outbreaks in mainland China affecting Taiwan, but also better attitudes toward meeting domestic needs (endorsing the government''s new policy on AI, and supporting a ban on slaughtering live poultry in markets).

title:
  Changing risk awareness and personal protection measures for low to high pathogenic avian influenza in live-poultry markets in Taiwan, 2007 to 2012

abstract:
  BACKGROUND: Outbreaks of low and high pathogenic avian influenza (LPAI, HPAI) H5N2 in chickens have occurred in Taiwan since 2003 and 2012, respectively. Fully understanding the different awareness, attitudes and protective behaviors adopted by workers in live-poultry markets (LPMWs) and local community residents (CRs) to face the challenges of LPAI and HPAI is very important to minimize viral adaptations to human populations. METHODS: A structural questionnaire containing information on respondents’ occupation, personal risk awareness, attitudes toward different policies, and preventative measures was administered. The two-stage survey (before and after HPAI H5N2 outbreaks) was conducted from 2007 to 2012, including: (1) 430 LPMWs and 418 CRs at LPMs from different geographical areas of Taiwan after the government announced outbreaks of LPAI H5N2 during 2007–2009, and (2) 73 LPMWs and 152 CRs at two LPMs in central Taiwan after the HPAI H5N2 outbreaks in 2012. The chi-squared test and logistic regression were applied for univariate and multivariate analyses, respectively. RESULTS: Before HPAI-H5N2 outbreaks, higher educated respondents demonstrated greater risk awareness and concerns regarding AI. However, LPM-workers protected themselves less from AI viruses (AIVs) and had lower acceptance of human or avian influenza vaccines. Most importantly, the participants who opposed (versus agreed with) the policy on banning live-poultry slaughtering at LPMs reported lower awareness of government prevention and control policies [Odds Ratio (OR): 0.76, 95 % Confidence Interval (CI): 0.56–1.01] or practiced preventive measures (OR: 0.42, 95 % CI: 0.25–0.70). After HPAI-H5N2 outbreaks, the risk awareness about AI in central Taiwan significantly increased [LPAI to HPAI LPMWs: 34.6 to 65.6 %, p < 0.05; CRs: 44.0 to 76.5 %, p < 0.05] and LPMWs’ belief in the effectiveness of vaccination to prevent human or avian influenza virus infection strikingly decreased (92.3 to 68.5 %, p < 0.05). CONCLUSIONS: Risk awareness depends on high or low pathogenicity of AIVs, working in LPMs, levels of education, age, and proximity to the sites of severe AI outbreaks. Regardless of novel LPAI or HPAI virus reassortants that pose public health risks, prompt and clear risk communication focusing on both correct information about AIVs and the most appropriate preventive measures are important for effective prevention of human infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-015-0987-8) contains supplementary material, which is available to authorized users.


id: cord-271105-eyigl0wz
author: Ionidis, Georgios
date: 2016-02-11
txt: ./txt/cord-271105-eyigl0wz.txt
cache: ./cache/cord-271105-eyigl0wz.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-016-1410-9
doi: 10.1186/s12879-016-1410-9
summary:
  Under the Guideline of Deutsche Vereinigung zur Bekämpfung der Viruskrankeiten e.V. and the Robert Koch-Institute (DVV/RKI Guideline) [22] , disinfectants achieving at least 4 log 10 titer reduction factor (RF of 4) against vaccinia virus and bovine viral diarrhea virus (BVDV) are active against all enveloped viruses (limited spectrum virucidal) [23, 24] . The different formulations of the new hand rub based on ethanol, citric acid and urea were screened undiluted (80.0 % due to the addition of test virus suspension and interfering substance) against PV, AdV and polyomavirus SV40 as non-enveloped test viruses of the Guideline of DVV/RKI in the presence of FCS with a fixed exposure time of 60 s. Consequently, the formulation with the sufficient virucidal activity containing 69.39 % w/w ethanol, 3.69 % w/w 2-propanol, 2.0 % urea and 2.0 % citric acid was tested against several non-enveloped (MNV, AdV, PV, polyomavirus SV40) and enveloped viruses (BVDV, vaccinia virus strain Elstree) in the presence or absence of FCS according to Guideline of DVV/RK or in clean conditions according to EN 14476.

title:
  Development and virucidal activity of a novel alcohol-based hand disinfectant supplemented with urea and citric acid

abstract:
  BACKGROUND: Hand disinfectants are important for the prevention of virus transmission in the health care system and environment. The development of broad antiviral spectrum hand disinfectants with activity against enveloped and non-enveloped viruses is limited due to a small number of permissible active ingredients able to inactivate viruses. METHODS: A new hand disinfectant was developed based upon 69.39 % w/w ethanol and 3.69 % w/w 2-propanol. Different amounts of citric acid and urea were added in order to create a virucidal claim against poliovirus (PV), adenovirus type 5 (AdV) and polyomavirus SV40 (SV40) as non-enveloped test viruses in the presence of fetal calf serum (FCS) as soil load. The exposure time was fixed to 60 s. RESULTS: With the addition of 2.0 % citric acid and 2.0 % urea an activity against the three test viruses was achieved demonstrating a four log(10) reduction of viral titers. Furthermore, this formulation was able to inactivate PV, AdV, SV40 and murine norovirus (MNV) in quantitative suspension assays according to German and European Guidelines within 60 s creating a virucidal claim. For inactivation of vaccinia virus and bovine viral diarrhea virus 15 s exposure time were needed to demonstrate a 4 log(10) reduction resulting in a claim against enveloped viruses. Additionally, it is the first hand disinfectant passing a carrier test with AdV and MNV. CONCLUSIONS: In conclusion, this new formulation with a low alcohol content, citric acid and urea is capable of inactivating all enveloped and non-enveloped viruses as indicated in current guidelines and thereby contributing as valuable addition to the hand disinfection portfolio.


id: cord-271813-nroflfmc
title: Positive results for patients with COVID-19 discharged form hospital in Chongqing, China
author: Deng, Wang
date: 2020-06-19
txt: ./txt/cord-271813-nroflfmc.txt
cache: ./cache/cord-271813-nroflfmc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32560694/
doi: 10.1186/s12879-020-05151-y
summary:
  METHODS: In the study, 576 patients with COVID-19 discharged from hospital in Chongqing, China from January 24, 2020, to March 10, 2020 were evaluated by viral nucleic acid tests for severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) to determine if they could be released from quarantine. CONCLUSIONS: Multi-site screening of SARS-CoV-2 including nasal and pharyngeal swabs, stool and sputum specimens could be considered to improve the diagnosis, treatment and infection control in patients with COVID-19. Among them, 61 patients had positive results of SARS-CoV-2 by real-time reverse transcriptase polymerase chain reaction (RT-PCR) test, which provided the important information and clinical evidence for the improved management of patients recovered from COVID-19. The study revealed the clinical features of recovered patients with the recurrence of positive results of SARS-CoV-2.Multi-site screening including nasal and pharyngeal swabs, stool and sputum specimens could be considered to improve the diagnosis, treatment and infection control in patients with COVID-19.

abstract:
  BACKGROUND: Since December 2019, over 80,000 patients with coronavirus disease 2019 (COVID-19) have been confirmed in China. With the increasing number of recovered patients, more attention should be paid to the follow-up of these patients. METHODS: In the study, 576 patients with COVID-19 discharged from hospital in Chongqing, China from January 24, 2020, to March 10, 2020 were evaluated by viral nucleic acid tests for severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) to determine if they could be released from quarantine. Among the 576 patients, 61 patients (10.6%) had positive RT-PCR test results of SARS-CoV-2. We aimed to analyze the demographics, clinical characteristics and treatment of 61 patients. RESULTS: These positive patients were characterized by older age, chronic medical illness and mild conditions. 38 (62.3%) patients who were asymptomatic without abnormalities on chest radiographs were found in the positive with COVID-19. Also, they showed positive results of stool or sputum specimens with negative results of nasal and pharyngeal swab specimens. The median duration of positive result of SARS-CoV-2 was varied from 3 days to 35 days in the patients discharged from hospital with no family member infection. CONCLUSIONS: Multi-site screening of SARS-CoV-2 including nasal and pharyngeal swabs, stool and sputum specimens could be considered to improve the diagnosis, treatment and infection control in patients with COVID-19. Our findings provide the important information and clinical evidence for the improved management of patients recovered from COVID-19.


id: cord-272194-h7xnr389
author: Wiegers, Hanke M. G.
date: 2019-11-06
url: https://www.ncbi.nlm.nih.gov/pubmed/31694565/
doi: 10.1186/s12879-019-4468-3
title:
  Bacterial co-infection of the respiratory tract in ventilated children with bronchiolitis; a retrospective cohort study

abstract:
  BACKGROUND: Viral bronchiolitis is the most common cause of respiratory failure requiring invasive ventilation in young children. Bacterial co-infections may complicate and prolong paediatric intensive care unit (PICU) stay. Data on prevalence, type of pathogens and its association with disease severity are limited though. These data are especially important as bacterial co-infections may be treated using antibiotics and could reduce disease severity and duration of PICU stay. We investigated prevalence of bacterial co-infection and its association with disease severity and PICU stay. METHODS: Retrospective cohort study of the prevalence and type of bacterial co-infections in ventilated children performed in a 14-bed tertiary care PICU in The Netherlands. Children less than 2 years of age admitted between December 2006 and November 2014 with a diagnosis of bronchiolitis and requiring invasive mechanical ventilation were included. Tracheal aspirates (TA) and broncho-alveolar lavages (BAL) were cultured and scored based on the quantity of bacteria colony forming units (CFU) as: co-infection (TA > 10(^5)/BAL > 10(^4) CFU), low bacterial growth (TA < 10(^5)/BAL < 10(^4) CFU), or negative (no growth). Duration of mechanical ventilation and PICU stay were collected using medical records and compared against the presence of co-infection using univariate and multivariate analysis. RESULTS: Of 167 included children 63 (37.7%) had a bacterial co-infection and 67 (40.1%) low bacterial growth. Co-infections occurred within 48 h from intubation in 52 out 63 (82.5%) co-infections. H.influenza (40.0%), S.pneumoniae (27.1%), M.catarrhalis (22.4%), and S.aureus (7.1%) were the most common pathogens. PICU stay and mechanical ventilation lasted longer in children with co-infections than children with negative cultures (9.1 vs 7.7 days, p = 0.04 and 8.1vs 6.5 days, p = 0.02). CONCLUSIONS: In this large study, bacterial co-infections occurred in more than a third of children requiring invasive ventilation for bronchiolitis and were associated with longer PICU stay and mechanical ventilation. These findings support a clinical trial of antibiotics to test whether antibiotics can reduce duration of PICU stay.


id: cord-272207-jtvf257r
author: Liao, Qiuyan
date: 2014-03-27
txt: ./txt/cord-272207-jtvf257r.txt
cache: ./cache/cord-272207-jtvf257r.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-14-169
doi: 10.1186/1471-2334-14-169
summary:
  This study was aimed to compare the strength of associations between different cognitive and affective measures of risk and self-reported protective behaviors in a series of ten cross-sectional surveys conducted throughout the first wave of influenza A/H1N1 pandemic. RESULTS: Excepting state anxiety, other affective measures including "anticipated worry", "experienced worry" and "current worry" specific to A/H1N1 risk were consistently and strongly associated with adoption of protective behaviors across different survey periods. This finding is consistent with those from other studies conducted during both SARS [6] and pandemic A/H1N1 [10, 24] , suggesting that affective components contribute significantly to adoption of protective behaviors in response to the threat during epidemics over and above simpler cognitive risk estimates. This study found that the proportions of missing data for purer cognitive risk perception measures, particularly perceived absolute/relative susceptibility to A/H1N1 were greater than for affect-loaded measures, suggesting that respondents may face greater Figure 3 Associations between psychological responses and disinfecting household frequently during A/H1N1 pandemic.

title:
  Anxiety, worry and cognitive risk estimate in relation to protective behaviors during the 2009 influenza A/H1N1 pandemic in Hong Kong: ten cross-sectional surveys

abstract:
  BACKGROUND: Few studies have investigated associations between psychological and behavioral indices throughout a major epidemic. This study was aimed to compare the strength of associations between different cognitive and affective measures of risk and self-reported protective behaviors in a series of ten cross-sectional surveys conducted throughout the first wave of influenza A/H1N1 pandemic. METHODS: All surveys were conducted using questionnaire-based telephone interviews, with random digit dialing to recruit adults from the general population. Measures of anxiety and worry (affective) and perceived risk (cognitive) regarding A/H1N1 were made in 10 serial surveys. Multivariate logistic regression models were used to estimate the cognitive/affective-behavioral associations in each survey while multilevel logistic models were conducted to estimate the average effects of each cognitive/affective measure on adoption of protective behaviors throughout the ten surveys. RESULTS: Excepting state anxiety, other affective measures including “anticipated worry”, “experienced worry” and “current worry” specific to A/H1N1 risk were consistently and strongly associated with adoption of protective behaviors across different survey periods. However, the cognitive-behavioral associations were weaker and inconsistent across the ten surveys. Perceived A/H1N1 severity relative to SARS had stronger associations with adoption of protective behaviors in the late epidemic periods than in the early epidemic periods. CONCLUSION: Risk-specific worries appear to be significantly associated with the adoption of protective behaviors at different epidemic stages, whereas cognitive measures may become more important in understanding people’s behavioral responses later in epidemics. Future epidemic-related psycho-behavioral research should include more affective-loaded measures of risk.


id: cord-272240-s1gnwb2s
author: Li, Tiegang
date: 2014-01-02
txt: ./txt/cord-272240-s1gnwb2s.txt
cache: ./cache/cord-272240-s1gnwb2s.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-14-4
doi: 10.1186/1471-2334-14-4
summary:
  Previous studies have demonstrated the positive correlation between a willingness to adhere to the recommendations around infection control practices and perceived infectiousness and severity of the disease [8] [9] [10] , perceptions about the effectiveness of control measures [11] , and trust in the information being provided by national and international public health authorities [12] . Because a considerable number of H7N9 patients engaged in food-related work before symptom onset (including chef, food transporter, poultry seller and slaughter), we conducted face-to-face interviews on attitudes, practices and information needs among employees of food production and operation in Guangzhou, with an effort to assess the preparedness and response of the public, and to facilitate the development of effective prevention strategies against H7N9 infection. In a previous study designed to assess the implications of public understanding of avian influenza, researchers found that the majority of participants did not believe a pandemic would occur, and believed that dealing with the disease was the responsibility of the government [14] .

title:
  Attitudes, practices and information needs regarding novel influenza A (H7N9) among employees of food production and operation in Guangzhou, Southern China: a cross-sectional study

abstract:
  BACKGROUND: As of 30 May 2013, 132 human infections with avian influenza A (H7N9) had been reported in 10 Chinese cities. On 17 May 2013, because a chicken infection with H7 subtype avian influenza virus was detected in Guanzhou, Guangzhou became the 11th city to conduct emergency response operations. The goal of this study was to identify attitudes, practices and information needs among employees of food production and operation in Guangzhou. METHODS: A cross-sectional survey of face-to-face interviews was used during 17–24 June 2013. All adults seeking health examination in Guangzhou Center for Disease Control and Prevention who had lived in Guangzhou for at least 3 months, were engaged in food production and operation, and agreed to participate were interviewed. RESULTS: Of 1,450 participants, 69.72% worried about being infected with the A/H7N9 and 74.41% stated that they had searched for information about A/H7N9. The internet (76.92%), television (67.56%), and newspapers (56.26%) were the main methods of obtaining information; the use of these methods differed significantly by various demographic variables (P < 0.05). More than one-fifth of participants complained that the information was not timely enough (20.28%) and was intentionally concealed by the government (20.76%). Nearly one-third (32.35%) did not believe that the government could control the A/H7N9 epidemic. Most participants (80.76%) reported washing hands more frequently than before, while over one-third (37.17%) stated no longer buying poultry. A total of 84.00% indicated a willingness to receive an A/H7N9 vaccine, and the primary reason for not being willing was concern about safety (58.19%). A history of influenza vaccination and worry about being infected with the A/H7N9 were significantly associated with intention to receive an A/H7N9 vaccine (P < 0.05). CONCLUSIONS: Our findings provide insight into the attitudes and practices of employees of food production and operation 3 months after the first human A/H7N9 case reported in China, and 1 month after infected chickens were identified in Guangzhou. Distrust in the health department should be addressed, and more effort should be made to improve compliance of proper preventive measures to reduce panic among the public. The information needs should be taken into account in the next step of health education.


id: cord-274123-wgigtgl9
author: Dube, Felix S.
date: 2016-10-24
txt: ./txt/cord-274123-wgigtgl9.txt
cache: ./cache/cord-274123-wgigtgl9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27776489/
doi: 10.1186/s12879-016-1934-z
summary:
  title: Respiratory microbes present in the nasopharynx of children hospitalised with suspected pulmonary tuberculosis in Cape Town, South Africa We have recently shown [5] that specific pathogens (including Bordetella pertussis, influenza virus, respiratory syncyntial virus [RSV], adenovirus, parainfluenzavirus, bocavirus) are detected significantly more frequently from the nasopharynx (NP) of children with pneumonia than age-matched controls, and so are likely to play an important role in pneumonia aetiology. This is the first comprehensive detailed study of the diversity of respiratory microbes detected in children presenting with suspected PTB in a TB endemic setting and showed that multiple potential pathogens are present in th nasopharynx of such children. In conclusion, this study describes the detection of multiple respiratory microbes in the nasopharynx of children hospitalised with suspected PTB. pneumoniae, hMPV, coronavirus O43, influenza C virus, rhinovirus and cytomegalovirus formed the dominant microbial profile in children with PTB but this failed to reach statistical significance on testing of each individual microbe.

title:
  Respiratory microbes present in the nasopharynx of children hospitalised with suspected pulmonary tuberculosis in Cape Town, South Africa

abstract:
  BACKGROUND: Lower respiratory tract infection in children is increasingly thought to be polymicrobial in origin. Children with symptoms suggestive of pulmonary tuberculosis (PTB) may have tuberculosis, other respiratory tract infections or co-infection with Mycobacterium tuberculosis and other pathogens. We aimed to identify the presence of potential respiratory pathogens in nasopharyngeal (NP) samples from children with suspected PTB. METHOD: NP samples collected from consecutive children presenting with suspected PTB at Red Cross Children’s Hospital (Cape Town, South Africa) were tested by multiplex real-time RT-PCR. Mycobacterial liquid culture and Xpert MTB/RIF was performed on 2 induced sputa obtained from each participant. Children were categorised as definite-TB (culture or qPCR [Xpert MTB/RIF] confirmed), unlikely-TB (improvement of symptoms without TB treatment on follow-up) and unconfirmed-TB (all other children). RESULTS: Amongst 214 children with a median age of 36 months (interquartile range, [IQR] 19–66 months), 34 (16 %) had definite-TB, 86 (40 %) had unconfirmed-TB and 94 (44 %) were classified as unlikely-TB. Moraxella catarrhalis (64 %), Streptococcus pneumoniae (42 %), Haemophilus influenzae spp (29 %) and Staphylococcus aureus (22 %) were the most common bacteria detected in NP samples. Other bacteria detected included Mycoplasma pneumoniae (9 %), Bordetella pertussis (7 %) and Chlamydophila pneumoniae (4 %). The most common viruses detected included metapneumovirus (19 %), rhinovirus (15 %), influenza virus C (9 %), adenovirus (7 %), cytomegalovirus (7 %) and coronavirus O43 (5.6 %). Both bacteria and viruses were detected in 73, 55 and 56 % of the definite, unconfirmed and unlikely-TB groups, respectively. There were no significant differences in the distribution of respiratory microbes between children with and without TB. Using quadratic discriminant analysis, human metapneumovirus, C. pneumoniae, coronavirus 043, influenza virus C virus, rhinovirus and cytomegalovirus best discriminated children with definite-TB from the other groups of children. CONCLUSIONS: A broad range of potential respiratory pathogens was detected in children with suspected TB. There was no clear association between TB categorisation and detection of a specific pathogen. Further work is needed to explore potential pathogen interactions and their role in the pathogenesis of PTB. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-016-1934-z) contains supplementary material, which is available to authorized users.


id: cord-274438-tgslabi2
author: Schnee, Sarah Valerie
date: 2017-12-13
txt: ./txt/cord-274438-tgslabi2.txt
cache: ./cache/cord-274438-tgslabi2.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-017-2855-1
doi: 10.1186/s12879-017-2855-1
summary:
  title: Performance of the Alere i RSV assay for point-of-care detection of respiratory syncytial virus in children False negative Alere i RSV test results mostly occurred in samples with low viral load (mean CT value 31.1; CI(95) 29.6 – 32.6). Mann-Whitney-U-test was applied to compare C T values in samples with true positive versus false negative Alere i RSV result. In comparison to the RT-PCR reference standard, the Alere i RSV test result was true positive in 213 and true negative in 278 samples, respectively. The Alere i RSV performed well in the point-of-care setting, and sensitive test results were obtained across all pediatric age groups within 13 min. Evaluation of Alere i RSV for rapid detection of respiratory syncytial virus in children hospitalized with acute respiratory tract infection Host and viral factors affecting clinical performance of a rapid diagnostic test for respiratory Syncytial virus in hospitalized children

title:
  Performance of the Alere i RSV assay for point-of-care detection of respiratory syncytial virus in children

abstract:
  BACKGROUND: Respiratory syncytial virus (RSV) is the most important cause of severe acute respiratory tract infection in young children. Alere i RSV is a novel molecular rapid test which identifies respiratory syncytial virus in less than 13 min. METHODS: We evaluated the clinical performance of the Alere i RSV assay in a pediatric point-of-care setting during winter season 2016 / 2017. Test results from 518 nasopharyngeal swab samples were compared to a real-time reverse transcription PCR reference standard. RESULTS: The overall sensitivity and specificity of the Alere i RSV test assay was 93% (CI(95) 89% – 96%) and 96% (CI(95) 93% – 98%), respectively. Alere i RSV performed well in children of all age groups. An optimal sensitivity of 98% (CI(95) 94% - 100%) and specificity of 96% (CI(95) 90% - 99%) was obtained in children < 6 months. In children ≥ 2 years, sensitivity and specificity remained at 87% (CI(95) 73% – 96%) and 98% (CI(95) 92% – 100%), respectively. False negative Alere i RSV test results mostly occurred in samples with low viral load (mean CT value 31.1; CI(95) 29.6 – 32.6). The Alere i RSV assay is easy to use and can be operated after minimal initial training. Test results are available within 13 min, with most RSV positive samples being identified after approximately 5 min. CONCLUSION: The Alere i RSV assay has the potential to facilitate the detection of RSV in pediatric point-of-care settings. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-017-2855-1) contains supplementary material, which is available to authorized users.


id: cord-274749-ji91qq9q
author: Lagare, Adamou
date: 2015-11-14
txt: ./txt/cord-274749-ji91qq9q.txt
cache: ./cache/cord-274749-ji91qq9q.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-015-1251-y
doi: 10.1186/s12879-015-1251-y
summary:
  The viruses most frequently detected in children with ARIs include respiratory syncytial virus (RSV), influenza virus (INF) types A and B, adenovirus (AV), parainfluenza virus (PIV), human metapneumovirus (HMPV) and rhinovirus (RV) [3] [4] [5] ; however, the clinical presentations of respiratory tract infections are similar, making it difficult to distinguish between etiologic agents without a laboratory diagnosis [6] . We aimed to document the prevalence of selected viral and bacterial infections among children <5 years of age hospitalized with severe acute respiratory illness (SARI) at selected hospitals in Niger from January 2010 through December 2012. We report the detection rate of selected viral and bacterial pathogens among children <5 years of age hospitalized with SARI in Niger. This study reports the detection rate of viral and bacterial pathogens among children <5 years of age hospitalized with SARI in Niger.

title:
  Viral and bacterial etiology of severe acute respiratory illness among children < 5 years of age without influenza in Niger

abstract:
  BACKGROUND: Globally, pneumonia is the leading cause of morbidity and mortality in children, with the highest burden experienced in sub-Saharan Africa and Asia. However, there is a dearth of information on the etiology of severe acute respiratory illness (SARI) in Africa, including Niger. METHODS: We implemented a retrospective study as part of national influenza sentinel surveillance in Niger. We randomly selected a sample of nasopharyngeal specimens collected from children <5 years of age hospitalized with SARI from January 2010 through December 2012 in Niger. The samples were selected from individuals that tested negative by real-time reverse transcription polymerase chain reaction (rRT-PCR) for influenza A and B virus. The samples were analyzed using the Fast Track Diagnostic Respiratory Pathogens 21plus Kit (BioMérieux, Luxemburg), which detects 23 respiratory pathogens including 18 viral and 5 bacterial agents. RESULTS: Among the 160 samples tested, 138 (86 %) tested positive for at least one viral or bacterial pathogen; in 22 (16 %) sample, only one pathogen was detected. We detected at least one respiratory virus in 126 (78 %) samples and at least one bacterium in 102 (64 %) samples. Respiratory syncytial virus (56/160; 35 %), rhinovirus (47/160; 29 %) and parainfluenza virus (39/160; 24 %) were the most common viral pathogens detected. Among bacterial pathogens, Streptococcus pneumoniae (90/160; 56 %) and Haemophilus influenzae type b (20/160; 12 %) predominated. CONCLUSIONS: The high prevalence of certain viral and bacterial pathogens among children <5 years of age with SARI highlights the need for continued and expanded surveillance in Niger.


id: cord-274763-i6e3g3te
author: Liu, Wen-Kuan
date: 2018-07-16
txt: ./txt/cord-274763-i6e3g3te.txt
cache: ./cache/cord-274763-i6e3g3te.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30012099/
doi: 10.1186/s12879-018-3225-3
summary:
  title: Epidemiology of HBoV1 infection and relationship with meteorological conditions in hospitalized pediatric patients with acute respiratory illness: a 7-year study in a subtropical region BACKGROUND: Human bocavirus 1 (HBoV1) is an important cause of acute respiratory illness (ARI), yet the epidemiology and effect of meteorological conditions on infection is not fully understood. METHODS: Samples from 11,399 hospitalized pediatric patients (≤14 years old), with ARI were tested for HBoV1 and other common respiratory pathogens using real-time PCR, between July 2009 and June 2016. We collected meteorological data for Guangzhou, including monthly mean temperature, mean relative humidity, rainfall, mean wind speed, mean air pressure, mean vapor pressure and sunshine duration for a 7-year period, to explore the correlation between meteorological conditions and prevalence of HBoV1. Clinical and epidemiological profiles of lower respiratory tract infection in hospitalized children due to human bocavirus in a subtropical area of China

title:
  Epidemiology of HBoV1 infection and relationship with meteorological conditions in hospitalized pediatric patients with acute respiratory illness: a 7-year study in a subtropical region

abstract:
  BACKGROUND: Human bocavirus 1 (HBoV1) is an important cause of acute respiratory illness (ARI), yet the epidemiology and effect of meteorological conditions on infection is not fully understood. To investigate the distribution of HBoV1 and determine the effect of meteorological conditions, hospitalized pediatric patients were studied in a subtropical region of China. METHODS: Samples from 11,399 hospitalized pediatric patients (≤14 years old), with ARI were tested for HBoV1 and other common respiratory pathogens using real-time PCR, between July 2009 and June 2016. In addition, local meteorological data were collected. RESULTS: Of the 11,399 patients tested, 5606 (49.2%) were positive for at least one respiratory pathogen. Two hundred forty-eight of 11,399 (2.2%) were positive for HBoV1 infection. Co-infection was common in HBoV1-positive patients (45.2%, 112/248). A significant difference in the prevalence of HBoV1 was found in patients in different age groups (p < 0.001), and the peak prevalence was found in patients aged 7–12 months (4.7%, 56/1203). Two HBoV1 prevalence peaks were found in summer (between June and September) and winter (between November and December). The prevalence of HBoV1 was significantly positively correlated with mean temperature and negatively correlated with mean relative humidity, and the mean temperature in the preceding month had better explanatory power than the current monthly temperature. CONCLUSIONS: This study provides a better understanding of the characteristics of HBoV1 infection in children in subtropical regions. Data from this study provide useful information for the future control and prevention of HBoV1 infections.


id: cord-275211-1b56a6zc
title: Epidemiology and clinical presentation of the four human parainfluenza virus types
author: Liu, Wen-Kuan
date: 2013-01-23
txt: ./txt/cord-275211-1b56a6zc.txt
cache: ./cache/cord-275211-1b56a6zc.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-13-28
doi: 10.1186/1471-2334-13-28
summary:
  To analyse epidemiologic and clinical characteristics of the four types of human parainfluenza viruses (HPIVs), patients with acute respiratory tract illness (ARTI) were studied in Guangzhou, southern China. CONCLUSIONS: HPIV infection led to a wide spectrum of symptoms, and similar clinical manifestations were found in the patients with four different types of HPIVs. The study suggested pathogenic activity of HPIV in gastrointestinal illness. The HPIV-1, HPIV-2 and HPIV-3 are second only to respiratory syncytial virus (RSV) as a cause of hospitalizations (2%-17%) for acute respiratory infection among children aged younger than 5 years in the United States [1, [8] [9] [10] . The aims of this study were to explore the epidemiologic features and clinical manifestations of HPIVs and other common respiratory pathogens in children and adults with acute respiratory tract illness (ARTI) in Guangzhou, southern China, and to uncover clues that might help to establish clinical distinctions between different HPIV types.

abstract:
  BACKGROUND: Human parainfluenza viruses (HPIVs) are important causes of upper respiratory tract illness (URTI) and lower respiratory tract illness (LRTI). To analyse epidemiologic and clinical characteristics of the four types of human parainfluenza viruses (HPIVs), patients with acute respiratory tract illness (ARTI) were studied in Guangzhou, southern China. METHODS: Throat swabs (n=4755) were collected and tested from children and adults with ARTI over a 26-month period, and 4447 of 4755 (93.5%) patients’ clinical presentations were recorded for further analysis. RESULTS: Of 4755 patients tested, 178 (3.7%) were positive for HPIV. Ninety-nine (2.1%) samples were positive for HPIV-3, 58 (1.2%) for HPIV-1, 19 (0.4%) for HPIV-2 and 8 (0.2%) for HPIV-4. 160/178 (88.9%) HPIV-positive samples were from paediatric patients younger than 5 years old, but no infant under one month of age was HPIV positive. Seasonal peaks of HPIV-3 and HPIV-1 occurred as autumn turned to winter and summer turned to autumn. HPIV-2 and HPIV-4 were detected less frequently, and their frequency of isolation increased when the frequency of HPIV-3 and HPIV-1 declined. HPIV infection led to a wide spectrum of symptoms, and more “hoarseness” (p=0.015), “abnormal pulmonary breathing sound” (p<0.001), “dyspnoea” (p<0.001), “pneumonia” (p=0.01), and “diarrhoea” (p<0.001) presented in HPIV-positive patients than HPIV-negative patients. 10/10 (100%) HPIV-positive adult patients (≥14 years old) presented with systemic influenza-like symptoms, while 90/164 (54.9%) HPIV-positive paediatric patients (<14 years old) presented with these symptoms (p=0.005). The only significant difference in clinical presentation between HPIV types was “Expectoration” (p<0.001). Co-infections were common, with 33.3%–63.2% of samples positive for the four HPIV types also testing positive for other respiratory pathogens. However, no significant differences were seen in clinical presentation between patients solely infected with HPIV and patients co-infected with HPIV and other respiratory pathogens. CONCLUSIONS: HPIV infection led to a wide spectrum of symptoms, and similar clinical manifestations were found in the patients with four different types of HPIVs. The study suggested pathogenic activity of HPIV in gastrointestinal illness. The clinical presentation of HPIV infection may differ by patient age.


id: cord-276015-id15u3br
author: Beran, Jiří
date: 2016-11-07
url: https://www.ncbi.nlm.nih.gov/pubmed/27821093/
doi: 10.1186/s12879-016-1965-5
title:
  Inosine pranobex is safe and effective for the treatment of subjects with confirmed acute respiratory viral infections: analysis and subgroup analysis from a Phase 4, randomised, placebo-controlled, double-blind study

abstract:
  BACKGROUND: Inosine pranobex (Isoprinosine®) is an immunomodulatory drug approved in several countries for the treatment of viral infections. This study compared the efficacy and safety of inosine pranobex versus placebo in subjects with clinically diagnosed influenza-like illness, including subjects with laboratory-confirmed acute respiratory viral infections. Subgroup analyses evaluated the efficacy of inosine pranobex compared to placebo in otherwise healthy (without related ongoing disease) subjects that were less than 50 years of age and healthy subjects that were at least 50 years of age. The effect of body mass index (BMI) was evaluated in subjects less than 50 years of age. METHODS: A total of 463 subjects were randomly assigned to receive inosine pranobex (n = 231) or placebo (n = 232) in this Phase 4, randomised, double-blind, multicentre study. The primary efficacy endpoint was time to resolution of all influenza-like symptoms present at baseline to none. Safety was evaluated through analysis of adverse events, vital signs, and physical examinations. RESULTS: The difference in time to resolution of all influenza-like symptoms between treatment groups was not statistically significant but showed a faster improvement in subjects in the inosine pranobex group versus those in the placebo group - Hazard Ratio = 1.175; (95 % CI: 0.806–1.714). P-value = 0.324. In the subgroup analysis for subjects less than 50 years of age, statistically significant differences in time to resolution of influenza-like symptoms that favoured the inosine pranobex group over the placebo group were observed in those without related ongoing disease and those who were non-obese (BMI <30 kg/m(2)). The differences between the inosine pranobex and placebo groups in subjects at least 50 years of age without related ongoing disease and in subjects less than 50 years of age who were obese (BMI ≥30 kg/m(2)) were not statistically significant. Inosine pranobex was generally well tolerated, and no deaths were reported. CONCLUSIONS: The study results indicate the safety of inosine pranobex for the treatment of subjects with confirmed acute respiratory viral infections and confirm the efficacy of inosine pranobex versus placebo in healthy non-obese subjects less than 50 years of age with clinically diagnosed influenza-like illnesses. TRIAL REGISTRATION: EWO-ISO-2014/1, EudraCT 2014-001863-11; Date of registration: 29 APR 2014; Detail information web link: https://www.clinicaltrialsregister.eu/ctr-search/trial/2014-001863-11/results ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-016-1965-5) contains supplementary material, which is available to authorized users.


id: cord-276857-i948aq4b
title: A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study
author: Chung, Grace TY
date: 2005-10-18
txt: ./txt/cord-276857-i948aq4b.txt
cache: ./cache/cord-276857-i948aq4b.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16229749/
doi: 10.1186/1471-2334-5-87
summary:
  We present here a simple and rapid assay for the screening of SARS-coronavirus genotypes based on the use of fluorogenic oligonucleotide probes for allelic discrimination. Genotyping of the SARS-coronavirus isolates obtained from these patients were carried out by the allelic discrimination assays and confirmed by direct sequencing. In-depth analysis of the available sequence data on SARS-CoV also revealed that the viral isolates could be readily subclassified into several major genotypes based on nucleotide variations at specific genomic positions [8, 12] . In this study, we demonstrate the feasibility of the adoption of allelic discrimination assays based on the use of fluorogenic oligonucleotide probes for the genotyping of SARS-CoV isolates. Our study has clearly demonstrated the feasibility of using allelic discrimination assays as a method for genetic characterization of SARS-CoV genotypes in patients. Genotype of SARS-CoV culture isolates from 30 patients determined by Taqman Allelic Discrimination assays Petric M, Skowronski DM

abstract:
  BACKGROUND: The Severe Acute Respiratory Syndrome (SARS) was a newly emerged infectious disease which caused a global epidemic in 2002–2003. Sequence analysis of SARS-coronavirus isolates revealed that specific genotypes predominated at different periods of the epidemic. This information can be used as a footprint for tracing the epidemiology of infections and monitor viral evolution. However, direct sequencing analysis of a large number of clinical samples is cumbersome and time consuming. We present here a simple and rapid assay for the screening of SARS-coronavirus genotypes based on the use of fluorogenic oligonucleotide probes for allelic discrimination. METHODS: Thirty SARS patients were recruited. Allelic discrimination assays were developed based on the use of fluorogenic oligonucleotide probes (TaqMan). Genotyping of the SARS-coronavirus isolates obtained from these patients were carried out by the allelic discrimination assays and confirmed by direct sequencing. RESULTS: Genotyping based on the allelic discrimination assays were fully concordant with direct sequencing. All of the 30 SARS-coronavirus genotypes studied were characteristic of genotypes previously documented to be associated with the latter part of the epidemic. Seven of the isolates contained a previously reported major deletion but in patients not epidemiologically related to the previously studied cohort. CONCLUSION: We have developed a simple and accurate method for the characterization and screening of SARS-coronavirus genotypes. It is a promising tool for the study of epidemiological relationships between documented cases during an outbreak.


id: cord-277010-2iecsho0
author: Wen, Xiaohong
date: 2019-01-08
txt: ./txt/cord-277010-2iecsho0.txt
cache: ./cache/cord-277010-2iecsho0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30621623/
doi: 10.1186/s12879-018-3668-6
summary:
  title: Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study Similarly, the positive rate of cases with a single virus infection was highest in the young children (65.5%) and lowest in adults of 18-60 years of age (38.5%). The proportion of respiratory viruses notably differed across different age groups; the virus positive rate was the highest in young children under 5 years but was lowest in adults (18~60 years) in this study. Therefore, all positive RhV and/or EV specimens and 10 FluA virus specimens with random selection were identified Table 2 Age distribution of viruses from outpatients with ARIs ARIs, acute respiratory infections by sequencing assay, respectively, and among them, four RhV positive and 3 EV positive specimens were not sequenced due to low viral load in the specimens. In summary, this study provides important epidemiologic data regarding the clinical characteristics, viral spectrum, age distribution and seasonality of viruses in outpatients with ARIs in Huzhou, China.

title:
  Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study

abstract:
  BACKGROUND: Viruses are commonly found in patients with acute respiratory infections (ARIs). However, the viral etiologies and clinical characteristics of outpatients with ARIs are poorly understood in China. Here, we identified the viral etiologies in outpatients with ARIs in Huzhou, China. RESULTS: Our results indicated that of 426 outpatients, 246 were positive for viruses. Of them, 221 were positive for a single virus, including influenza A, which comprised H3N2 (28.5%) and pandemic H1N1 (2009) (19.0%), enterovirus (10.4%), and influenza B (8.6%). Other single viruses were detected at less than 8.0%. Twenty-five patients were positively coinfected with two viruses. The prevalent viruses in coinfections were rhinovirus and H3N2 virus (28.0%). Viruses were major pathogens in young children (< 5 years) (75.0%). Coinfections were prevalent in older adults (11.9%) and young children (9.5%). Virus-positive outpatients presented higher temperatures and more sore throat, fatigue and shortness of breath than virus-negative outpatients. ARIs and most virus detections peaked during the winter, but enteroviruses emerged between April and September. CONCLUSION: Viruses are major agents of ARIs among outpatients in Huzhou, China. There was a variation in the distribution of viruses across different age groups and seasons. These findings are beneficial for planning prevention and treatment services for outpatients with ARIs.


id: cord-278508-h145cxlp
author: Streng, Andrea
date: 2015-12-18
url: https://doi.org/10.1186/s12879-015-1293-1
doi: 10.1186/s12879-015-1293-1
title:
  Continued high incidence of children with severe influenza A(H1N1)pdm09 admitted to paediatric intensive care units in Germany during the first three post-pandemic influenza seasons, 2010/11–2012/13

abstract:
  BACKGROUND: Previous influenza surveillance at paediatric intensive care units (PICUs) in Germany indicated increased incidence of PICU admissions for the pandemic influenza subtype A(H1N1)pdm09. We investigated incidence and clinical characteristics of influenza in children admitted to PICUs during the first three post-pandemic influenza seasons, using active screening. METHODS: We conducted a prospective surveillance study in 24 PICUs in Bavaria (Germany) from October 2010 to September 2013. Influenza cases among children between 1 month and 16 years of age admitted to these PICUs with acute respiratory infection were confirmed by PCR analysis of respiratory secretions. RESULTS: A total of 24/7/20 influenza-associated PICU admissions were recorded in the post-pandemic seasons 1/2/3; incidence estimates per 100,000 children were 1.72/0.76/1.80, respectively. Of all 51 patients, 80 % had influenza A, including 65 % with A(H1N1)pdm09. Influenza A(H1N1)pdm09 was almost absent in season 2 (incidence 0.11), but dominated PICU admissions in seasons 1 (incidence 1.35) and 3 (incidence 1.17). Clinical data was available for 47 influenza patients; median age was 4.8 years (IQR 1.6–11.0). The most frequent diagnoses were influenza-associated pneumonia (62 %), bronchitis/bronchiolitis (32 %), secondary bacterial pneumonia (26 %), and ARDS (21 %). Thirty-six patients (77 %) had underlying medical conditions. Median duration of PICU stay was 3 days (IQR 1–11). Forty-seven per cent of patients received mechanical ventilation, and one patient (2 %) extracorporeal membrane oxygenation; 19 % were treated with oseltamivir. Five children (11 %) had pulmonary sequelae. Five children (11 %) died; all had underlying chronic conditions and were infected with A(H1N1)pdm09. In season 3, patients with A(H1N1)pdm09 were younger than in season 1 (p = 0.020), were diagnosed more often with bronchitis/bronchiolitis (p = 0.004), and were admitted to a PICU later after the onset of influenza symptoms (p = 0.041). CONCLUSIONS: Active screening showed a continued high incidence of A(H1N1)pdm09-associated PICU admissions in the post-pandemic seasons 1 and 3, and indicated possible underestimation of incidence in previous German studies. The age shift of severe A(H1N1)pdm09 towards younger children may be explained by increasing immunity in the older paediatric population. The high proportion of patients with underlying chronic conditions indicates the importance of consistent implementation of the current influenza vaccination recommendations for risk groups in Germany.


id: cord-281916-v6u5mr2i
author: Bonnin, Paul
date: 2016-08-09
txt: ./txt/cord-281916-v6u5mr2i.txt
cache: ./cache/cord-281916-v6u5mr2i.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-016-1730-9
doi: 10.1186/s12879-016-1730-9
summary:
  METHODS: Our study included 800 upper respiratory tract specimens of which 400 negative and 400 positive for viral detection in multiplex PCR. If a rich cell collection appears to be an important prerequisite for the quality of respiratory viral diagnosis, there is currently no information on a possible cellularity threshold that would validate the result of the viral molecular detection. These 800 aliquots were selected in the laboratory samples bank according to their results in virological diagnosis: 400 Positive and 400 Negative for molecular detection of respiratory panel using the RespiFinder ® Smart_22_Fast technique (Pathofinder, Maastricht, Netherlands). The main objectives of this work have been to study the cellularity of these clinical respiratory specimens, to propose a possible definition of what is commonly called "cellular richness," and to measure the impact of this marker on the molecular viral diagnosis. (2014) performed a molecular cell quantification using real time PCR in order to validate viral detection on nasal swabs.

title:
  Study and interest of cellular load in respiratory samples for the optimization of molecular virological diagnosis in clinical practice

abstract:
  BACKGROUND: Respiratory viral diagnosis of upper respiratory tract infections has largely developed through multiplex molecular techniques. Although the sensitivity of different types of upper respiratory tract samples seems to be correlated to the number of sampled cells, this link remains largely unexplored. METHODS: Our study included 800 upper respiratory tract specimens of which 400 negative and 400 positive for viral detection in multiplex PCR. All samples were selected and matched for age in these 2 groups. For the positive group, samples were selected for the detected viral species. RESULTS: Among the factors influencing the cellularity were the type of sample (p < 0.0001); patient age (p < 0.001); viral positive or negative nature of the sample (p = 0.002); and, for the positive samples, the number of viral targets detected (0.004 < p < 0.049) and viral species. CONCLUSION: The cellular load of upper respiratory samples is multifactorial and occurs for many in the sensitivity of molecular detection. However it was not possible to determine a minimum cellularity threshold allowing molecular viral detection. The differences according to the type of virus remain to be studied on a larger scale.


id: cord-282533-w6kl74c8
author: Li, Jin
date: 2018-10-11
url: https://doi.org/10.1186/s12879-018-3429-6
doi: 10.1186/s12879-018-3429-6
title:
  Rapid detection of respiratory organisms with the FilmArray respiratory panel in a large children’s hospital in China

abstract:
  BACKGROUND: Respiratory tract infections (RTIs) are the most common illness in children, and rapid diagnosis is required for the optimal management of RTIs, especially severe infections. METHODS: Nasopharyngeal swab or sputum specimens were collected from children aged 19 days to 15 years who were admitted to a hospital in Shanghai and diagnosed with RTIs. The specimens were tested with the FilmArray Respiratory Panel, a multiplex PCR assay that detects 16 viruses, Mycoplasma pneumoniae (M. pneumoniae), Bordetella pertussis (B. pertussis) and Chlamydophila pneumoniae (C. pneumoniae). RESULTS: Among the 775 children studied, 626 (80.8%, 626/775) tested positive for at least one organism, and multiple organisms were detected in 198 (25.5%). Rhinoviruses/enteroviruses (25.5%, 198/775) were detected most often, followed by respiratory syncytial virus (19.5%, 151/775), parainfluenza virus 3 (14.8%, 115/775), influenza A or B (10.9%), adenovirus (10.8%), M. pneumoniae (10.6%) and B. pertussis (6.3%). The prevalence of organisms differed by age, and most of the viruses were more common in winter. Of the 140 children suspected of having pertussis, 35.0% (49/140) tested positive for B. pertussis. CONCLUSIONS: FilmArray RP allows the rapid simultaneous detection of a wide number of respiratory organisms, with limited hands-on time, in Chinese pediatric patients with RTIs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3429-6) contains supplementary material, which is available to authorized users.


id: cord-282898-hsqvkm2i
author: Matsuda, Kentaro
date: 2013-12-16
txt: ./txt/cord-282898-hsqvkm2i.txt
cache: ./cache/cord-282898-hsqvkm2i.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-13-591
doi: 10.1186/1471-2334-13-591
summary:
  title: Gene and cytokine profile analysis of macrolide-resistant Mycoplasma pneumoniae infection in Fukuoka, Japan Serum IFN-gamma, IL-6 and IP-10 levels were significantly higher in patients infected by the macrolide-resistance genotypes than in those infected by the no-mutation strains (comparison of A2063G vs. pneumoniae isolated from clinical samples antimicrobial agent when compared with the patients infected not only by macrolide-sensitive strains (p = 0.001) but also by A2063T transversion strains (p = 0.02). Characteristics of macrolide-resistant Mycoplasma pneumoniae strains isolated from patients and induced with erythromycin in vitro High prevalence of macrolide resistance in Mycoplasma pneumoniae isolates from adult and adolescent patients with respiratory tract infection in China Nationwide surveillance of macrolide-resistant Mycoplasma pneumoniae infection in pediatric patients Characterization and molecular analysis of macrolide-resistant Mycoplasma pneumoniae clinical isolates obtained in Japan A comparative clinical study of macrolide-sensitive and macrolide-resistant Mycoplasma pneumoniae infections in pediatric patients Gene and cytokine profile analysis of macrolide-resistant Mycoplasma pneumoniae infection in Fukuoka

title:
  Gene and cytokine profile analysis of macrolide-resistant Mycoplasma pneumoniae infection in Fukuoka, Japan

abstract:
  BACKGROUND: Recent epidemiologic data suggest that the prevalence of macrolide resistant Mycoplasma pneumoniae (MR-M. pneumoniae) is increasing rapidly worldwide. This study assessed the present status of M. pneumoniae infection in Japan and clinical end-points to distinguish children with MR-M. pneumoniae. METHODS: During an outbreak of M. pneumoniae infections in Fukuoka, Japan in 2010–11, a total of 105 children with clinically suspected M. pneumoniae infection were enrolled. M. pneumoniae was analyzed for macrolide resistance in domain V of the 23S rRNA gene. Sixty -five patients with PCR positive for M. pneumoniae were analyzed with regard to clinical symptoms, efficacy of several antimicrobial agents and several laboratory data. RESULTS: Causative pathogens were detected in 81.0% (85 of 105) and M. pneumoniae was identified 61.9% (65 of 105). The resistance rate of M. pneumoniae was 89.2% (58 of 65) in this general pediatric outpatient setting. Patients infected with MR-M. pneumoniae showed longer times to resolution of fever and required frequent changes of the initially prescribed macrolide to another antimicrobial agent. We observed three different genotypes of M. pneumoniae including the rarely reported A2063T mutation (A2063G: 31 strains, A2063T: 27 strains, no mutation: 7 strains). Drug susceptibility testing showed different antimicrobial susceptibility profiles for each genotype. Serum IFN-gamma, IL-6 and IP-10 levels were higher in patients with MR-genotypes than in those infected with no-mutation strains (p < 0.001). CONCLUSIONS: Macrolide resistance is more common than previously thought and a small epidemic of rarely reported A2063T mutation was observed in Fukuoka, Japan. Furthermore our results reveal the possibility that levels of certain inflammatory cytokines may be a candidate to predict MR-M.pneumoniae infection.


id: cord-283190-fc05u8mx
author: Neupane, Dinesh
date: 2012-03-30
txt: ./txt/cord-283190-fc05u8mx.txt
cache: ./cache/cord-283190-fc05u8mx.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-12-76
doi: 10.1186/1471-2334-12-76
summary:
  In early 2006 the Government of Nepal established the Avian Influenza Control Project (AICP) and endorsed a Joint Health and Agriculture National Avian Influenza and Influenza Pandemic Preparedness and Response Plan (NAIIPPRP) [4, 9] which placed particular emphasis on precautionary behaviours of poultry workers as well as the knowledge and attitudes which drive such practices. The objectives of the present study were 1) to identify levels of knowledge about preventive behaviours as well as actual preventive behaviours with regard to avian influenza in Nepalese poultry workers, 2) to investigate factors associated with knowing about and practising preventive behaviours against AI, among them sociodemographic characteristics, media use (health information from TV and newspapers), and experience of fear. Afterwards study participants were asked to indicate how often they were using the following preventive measures when dealing with poultry: washing hands with soap and water, donning gloves, face masks, boots/boots covers, putting on protective body garments, and washing and disinfecting utensils and surfaces (five-step-answering format from "always" to "never").

title:
  Knowledge, attitudes and practices related to avian influenza among poultry workers in Nepal: a cross sectional study

abstract:
  BACKGROUND: Avian influenza is a considerable threat to global public health. Prevention and control depend on awareness and protective behaviours of the general population as well as high risk-groups. This study aims to explore the knowledge, attitudes and practices related to avian influenza among poultry workers in Nepal. METHODS: The study was based on a cross-sectional study design, using a structured questionnaire administered in face-to-face interviews with 96 poultry workers age 15 and above from the Rupandehi district in Nepal. RESULTS: The majority of respondents were male (80%), mean age was 35 (SD = 11.6). Nearly everybody was aware that AI cases had been detected in Nepal and that poultry workers were at risk for infection. The major sources of AI information were radio, TV and newspapers. Knowledge about preventive measures was high with regard to some behaviours (hand washing), but medium to low with regard to others (using cleaning and disinfecting procedures or protective clothing). Poultry workers who got their information from TV and newspapers and those who were more afraid of contracting AI had higher knowledge than those who did not. Being employed as compared to being an owner of a poultry farm as well as having a high level of knowledge was associated with practising more preventive behaviours. While on one hand many specific government control measures found a high degree of acceptance, a majority of study participants also thought that government control and compensation measures as a whole were insufficient. CONCLUSIONS: The study provides information about knowledge and practices regarding avian influenza among poultry workers in Nepal. It highlights the importance of targeting lack of knowledge as well as structural-material barriers to successfully build preparedness for a major outbreak situation.


id: cord-283450-w6scpc65
title: The United States and Canada as a coupled epidemiological system: An example from hepatitis A
author: Amariei, Raluca
date: 2008-02-28
url: https://www.ncbi.nlm.nih.gov/pubmed/18307785/
doi: 10.1186/1471-2334-8-23
abstract:
  BACKGROUND: Hepatitis A (HA) is a low-incidence, non-endemic disease in Canada and the United States (US). However, a large difference in HA incidence between Canada and HA-endemic countries has made travel an important contributor to hepatitis A prevalence in Canada. There is also a (smaller) incidence differential between Canada and the US. Although the US has only moderately higher HA incidence, the volume of travel by Canadians to the US is many times higher than travel volume to endemic countries. Hence, travel to the US may constitute a source of low to moderate risk for Canadian travelers. To our knowledge, travel to the US has never been included as a potential risk factor for HA infection in Canadian epidemiologic analyses. The objective of this study was to use dynamic models to investigate the possible effects on hepatitis A incidence in Canada due to (1) implementing vaccination in the US, and (2) varying the volume of travel by Canadians to the US. METHODS: We developed and analyzed age-structured compartmental models for the transmission and vaccination of hepatitis A, for both Canada and the US. Models were parameterized using data on seroprevalence, case reporting, and travel patterns. The potential effect of hepatitis A prevalence in the US on hepatitis A prevalence in Canada was captured through a term representing infection of Canadians due to travel in the US. RESULTS: The model suggests that approximately 22% of HA cases in Canada in the mid 1990s may have been attributable to travel to the US. A universal vaccination programme that attained 70% coverage in young children in the US in the mid 1990s could have reduced Canadian incidence by 21% within 5 years. CONCLUSION: Since not all necessary data were available to parameterize the model, the results should be considered exploratory. However, the analysis shows that, under plausible assumptions, the US may be more important for determining HA prevalence in Canada than is currently supposed. As international travel continues to grow, making vaccination policies ever more relevant to populations beyond a country's borders, such multi-country models will most likely come into wider use as predictive aids for policy development.


id: cord-284393-s9qp9a4e
author: Wei, Yiping
date: 2020-07-29
txt: ./txt/cord-284393-s9qp9a4e.txt
cache: ./cache/cord-284393-s9qp9a4e.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-020-05252-8
doi: 10.1186/s12879-020-05252-8
summary:
  title: Clinical characteristics of 276 hospitalized patients with coronavirus disease 2019 in Zengdu District, Hubei Province: a single-center descriptive study BACKGROUND: We aimed to report the epidemiological and clinical characteristics of hospitalized patients with coronavirus disease-19 (COVID-19) in Zengdu District, Hubei Province, China. Our study on 276 inpatients in Zengdu Hhospital confirms that COVID-19 patients in the areas surrounding the core COVID-19 outbreak region showed mainly mild and moderate illness with fever and lymphocytopenia as the main clinical features. Moreover, compared to studies in which only seriously ill COVID-19 patients were admitted, our admission criteria better reflect the disease characteristics in the area around the outbreak point, so as to provide a decision-making reference for hospitals in the residential area to decide which patients should stay at home for observation and which high-risk patients should be hospitalized in a timely manner. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China

title:
  Clinical characteristics of 276 hospitalized patients with coronavirus disease 2019 in Zengdu District, Hubei Province: a single-center descriptive study

abstract:
  BACKGROUND: We aimed to report the epidemiological and clinical characteristics of hospitalized patients with coronavirus disease-19 (COVID-19) in Zengdu District, Hubei Province, China. METHODS: Clinical data on COVID-19 inpatients in Zengdu Hospital from January 27 to March 11, 2020 were collected; this is a community hospital in an area surrounding Wuhan and supported by volunteer doctors. All hospitalized patients with COVID-19 were included in this study. The epidemiological findings, clinical features, laboratory findings, radiologic manifestations, and clinical outcomes of these patients were analyzed. The patients were followed up for clinical outcomes until March 22, 2020. Severe COVID-19 cases include severe and critical cases diagnosed according to the seventh edition of China’s COVID-19 diagnostic guidelines. Severe and critical COVID-19 cases were diagnosed according to the seventh edition of China’s COVID-19 diagnostic guidelines. RESULTS: All hospitalized COVID-19 patients, 276 (median age: 51.0 years), were enrolled, including 262 non-severe and 14 severe patients. The proportion of patients aged over 60 years was higher in the severe group (78.6%) than in the non-severe group (18.7%, p < 0.01). Approximately a quarter of the patients (24.6%) had at least one comorbidity, such as hypertension, diabetes, or cancer, and the proportion of patients with comorbidities was higher in the severe group (85.7%) than in the non-severe group (21.4%, p < 0.01). Common symptoms included fever (82.2% [227/276]) and cough (78.0% [218/276]). 38.4% (106/276) of the patients had a fever at the time of admission. Most patients (94.9% [204/276]) were cured and discharged; 3.6% (10/276) deteriorated to a critical condition and were transferred to another hospital. The median COVID-19 treatment duration and hospital stay were 14.0 and 18.0 days, respectively. CONCLUSIONS: Most of the COVID-19 patients in Zengdu had mild disease. Older patients with underlying diseases were at a higher risk of progression to severe disease. The length of hospital-stay and antiviral treatment duration for COVID-19 were slightly longer than those in Wuhan. This work will contribute toward an understanding of COVID-19 characteristics in the areas around the core COVID-19 outbreak region and serve as a reference for decision-making for epidemic prevention and control in similar areas.


id: cord-285976-l7voruz7
title: Small-area spatial statistical analysis of malaria clusters and hotspots in Cameroon;2000–2015
author: Tewara, Marlvin Anemey
date: 2018-12-07
url: https://doi.org/10.1186/s12879-018-3534-6
doi: 10.1186/s12879-018-3534-6
abstract:
  BACKGROUND: Malaria prevalence in Cameroon is a major public health problem both at the regional and urban-rural geographic scale. In 2016, an estimated 1.6 million confirmed cases, and 18,738 cases were reported in health facilities and communities respectively, with about 8000 estimated deaths. Several studies have estimated malaria prevalence in Cameroon using the analytical techniques at the regional scale. We aimed at identifying malaria clusters and hotspots at the urban-rural geographic scale from the Demographic and Health Survey (DHS) data for households between 2000 and 2015 using ArcGIS for intervention programs. METHODS: To identify malaria hotspots and analyze the pattern of distribution, we used the optimized hotspots toolset and spatial autocorrelation respectively in ArcGIS 10.3 for desktop. We also used Pearson’s Correlation analysis to identify associative environmental factors using the R-software 3.4.1. RESULTS: The spatial distribution of malaria showed statistically significant clustered pattern for the year 2000 and 2015 with Moran’s indexes 0.126 (P < 0.001) and 0.187 (P < 0.001) respectively. Meanwhile, the years 2005 and 2010 with Moran’s indexes 0.001 (P = 0.488) and 0.002 (P = 0.318) respectively, had a random malaria distribution pattern. There exist varying degrees of malaria clusters and statistically significant hotspots in the urban-rural areas of the 12 administrative regions. Malaria cases were associated with population density and some environmental covariates; rainfall, enhanced vegetation index and composite lights (P < 0.001). CONCLUSION: This study identified urban-rural areas with high and low malaria clusters and hotspots. Our maps can be used as supportive tools for effective malaria control and elimination, and investments in malaria programs and research, malaria prevention, diagnosis and treatment, surveillance, should pay more attention to urban-rural geographic scale.


id: cord-286843-8qh1pblc
title: Impact of microbial Aetiology on mortality in severe community-acquired pneumonia
author: Quah, Jessica
date: 2018-09-04
txt: ./txt/cord-286843-8qh1pblc.txt
cache: ./cache/cord-286843-8qh1pblc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30180811/
doi: 10.1186/s12879-018-3366-4
summary:
  Univariate and multivariate logistic regression showed that serum procalcitonin, APACHE II severity score and mixed viral-bacterial infection were associated with increased risk of hospital mortality. Postulated prohibitive factors against the routine performance of viral diagnostics tests in patients with severe CAP may include a lack of clear clinical guidelines, perceived low cost-effectiveness and the paucity of effective anti-viral therapies for respiratory viruses other than influenza. Our primary hypothesis was that respiratory viruses were important causative pathogens in severe CAP and was associated with increased mortality when present with bacterial pathogens in mixed viral-bacterial co-infections. performed a prospective observational study on physician practices in the use of respiratory virus diagnostics demonstrating that despite clinical guideline recommendations on testing of respiratory viruses during influenza season, less than half of patients admitted to the intensive care unit with pneumonia were tested for viral pathogens [14] .

abstract:
  BACKGROUND: The impact of different classes of microbial pathogens on mortality in severe community-acquired pneumonia is not well elucidated. Previous studies have shown significant variation in the incidence of viral, bacterial and mixed infections, with conflicting risk associations for mortality. We aimed to determine the risk association of microbial aetiologies with hospital mortality in severe CAP, utilising a diagnostic strategy incorporating molecular testing. Our primary hypothesis was that respiratory viruses were important causative pathogens in severe CAP and was associated with increased mortality when present with bacterial pathogens in mixed viral-bacterial co-infections. METHODS: A retrospective cohort study from January 2014 to July 2015 was conducted in a tertiary hospital medical intensive care unit in eastern Singapore, which has a tropical climate. All patients diagnosed with severe community-acquired pneumonia were included. RESULTS: A total of 117 patients were in the study. Microbial pathogens were identified in 84 (71.8%) patients. Mixed viral-bacterial co-infections occurred in 18 (15.4%) of patients. Isolated viral infections were present in 32 patients (27.4%); isolated bacterial infections were detected in 34 patients (29.1%). Hospital mortality occurred in 16 (13.7%) patients. The most common bacteria isolated was Streptococcus pneumoniae and the most common virus isolated was Influenza A. Univariate and multivariate logistic regression showed that serum procalcitonin, APACHE II severity score and mixed viral-bacterial infection were associated with increased risk of hospital mortality. Mixed viral-bacterial co-infections were associated with an adjusted odds ratio of 13.99 (95% CI 1.30–151.05, p = 0.03) for hospital mortality. CONCLUSIONS: Respiratory viruses are common organisms isolated in severe community-acquired pneumonia. Mixed viral-bacterial infections may be associated with an increased risk of mortality.


id: cord-287367-1sdt9zz8
author: Andrews, Denise
date: 2017-10-10
url: https://doi.org/10.1186/s12879-017-2784-z
doi: 10.1186/s12879-017-2784-z
title:
  Multiplex PCR point of care testing versus routine, laboratory-based testing in the treatment of adults with respiratory tract infections: a quasi-randomised study assessing impact on length of stay and antimicrobial use

abstract:
  BACKGROUND: Laboratory-based respiratory pathogen (RP) results are often available too late to influence clinical decisions such as hospitalisation or antibiotic treatment due to time delay in transport of specimens and testing schedules. Ward-based i.e. point of care (POC) testing providing rapid results may alter the clinical management pathway. METHODS: FilmArray® RP polymerase chain reaction (PCR) systems were placed in three in-patient and out-patient medical areas. Patients presenting with influenza-like illness /upper respiratory tract infection +/− lower RTI were recruited between January–July 2015. FilmArray® POC testing occurred on even days of the month (intervention) or routine, laboratory-based RP PCR testing +/− atypical serology on odd days (control). The primary outcome was length of hospital stay. The secondary outcomes were impact on the use of antimicrobials, readmissions, all-cause mortality, length of ward stay and turn-around time (TAT) (time to result from admission). RESULTS: Of 606 eligible patients, 545 (89.9%) were included; 211 in the control arm and 334 in the intervention arm. 20% of control arm patients and 24% of intervention arm patients had an RP detected. POC testing was not associated with the primary outcome measure, length of stay, but reduced the TAT from 39.5 h to 19.0 h, p < 0.001. Only the prescribing decision differed between study arms, p < 0.001. When antivirals were given, the intervention was associated with a reduction in the median time to the first dose of 36 h and allowed appropriate treatment of mycoplasma infection. CONCLUSIONS: We found no association between respiratory PCR POC testing and length of stay or most of the secondary outcomes except the antimicrobial prescribing decision. This was probably due to a delay in initiating FilmArray® testing. Despite this, POC testing allowed time-critical antivirals to be given significantly faster, appropriate mycoplasma treatment and results were available considerably faster than routine, laboratory-based testing. Ward-staff of all grades performed POC testing without difficulty suggesting potential use across many divergent healthcare settings. Further studies evaluating the implementation of rapid respiratory PCR POC testing and the effect on length of stay and antimicrobial use are required. TRIAL REGISTRATION: ISRCTN10470967, Retrospectively Registered, 30/6/2015.


id: cord-287546-0x294f8t
title: An optimal control theory approach to non-pharmaceutical interventions
author: Lin, Feng
date: 2010-02-19
url: https://doi.org/10.1186/1471-2334-10-32
doi: 10.1186/1471-2334-10-32
abstract:
  BACKGROUND: Non-pharmaceutical interventions (NPI) are the first line of defense against pandemic influenza. These interventions dampen virus spread by reducing contact between infected and susceptible persons. Because they curtail essential societal activities, they must be applied judiciously. Optimal control theory is an approach for modeling and balancing competing objectives such as epidemic spread and NPI cost. METHODS: We apply optimal control on an epidemiologic compartmental model to develop triggers for NPI implementation. The objective is to minimize expected person-days lost from influenza related deaths and NPI implementations for the model. We perform a multivariate sensitivity analysis based on Latin Hypercube Sampling to study the effects of input parameters on the optimal control policy. Additional studies investigated the effects of departures from the modeling assumptions, including exponential terminal time and linear NPI implementation cost. RESULTS: An optimal policy is derived for the control model using a linear NPI implementation cost. Linear cost leads to a "bang-bang" policy in which NPIs are applied at maximum strength when certain state criteria are met. Multivariate sensitivity analyses are presented which indicate that NPI cost, death rate, and recovery rate are influential in determining the policy structure. Further death rate, basic reproductive number and recovery rate are the most influential in determining the expected cumulative death. When applying the NPI policy, the cumulative deaths under exponential and gamma terminal times are close, which implies that the outcome of applying the "bang-bang" policy is insensitive to the exponential assumption. Quadratic cost leads to a multi-level policy in which NPIs are applied at varying strength levels, again based on certain state criteria. Results indicate that linear cost leads to more costly implementation resulting in fewer deaths. CONCLUSIONS: The application of optimal control theory can provide valuable insight to developing effective control strategies for pandemic. Our findings highlight the importance of establishing a sensitive and timely surveillance system for pandemic preparedness.


id: cord-287931-cxqzac4a
title: An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens
author: Huang, Weiwei
date: 2013-09-20
txt: ./txt/cord-287931-cxqzac4a.txt
cache: ./cache/cord-287931-cxqzac4a.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-13-437
doi: 10.1186/1471-2334-13-437
summary:
  RESULTS: Using multiple probes designed to specifically detect a microbial genus or species, EOPM can correctly identify known pathogens at the species or genus level in blinded testing. To facilitate the application of EOPM in multiple surveillance sites for infectious diseases, we designed software with a user-friendly interface, which is supported by a statistical analysis method based on a comprehensive microbial sequence identification database. Analysis of the enrichment results at the genus level revealed Cardiovirus as the number one match, showing significant enrichment ( The microarray raw data of other symptom-causing pathogens, such as streptococcus and mycoplasma, identified by EOPM in peripheral blood in infectious patients, were also submitted to the GEO database. These microarray platforms use long oligonucleotide probes (60-70-mer) and random PCR amplification, and have successfully identified unexpected pathogens in infectious disease outbreaks, even discovering novel viruses with homology to known species [8, 11] .

abstract:
  BACKGROUND: Infectious diseases emerge frequently in China, partly because of its large and highly mobile population. Therefore, a rapid and cost-effective pathogen screening method with broad coverage is required for prevention and control of infectious diseases. The availability of a large number of microbial genome sequences generated by conventional Sanger sequencing and next generation sequencing has enabled the development of a high-throughput high-density microarray platform for rapid large-scale screening of vertebrate pathogens. METHODS: An easy operating pathogen microarray (EOPM) was designed to detect almost all known pathogens and related species based on their genomic sequences. For effective identification of pathogens from EOPM data, a statistical enrichment algorithm has been proposed, and further implemented in a user-friendly web-based interface. RESULTS: Using multiple probes designed to specifically detect a microbial genus or species, EOPM can correctly identify known pathogens at the species or genus level in blinded testing. Despite a lower sensitivity than PCR, EOPM is sufficiently sensitive to detect the predominant pathogens causing clinical symptoms. During application in two recent clinical infectious disease outbreaks in China, EOPM successfully identified the responsible pathogens. CONCLUSIONS: EOPM is an effective surveillance platform for infectious diseases, and can play an important role in infectious disease control.


id: cord-288372-48wao8a0
author: Dia, Ndongo
date: 2014-04-08
url: https://doi.org/10.1186/1471-2334-14-189
doi: 10.1186/1471-2334-14-189
title:
  Respiratory viruses associated with patients older than 50 years presenting with ILI in Senegal, 2009 to 2011

abstract:
  BACKGROUND: In Africa, especially in West Africa, studies about the prevalence and diversity of respiratory viruses (influenza and others) in elderly people are largely lacking. In studies done elsewhere, it is well established that older people, when compared with younger adults, are at greater risk of significant morbidity and mortality from complications arising from influenza. The main aim of this study was to determine the prevalence and the diversity of respiratory viruses associated with ILI cases in adults over 50 years old in Senegal. METHODS: The recruitment period of this study was from January 2009 to December 2011. 232 patients aged 50 years and above presenting ILI cases were enrolled. Nasal-pharyngeal and/or oral pharyngeal swabs were collected from patients. RNA was extracted from 200 μl of each sample followed by a two-step real-time RT-PCR. The Anyplex™ II RV16 Detection kit was used for viral detection. The kit enabled the simultaneous detection of the presence of 16 respiratory viruses. RESULTS: 150 viruses were detected: influenza viruses (44.7%) and rhinoviruses (26.7%) were the most prevalent. We detected 13 human parainfluenza viruses (8.7%), 7 human respiratory syncytial viruses (4.7%), 6 coronaviruses (4%), 5 human metapneumoviruses (3.3%), 5 human adenoviruses (3.3%) and 1 human bocavirus (0.7%). 14 cases (6%) of dual virus infections and one triple viral detection case were encountered. 56 (56.6%) viruses detected were found in the 50-64 year old age group, 59 (76.6%; P < 0.001) from 65–74 year old age group and 35 (62.5%) were detected in the ≥75 year old age group. The viral co-infections were more frequent in the 65-74 age group (9/15). CONCLUSIONS: This pilot study demonstrates a variety of respiratory viruses in the elderly. It also highlights a high prevalence of these viruses in this age group. We speculate from these results that the impact of respiratory viruses other than influenza on the elderly has been considerably underestimated. A more exhaustive study seems necessary in order to provide a more complete picture of the burden of respiratory viruses on morbidity among adults over 50 years old in the sub-Saharan context.


id: cord-288720-bd86zswo
author: Lin, Sheng
date: 2020-10-20
url: https://www.ncbi.nlm.nih.gov/pubmed/33081711/
doi: 10.1186/s12879-020-05493-7
title:
  Epidemiological and clinical characteristics of 161 discharged cases with coronavirus disease 2019 in Shanghai, China

abstract:
  BACKGROUND: In December 2019, the outbreak of coronavirus disease 2019 (COVID-19) began in Wuhan, China, and rapidly spread to other regions. We aimed to further describe the epidemiological and clinical characteristics of discharged COVID-19 cases and evaluate the public health interventions. METHODS: We collected epidemiological and clinical data of all discharged COVID-19 cases as of 17 February 2020 in Shanghai. The key epidemiological distributions were estimated and outcomes were also compared between patients whose illness were before 24 January and those whose illness were after 24 January. RESULTS: Of 161 discharged COVID-19 cases, the median age was 45 years, and 80 (49.7%) cases were male. All of the cases were categorized as clinical moderate type. The most common initial symptoms were fever (85.7%), cough (41.0%), fatigue (19.3%), muscle ache (17.4%), sputum production (14.9%), and there were six asymptomatic cases. 39 (24.2%) cases got infected in Shanghai, and three of them were second-generation cases of Shanghai native cases. The estimated median of the time from onset to first medical visit, admission, disease confirmation, and discharge for 161 cases was 1.0 day (95% CI, 0.6–1.2), 2.0 days (95% CI, 1.5–2.6), 5.2 days (95% CI, 4.6–5.7), 18.1 days (95% CI, 17.4–18.8), respectively. The estimated median of the time from admission to discharge was 14.0 days (95% CI, 13.3–14.6). The time from onset to first medical visit, admission and disease confirmation were all shortened after the Shanghai’s first-level public health emergency response. In Cox regression model, the significant independent covariates for the duration of hospitalization were age, the time from onset to admission and the first-level public health emergency response. CONCLUSIONS: Local transmission had occurred in Shanghai in late January 2020. The estimated median of the time from onset to discharge of moderate COVID-19 was 18.1 days in Shanghai. Time intervals from onset to first medical visit, admission and disease confirmation were all shortened after the Shanghai’s first-level public health emergency response. Age, the first-level public health emergency response and the time from onset to admission were the impact factors for the duration of hospitalization.


id: cord-288972-dc6xbxha
title: Entry screening to delay local transmission of 2009 pandemic influenza A (H1N1)
author: Cowling, Benjamin J
date: 2010-03-30
txt: ./txt/cord-288972-dc6xbxha.txt
cache: ./cache/cord-288972-dc6xbxha.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-10-82
doi: 10.1186/1471-2334-10-82
summary:
  BACKGROUND: After the WHO issued the global alert for 2009 pandemic influenza A (H1N1), many national health agencies began to screen travelers on entry in airports, ports and border crossings to try to delay local transmission. METHODS: We reviewed entry screening policies adopted by different nations and ascertained dates of official report of the first laboratory-confirmed imported H1N1 case and the first laboratory-confirmed untraceable or ''local'' H1N1 case. To explore potential delays in local H1N1 transmission associated with entry screening, we ascertained dates of official report of the first laboratory-confirmed imported H1N1 case and the first laboratory-confirmed untraceable or ''local'' H1N1 case (i.e. a case not otherwise epidemiologically linked with international travel, contact with an imported case or their secondary infectees) and the interval between these two events. Additional file 1: Use of entry screening* and interval between confirmation of first imported pandemic influenza A (H1N1) case and confirmation of first untraceable local case

abstract:
  BACKGROUND: After the WHO issued the global alert for 2009 pandemic influenza A (H1N1), many national health agencies began to screen travelers on entry in airports, ports and border crossings to try to delay local transmission. METHODS: We reviewed entry screening policies adopted by different nations and ascertained dates of official report of the first laboratory-confirmed imported H1N1 case and the first laboratory-confirmed untraceable or 'local' H1N1 case. RESULTS: Implementation of entry screening policies was associated with on average additional 7-12 day delays in local transmission compared to nations that did not implement entry screening, with lower bounds of 95% confidence intervals consistent with no additional delays and upper bounds extending to 20-30 day additional delays. CONCLUSIONS: Entry screening may lead to short-term delays in local transmission of a novel strain of influenza virus. The resources required for implementation should be balanced against the expected benefits of entry screening.


id: cord-290432-4dli5emd
author: O’Grady, Kerry-Ann F.
date: 2017-04-04
txt: ./txt/cord-290432-4dli5emd.txt
cache: ./cache/cord-290432-4dli5emd.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28376882/
doi: 10.1186/s12879-017-2349-1
summary:
  We aimed to describe the prevalence of upper airway viruses and bacteria in symptomatic and asymptomatic urban-based Australian Indigenous children aged less than 5 years. METHODS: A cross-sectional analysis of data collected at baseline in an ongoing prospective cohort study of urban Aboriginal and Torres Strait Islander children registered with a primary health care service in the northern suburbs of Brisbane, Australia. Thus, in 164 urban-based Indigenous children presenting to an urban primary health care service, we described the prevalence of upper airway respiratory viruses and bacteria. We analysed data from a cohort of urban Aboriginal and Torres Strait Islander children aged less than 5 years collected at time of enrolment into a prospective study of ARIwC. In a study of upper airway viruses and bacteria in Central Australian Aboriginal children hospitalised for pneumonia [8] , a population with high rates of hospitalised lower ARI [15] and nasal colonisation [16] , the [8] .

title:
  Upper airway viruses and bacteria in urban Aboriginal and Torres Strait Islander children in Brisbane, Australia: a cross-sectional study

abstract:
  BACKGROUND: Respiratory morbidity in Australian Indigenous children is higher than their non-Indigenous counterparts, irrespective of urban or remote residence. There are limited studies addressing acute respiratory illness (ARI) in urban Indigenous children, particularly those that address the upper airway microbiome and its relationship to disease. We aimed to describe the prevalence of upper airway viruses and bacteria in symptomatic and asymptomatic urban-based Australian Indigenous children aged less than 5 years. METHODS: A cross-sectional analysis of data collected at baseline in an ongoing prospective cohort study of urban Aboriginal and Torres Strait Islander children registered with a primary health care service in the northern suburbs of Brisbane, Australia. Clinical, demographic and epidemiological data and bilateral anterior nasal swabs were collected on enrolment. Polymerase chain reaction was performed on nasal swabs to detect 17 respiratory viruses and 7 bacteria. The primary outcome was the prevalence of these microbes at enrolment. Logistic regression was performed to investigate differences in microbe prevalence between children with and without acute respiratory illness with cough as a symptom (ARIwC) at time of specimen collection. RESULTS: Between February 2013 and October 2015, 164 children were enrolled. The median age at enrolment was 18.0 months (IQR 7.2–34.3), 49.4% were boys and 56 children (34.2%) had ARIwC. Overall, 133/164 (81%) nasal swabs were positive for at least one organism; 131 (79.9%) for any bacteria, 59 (36.2%) for any virus and 57 (34.8%) for both viruses and bacteria. Co-detection of viruses and bacteria was more common in females than males (61.4% vs 38.6%, p = 0.044). No microbes, alone or in combination, were significantly associated with the presence of ARIwC. CONCLUSIONS: The prevalence of upper airways microbes in asymptomatic children is similar to non-Indigenous children with ARIwC from the same region. Determining the aetiology of ARIwC in this community is complicated by the high prevalence of multiple respiratory pathogens in the upper airways. STUDY REGISTRATION: Australia New Zealand Clinical Trial Registry Registration Number: 12,614,001,214,628. Retrospectively registered. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-017-2349-1) contains supplementary material, which is available to authorized users.


id: cord-291393-iht5zndl
author: De Angelis, Giulia
date: 2020-10-19
url: https://www.ncbi.nlm.nih.gov/pubmed/33076874/
doi: 10.1186/s12879-020-05504-7
title:
  Confirmed or unconfirmed cases of 2019 novel coronavirus pneumonia in Italian patients: a retrospective analysis of clinical features

abstract:
  BACKGROUND: Since December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged as a novel etiologic agent of viral pneumonia. We aimed to compare clinical features of 165 Italian patients with laboratory confirmed or unconfirmed 2019-nCoV pneumonia. METHODS: On March 31, 2020, hospitalized patients who presented with fever and/or respiratory symptoms, exposures, and presence of lung imaging features consistent with 2019-nCoV pneumonia were included. Before admission to a hospital ward, patients underwent RT-PCR based SARS-CoV-2 RNA detection in their nasopharyngeal swab samples. RESULTS: Of 165 patients studied, 119 had positive RT-PCR results and 46 were RT-PCR negative for 2 days or longer (i.e., when the last swab sample was obtained). The median age was 70 years (IQR, 58–78), and 123 (74.6%) of 165 patients had at least one comorbidity. The majority of patients (101/165, 61.2%) had a mild pneumonia, and the remaining patients (64/165, 38.8%) a severe/critical pneumonia. We did not find any substantial difference in symptoms, incubation periods, and radiographic/CT abnormalities as well as in many of the biological abnormalities recorded. However, at multivariable analysis, higher concentrations of hemoglobin (OR, 1.34; 95% CI, 1.11–1.65; P = 0.003) and lower counts of leukocytes (OR, 0.81; 95% CI, 0.72–0.90; P < 0.001) were statistically associated with confirmed COVID-19 diagnosis. While mortality rates were similar, patients with confirmed diagnosis were more likely to receive antivirals (95% vs 19.6%, P < 0.001) and to develop ARDS (63% vs 37%, P = 0.003) than those with unconfirmed COVID-19 diagnosis. CONCLUSIONS: Our findings suggest that unconfirmed 2019-nCoV pneumonia cases may be actually COVID-19 cases and that clinicians should be cautious when managing patients with presentations compatible with COVID-19.


id: cord-292609-e99y0l5a
author: Liu, Ye
date: 2010-08-06
url: https://doi.org/10.1186/1471-2334-10-234
doi: 10.1186/1471-2334-10-234
title:
  Ferret badger rabies origin and its revisited importance as potential source of rabies transmission in Southeast China

abstract:
  BACKGROUND: The frequent occurrence of ferret badger-associated human rabies cases in southeast China highlights the lack of laboratory-based surveillance and urges revisiting the potential importance of this animal in rabies transmission. To determine if the ferret badgers actually contribute to human and dog rabies cases, and the possible origin of the ferret badger-associated rabies in the region, an active rabies survey was conducted to determine the frequency of rabies infection and seroprevalence in dogs and ferret badgers. METHODS: A retrospective survey on rabies epidemics was performed in Zhejiang, Jiangxi and Anhui provinces in southeast China. The brain tissues from ferret badgers and dogs were assayed by fluorescent antibody test. Rabies virus was isolated and sequenced for phylogenetic analysis. The sera from ferret badgers and dogs were titrated using rabies virus neutralizing antibodies (VNA) test. RESULTS: The ferret badgers presented a higher percentage of rabies seroconversion than dogs did in the endemic region, reaching a maximum of 95% in the collected samples. Nine ferret badger-associated rabies viruses were isolated, sequenced, and were phylogenetically clustered as a separate group. Nucleotide sequence revealed 99.4-99.8% homology within the ferret badger isolates, and 83-89% homology to the dog isolates in the nucleoprotein and glycoprotein genes in the same rabies endemic regions. CONCLUSIONS: Our data suggest ferret badger-associated rabies has likely formed as an independent enzootic originating from dogs during the long-term rabies infestation in southeast China. The eventual role of FB rabies in public health remains unclear. However, management of ferret badger bites, rabies awareness and control in the related regions should be an immediate need.


id: cord-292828-29jbf9ik
author: Alsaleh, Asma N
date: 2014-01-09
txt: ./txt/cord-292828-29jbf9ik.txt
cache: ./cache/cord-292828-29jbf9ik.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-14-15
doi: 10.1186/1471-2334-14-15
summary:
  title: Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies. Importantly, when using highly sensitive polymerase chain reaction (PCR) assays the detection rates for respiratory viruses are similar in both anterior nasal swab specimens and samples collected by the more traditional method of nasopharyngeal aspiration [18, 19] . The ORChID project is an ongoing comprehensive community-based study using PCR assays to detect respiratory viruses in anterior nasal swab specimens taken weekly by parents from their infants throughout the first 2-years of life.

title:
  Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control

abstract:
  BACKGROUND: Carefully conducted, community-based, longitudinal studies are required to gain further understanding of the nature and timing of respiratory viruses causing infections in the population. However, such studies pose unique challenges for field specimen collection, including as we have observed the appearance of mould in some nasal swab specimens. We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays. METHODS: Anterior nasal swab samples were collected from infants participating in an ongoing community-based, longitudinal, dynamic birth cohort study. The samples were first collected from each infant shortly after birth and weekly thereafter. They were then mailed to the laboratory where they were catalogued, stored at -80°C and later screened by PCR for 17 respiratory viruses. The quality of specimen collection was assessed by screening for human deoxyribonucleic acid (DNA) using endogenous retrovirus 3 (ERV3). The impact of ERV3 load upon respiratory virus detection and the impact of visible mould observed in a subset of swabs reaching the laboratory upon both ERV3 loads and respiratory virus detection was determined. RESULTS: In total, 4933 nasal swabs were received in the laboratory. ERV3 load in nasal swabs was associated with respiratory virus detection. Reduced respiratory virus detection (odds ratio 0.35; 95% confidence interval 0.27-0.44) was observed in samples where the ERV3 could not be identified. Mould was associated with increased time of samples reaching the laboratory and reduced ERV3 loads and respiratory virus detection. CONCLUSION: Suboptimal sample collection and high levels of visible mould can impact negatively upon sample quality. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies.


id: cord-293858-dk4snw9r
author: Yang, Lin
date: 2019-02-14
url: https://www.ncbi.nlm.nih.gov/pubmed/30764779/
doi: 10.1186/s12879-019-3735-7
title:
  Comparison of influenza disease burden in older populations of Hong Kong and Brisbane: the impact of influenza and pneumococcal vaccination

abstract:
  BACKGROUND: Influenza and pneumococcal vaccine uptake in the older population aged 65 years or over of Hong Kong dramatically increased since the 2003 SARS outbreak. This study is aimed to evaluate the impact of increased coverage of influenza and pneumococcal vaccines by comparing the change of disease burden in the older population of Hong Kong, with the burden in the older population of Brisbane with relatively high vaccine coverage in the past fifteen years. METHODS: Time series segmented regression models were applied to weekly numbers of cause-specific mortality or hospitalization of Hong Kong and Brisbane. Annual excess rates of mortality or hospitalization associated with influenza in the older population were estimated for the pre-SARS (reference period), post-SARS and post-pandemic period, respectively. The rate ratios (RRs) between these periods were also calculated to assess the relative change of disease burden. RESULTS: Compared to the pre-SARS period, excess rates of mortality associated with influenza during the post-SARS period in Hong Kong decreased for cardiorespiratory diseases (RR = 0.90, 95% CI 0.80, 1.01), stroke (RR = 0.74, 95% CI 0.50, 1.09), and ischemic heart diseases (RR = 0.45, 95% CI 0.34, 0.58). The corresponding RRs in Brisbane were 0.79 (95% CI 0.54, 1.15), 0.33 (0.13, 0.80), and 1.09 (0.62, 1.90), respectively. Only the mortality of ischemic heart diseases showed a greater reduction in Hong Kong than in Brisbane. During the post-pandemic period, excess rates of all-cause mortality increased in Hong Kong, but to a lesser extent than in Brisbane (RR = 1.41 vs 2.39). CONCLUSION: A relative decrease (or less of an increase) of influenza disease burden was observed in the older population of Hong Kong after increased coverage of influenza and pneumococcal vaccines in this population, as compared to those of Brisbane where vaccination rates remained stable. The lack of significant findings in some disease categories highlights the challenges of evaluating the benefits of vaccination at the population level. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-019-3735-7) contains supplementary material, which is available to authorized users.


id: cord-294062-3esrg1jw
author: Tam, Clarence C.
date: 2018-09-14
url: https://doi.org/10.1186/s12879-018-3358-4
doi: 10.1186/s12879-018-3358-4
title:
  Association between semi-quantitative microbial load and respiratory symptoms among Thai military recruits: a prospective cohort study

abstract:
  BACKGROUND: Multiplex real-time polymerase chain reaction assays have improved diagnostic sensitivity for a wide range of pathogens. However, co-detection of multiple agents and bacterial colonization make it difficult to distinguish between asymptomatic infection or illness aetiology. We assessed whether semi-quantitative microbial load data can differentiate between symptomatic and asymptomatic states for common respiratory pathogens. METHODS: We obtained throat and nasal swab samples from military trainees at two Thai Army barracks. Specimens were collected at the start and end of 10-week training periods (non-acute samples), and from individuals who developed upper respiratory tract infection during training (acute samples). We analysed the samples using a commercial multiplex respiratory panel comprising 33 bacterial, viral and fungal targets. We used random effects tobit models to compare cycle threshold (Ct) value distributions from non-acute and acute samples. RESULTS: We analysed 341 non-acute and 145 acute swab samples from 274 participants. Haemophilus influenzae type B was the most commonly detected microbe (77.4% of non-acute and 64.8% of acute samples). In acute samples, nine specific microbe pairs were detected more frequently than expected by chance. Regression models indicated significantly lower microbial load in non-acute relative to acute samples for H. influenzae non-type B, Streptococcus pneumoniae and rhinovirus, although it was not possible to identify a Ct-value threshold indicating causal etiology for any of these organisms. CONCLUSIONS: Semi-quantitative measures of microbial concentration did not reliably differentiate between illness and asymptomatic colonization, suggesting that clinical symptoms may not always be directly related to microbial load for common respiratory infections. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3358-4) contains supplementary material, which is available to authorized users.


id: cord-296375-gf0mgz5x
title: Comparison of spatiotemporal characteristics of the COVID-19 and SARS outbreaks in mainland China
author: Zhang, Xi
date: 2020-10-30
txt: ./txt/cord-296375-gf0mgz5x.txt
cache: ./cache/cord-296375-gf0mgz5x.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-020-05537-y
doi: 10.1186/s12879-020-05537-y
summary:
  CONCLUSIONS: COVID-19 and SARS outbreaks exhibited distinct spatiotemporal clustering patterns at the provincial levels in mainland China, which may be attributable to changes in social and demographic factors, local government containment strategies or differences in transmission mechanisms. Therefore, in this study, by collecting the daily numbers of newly confirmed COVID-19 and SARS cases during the two epidemics, we aimed to determine the spatial behavior and temporal features of the COVID-19 spread in mainland China and compared them with respective features from the SARS epidemic using spatiotemporal analysis. Incident cases infected by COVID-19 were extracted from the daily briefings on novel coronavirus cases from January 20 to March 4, 2020, provided on the official website of the National Health Commission of the People''s Republic of China [5] . Incident cases of SARS were extracted from daily situation reports for mainland China from April 21 to August 3, 2003 , which were posted by China.org.cn (in Chinese) and were also provided by the National Health Commission.

abstract:
  BACKGROUND: Both coronavirus disease 2019 (COVID-19) and severe acute respiratory syndrome (SARS) are caused by coronaviruses and have infected people in China and worldwide. We aimed to investigate whether COVID-19 and SARS exhibited similar spatial and temporal features at provincial level in mainland China. METHODS: The number of people infected by COVID-19 and SARS were extracted from daily briefings on newly confirmed cases during the epidemics, as of Mar. 4, 2020 and Aug. 3, 2003, respectively. We depicted spatiotemporal patterns of the COVID-19 and SARS epidemics using spatial statistics such as Moran’s I and the local indicators of spatial association (LISA). RESULTS: Compared to SARS, COVID-19 had a higher overall incidence. We identified 3 clusters (predominantly located in south-central China; the highest RR = 135.08, 95% CI: 128.36–142.08) for COVID-19 and 4 clusters (mainly in Northern China; the highest RR = 423.51, 95% CI: 240.96–722.32) for SARS. Fewer secondary clusters were identified after the “Wuhan lockdown”. The LISA cluster map detected a significantly high-low (Hubei) and low-high spatial clustering (Anhui, Hunan, and Jiangxi, in Central China) for COVID-19. Two significant high-high (Beijing and Tianjin) and low-high (Hebei) clusters were detected for SARS. CONCLUSIONS: COVID-19 and SARS outbreaks exhibited distinct spatiotemporal clustering patterns at the provincial levels in mainland China, which may be attributable to changes in social and demographic factors, local government containment strategies or differences in transmission mechanisms. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-020-05537-y.


id: cord-296868-fn4gzsw1
title: Fever screening during the influenza (H1N1-2009) pandemic at Narita International Airport, Japan
author: Nishiura, Hiroshi
date: 2011-05-03
txt: ./txt/cord-296868-fn4gzsw1.txt
cache: ./cache/cord-296868-fn4gzsw1.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-11-111
doi: 10.1186/1471-2334-11-111
summary:
  The first contained confirmed influenza cases (n = 16) whose diagnosis took place at the airport during the early stages of the pandemic, and the second contained a selected and suspected fraction of passengers (self-reported or detected by an infrared thermoscanner; n = 1,049) screened from September 2009 to January 2010. The first dataset contained the limited number of confirmed cases infected with H1N1-2009 or other influenza viruses whose diagnosis took place at the airport during the very early stages of the 2009 pandemic, and the second dataset contained non-randomly sampled passengers, comprising a selected and suspected fraction of passengers (selfreported or detected by an infrared thermoscanner) arriving at Narita International Airport from September 2009 to January 2010 ( Figure 1 ).

abstract:
  BACKGROUND: Entry screening tends to start with a search for febrile international passengers, and infrared thermoscanners have been employed for fever screening in Japan. We aimed to retrospectively assess the feasibility of detecting influenza cases based on fever screening as a sole measure. METHODS: Two datasets were collected at Narita International Airport during the 2009 pandemic. The first contained confirmed influenza cases (n = 16) whose diagnosis took place at the airport during the early stages of the pandemic, and the second contained a selected and suspected fraction of passengers (self-reported or detected by an infrared thermoscanner; n = 1,049) screened from September 2009 to January 2010. The sensitivity of fever (38.0°C) for detecting H1N1-2009 was estimated, and the diagnostic performances of the infrared thermoscanners in detecting hyperthermia at cut-off levels of 37.5°C, 38.0°C and 38.5°C were also estimated. RESULTS: The sensitivity of fever for detecting H1N1-2009 cases upon arrival was estimated to be 22.2% (95% confidence interval: 0, 55.6) among nine confirmed H1N1-2009 cases, and 55.6% of the H1N1-2009 cases were under antipyretic medications upon arrival. The sensitivity and specificity of the infrared thermoscanners in detecting hyperthermia ranged from 50.8-70.4% and 63.6-81.7%, respectively. The positive predictive value appeared to be as low as 37.3-68.0%. CONCLUSIONS: The sensitivity of entry screening is a product of the sensitivity of fever for detecting influenza cases and the sensitivity of the infrared thermoscanners in detecting fever. Given the additional presence of confounding factors and unrestricted medications among passengers, reliance on fever alone is unlikely to be feasible as an entry screening measure.


id: cord-297024-90qq0xsw
title: How long do nosocomial pathogens persist on inanimate surfaces? A systematic review
author: Kramer, Axel
date: 2006-08-16
url: https://www.ncbi.nlm.nih.gov/pubmed/16914034/
doi: 10.1186/1471-2334-6-130
abstract:
  BACKGROUND: Inanimate surfaces have often been described as the source for outbreaks of nosocomial infections. The aim of this review is to summarize data on the persistence of different nosocomial pathogens on inanimate surfaces. METHODS: The literature was systematically reviewed in MedLine without language restrictions. In addition, cited articles in a report were assessed and standard textbooks on the topic were reviewed. All reports with experimental evidence on the duration of persistence of a nosocomial pathogen on any type of surface were included. RESULTS: Most gram-positive bacteria, such as Enterococcus spp. (including VRE), Staphylococcus aureus (including MRSA), or Streptococcus pyogenes, survive for months on dry surfaces. Many gram-negative species, such as Acinetobacter spp., Escherichia coli, Klebsiella spp., Pseudomonas aeruginosa, Serratia marcescens, or Shigella spp., can also survive for months. A few others, such as Bordetella pertussis, Haemophilus influenzae, Proteus vulgaris, or Vibrio cholerae, however, persist only for days. Mycobacteria, including Mycobacterium tuberculosis, and spore-forming bacteria, including Clostridium difficile, can also survive for months on surfaces. Candida albicans as the most important nosocomial fungal pathogen can survive up to 4 months on surfaces. Persistence of other yeasts, such as Torulopsis glabrata, was described to be similar (5 months) or shorter (Candida parapsilosis, 14 days). Most viruses from the respiratory tract, such as corona, coxsackie, influenza, SARS or rhino virus, can persist on surfaces for a few days. Viruses from the gastrointestinal tract, such as astrovirus, HAV, polio- or rota virus, persist for approximately 2 months. Blood-borne viruses, such as HBV or HIV, can persist for more than one week. Herpes viruses, such as CMV or HSV type 1 and 2, have been shown to persist from only a few hours up to 7 days. CONCLUSION: The most common nosocomial pathogens may well survive or persist on surfaces for months and can thereby be a continuous source of transmission if no regular preventive surface disinfection is performed.


id: cord-297029-b38sm4y9
author: Murillo-Zamora, Efrén
date: 2020-09-16
txt: ./txt/cord-297029-b38sm4y9.txt
cache: ./cache/cord-297029-b38sm4y9.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-020-05408-6
doi: 10.1186/s12879-020-05408-6
summary:
  Demographic characteristics (sex, age), tobacco use (current), personal history of chronic communicable disease (HIV infection, no/yes) and noncommunicable disease (no/yes: obesity [body mass index of 30 or higher], arterial hypertension, type 2 diabetes mellitus, asthma, chronic kidney disease, immunosuppression, chronic obstructive pulmonary disease, or cardiovascular illness) were collected from the surveillance system. In the multiple regression analysis (Table 2) , male gender (RR = 1.13, 95% CI 1.06-1.20) and older patients ([reference: 15-29 years old] 30-44, RR = 1.02, 95% CI 0.94-1.11; 45-59, RR = 1.26, 95% CI 1.15-1.38; 60 years or older, RR = 1.44, 95% CI 1.29-1.60), subjects to thoracic pain (RR = 1.16, 95% CI 1.10-1.24) or chronic kidney disease (RR = 1.31, 95% CI 1.04-1.64) were also more likely to present severe COVID-19.

title:
  Male gender and kidney illness are associated with an increased risk of severe laboratory-confirmed coronavirus disease

abstract:
  BACKGROUND: To identify factors predicting severe coronavirus disease 2019 (COVID-19) in adolescent and adult patients with laboratory-positive (quantitative reverse-transcription polymerase chain reaction) infection. METHOD: A retrospective cohort study took place, and data from 740 subjects, from all 32 states of Mexico, were analyzed. The association between the studied factors and severe (dyspnea requiring hospital admission) COVID-19 was evaluated through risk ratios (RRs) and 95% confidence intervals (CIs). RESULTS: Severe illness was documented in 28% of participants. In multiple analysis, male gender (RR = 1.13, 95% CI 1.06–1.20), advanced age ([reference: 15–29 years old] 30–44, RR = 1.02, 95% CI 0.94–1.11; 45–59, RR = 1.26, 95% CI 1.15–1.38; 60 years or older, RR = 1.44, 95% CI 1.29–1.60), chronic kidney disease (RR = 1.31, 95% CI 1.04–1.64) and thoracic pain (RR = 1.16, 95% CI 1.10–1.24) were associated with an increased risk of severe disease. CONCLUSIONS: To the best of our knowledge, this is the first study evaluating predictors of COVID-19 severity in a large subset of the Latin-American population. Male gender and kidney illness were independently associated with the risk of severe COVID-19. These results may be useful for health care protocols for the early detection and management of patients that may benefit from opportune and specialized supportive medical treatment.


id: cord-297494-6yxmaihl
author: Katsurada, Naoko
date: 2017-12-06
txt: ./txt/cord-297494-6yxmaihl.txt
cache: ./cache/cord-297494-6yxmaihl.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-017-2858-y
doi: 10.1186/s12879-017-2858-y
summary:
  However, influenza virus A and B were associated with three-fold higher mortality in patients with chronic respiratory disease but not with other comorbidities (ARR 3.38, 95% CI 1.54–7.42). We conducted this prospective multicentre study to determine the distribution of viruses associated with pneumonia in adults and to establish their virus-specific effects on pneumonia mortality stratified by age group and comorbidity status. To the best of our knowledge, this study is the first to systematically investigate virus-specific effects on pneumonia mortality by age group and comorbidity status among adults. In our study, multiple viruses were identified in 5.1% of virus-associated pneumonia and were associated with higher mortality than single viral infection in patients with chronic respiratory disease and other comorbidities. Systematic reviews have shown that multiple viral infections in patients with respiratory disease are not associated with disease severity [27, 28] ; however, the majority of previous studies included young children but not adults.

title:
  The impact of virus infections on pneumonia mortality is complex in adults: a prospective multicentre observational study

abstract:
  BACKGROUND: Various viruses are known to be associated with pneumonia. However, the impact of viral infections on adult pneumonia mortality remains unclear. This study aimed to clarify the effect of virus infection on pneumonia mortality among adults stratified by virus type and patient comorbidities. METHODS: This multicentre prospective study enrolled pneumonia patients aged ≥15 years from September 2011 to August 2014. Sputum samples were tested by in-house multiplex polymerase chain reaction assays to identify 13 respiratory viruses. Viral infection status and its effect on in-hospital mortality were examined by age group and comorbidity status. RESULTS: A total of 2617 patients were enrolled in the study and 77.8% was aged ≥65 years. 574 (21.9%) did not have comorbidities, 790 (30.2%) had chronic respiratory disease, and 1253 (47.9%) had other comorbidities. Viruses were detected in 605 (23.1%) patients. Human rhinovirus (9.8%) was the most frequently identified virus, followed by influenza A (3.9%) and respiratory syncytial virus (3.9%). Respiratory syncytial virus was more frequently identified in patients with chronic respiratory disease (4.7%) than those with other comorbidities (4.2%) and without comorbidities (2.1%) (p = 0.037). The frequencies of other viruses were almost identical between the three groups. Virus detection overall was not associated with increased mortality (adjusted risk ratio (ARR) 0.76, 95% CI 0.53–1.09). However, influenza virus A and B were associated with three-fold higher mortality in patients with chronic respiratory disease but not with other comorbidities (ARR 3.38, 95% CI 1.54–7.42). Intriguingly, paramyxoviruses were associated with dramatically lower mortality in patients with other comorbidities (ARR 0.10, 95% CI 0.01–0.70) but not with chronic respiratory disease. These effects were not affected by age group. CONCLUSIONS: The impact of virus infections on pneumonia mortality varies by virus type and comorbidity status in adults. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-017-2858-y) contains supplementary material, which is available to authorized users.


id: cord-298002-jvnwivrg
title: COVID-19 confirmed patients with negative antibodies results
author: Wang, Jian
date: 2020-09-22
txt: ./txt/cord-298002-jvnwivrg.txt
cache: ./cache/cord-298002-jvnwivrg.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32962655/
doi: 10.1186/s12879-020-05419-3
summary:
  CASE PRESENTATIONS: We present two cases of confirmed COVID-19 patients and characterize their initial symptoms, chest CT results, medication, and laboratory test results in detail (including RT-PCR, IgM/ IgG, cytokine and blood cell counts). CONCLUSION: Both of patients with confirmed COVID-19 pneumonia failed to produce either IgM or IgG even 40 to 50 days after their symptoms onset. During the outbreak of coronavirus 2019 (COVID-19) [1] [2] [3] , a small proportion of confirmed COVID-19 patients fail to produce IgM or IgG antibodies against SARS-CoV-2 even 40 days or longer periods of time after onset of their initial symptoms. From January 30 to March 15, 310 of COVID-19 patients who were positive for SARS-CoV-2 real time reverse-transcription PCR (RT-PCR) testing and received IgM and IgG detection at Wuhan Union Hospital (Wuhan, China) were enrolled. In this study, two patients with confirmed COVID-19 failed to produce either IgM or IgG even 40 to 50 days after their symptoms onset.

abstract:
  BACKGROUND: A new coronavirus disease 2019 (COVID-19) has escalated to a pandemic since its first outbreak in Wuhan, China. A small proportion of patients may have difficulty in generating IgM or IgG antibodies against SARS-CoV-2, and little attention has been paid to them. CASE PRESENTATIONS: We present two cases of confirmed COVID-19 patients and characterize their initial symptoms, chest CT results, medication, and laboratory test results in detail (including RT-PCR, IgM/ IgG, cytokine and blood cell counts). CONCLUSION: Both of patients with confirmed COVID-19 pneumonia failed to produce either IgM or IgG even 40 to 50 days after their symptoms onset. This work provides evidence demonstrating that at least a small proportion of patients may have difficulty in rapidly gaining immunity against SARS-CoV-2.


id: cord-298899-lkrmg5qr
author: Xie, Yewei
date: 2020-08-31
txt: ./txt/cord-298899-lkrmg5qr.txt
cache: ./cache/cord-298899-lkrmg5qr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32867706/
doi: 10.1186/s12879-020-05371-2
summary:
  To fill the research gaps mentioned above, this review article systematically summarizes global findings on the natural history, clinical spectrum, transmission patterns, laboratory findings, CT results, and risk factors of the COVID-19. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical course and risk factors for mortality of adult in patients with COVID-19 in Wuhan, China: a retrospective cohort study Clinical course and potential predicting factors of pneumonia of adult patients with coronavirus disease 2019 (COVID-19): a retrospective observational analysis of 193 confirmed cases in Thailand Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan Epidemiology, risk factors and clinical course of SARS-CoV-2 infected patients in a Swiss university hospital: an observational retrospective study

title:
  Epidemiologic, clinical, and laboratory findings of the COVID-19 in the current pandemic: systematic review and meta-analysis

abstract:
  BACKGROUND: The COVID-19 pandemic has affected the world deeply, with more than 14,000,000 people infected and nearly 600,000 deaths. This review aimed to summarize the epidemiologic traits, clinical spectrum, CT results and laboratory findings of the COVID-19 pandemic. METHODS: We scoped for relevant literatures published during 1st December 2019 to 16th July 2020 based on three databases using English and Chinese languages. We reviewed and analyzed the relevant outcomes. RESULTS: The COVID-19 pandemic was found to have a higher transmission rate compared to SARS and MERS and involved 4 stages of evolution. The basic reproduction number (R(0)) is 3.32 (95% CI:3.24–3.39), the incubation period was 5.24 days (95% CI:3.97–6.50, 5 studies) on average, and the average time for symptoms onset varied by countries. Common clinical spectrums identified included fever (38.1–39.0 °C), cough and fatigue, with Acute Respiratory Distress Syndrome (ARDS) being the most common complication reported. Body temperatures above 39.0 °C, dyspnea, and anorexia were more common symptoms in severe patients. Aged over 65 years old, having co-morbidities, and developing complications were the commonest high-risk factors associated with severe conditions. Leucopenia and lymphopenia were the most common signs of infection while liver and kidney damage were rare but may cause bad outcomes for patients. The bilateral, multifocal Ground-Glass Opacification (GGO) on peripheral, and the consolidative pulmonary opacity were the most frequent CT results and the tendency of mortality rates differed by region. CONCLUSIONS: We provided a bird’s-eye view of the COVID-19 during the current pandemic, which will help better understanding the key traits of the disease. The findings could be used for disease’s future research, control and prevention.


id: cord-299750-zkrlm3ds
author: Cui, Wei
date: 2010-05-31
txt: ./txt/cord-299750-zkrlm3ds.txt
cache: ./cache/cord-299750-zkrlm3ds.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/20513239/
doi: 10.1186/1471-2334-10-145
summary:
  We describe the clinical characteristics and factors associated with the death of patients who were hospitalized with 2009 H1N1 influenza pneumonia in Shenyang, China, from November to December 2009. Therefore, this report summarizes the clinical manifestations, clinical outcomes and the risk factors associated with death in hospitalized pneumonia patients associated with 2009 H1N1 influenza infections in Shenyang, China, during November to December 2009. They used a standardized form that included demographic data, seasonal influenza vaccination history for the previous year, smoking status, underlying medical conditions, clinical signs and symptoms, selected laboratory tests including C reactive protein (CRP), white blood cell classification and count, lactic dehydrogenase (LDH), creatine kinase (CK), glutamic-oxaloacetic transaminase (AST), glutamic alanine aminotransferase (ALT), albumin (Alb), CD4, CD8 and CD3 T cell counts, blood gas analyses, blood or sputum cultures, radiographic findings, intervals between symptom onset and initiation of oseltamivir therapy, treatment course and length of stay.

title:
  Factors associated with death in hospitalized pneumonia patients with 2009 H1N1 influenza in Shenyang, China

abstract:
  BACKGROUND: During the spring of 2009, a pandemic influenza A (H1N1) virus emerged and spread globally. We describe the clinical characteristics and factors associated with the death of patients who were hospitalized with 2009 H1N1 influenza pneumonia in Shenyang, China, from November to December 2009. METHODS: We carried out a retrospective chart review of 68 patients who were hospitalized with pneumonia and confirmed to have 2009 H1N1 virus infection by a real time RT-PCR assay of respiratory specimens. RESULTS: Of the 68 patients we studied, 30 (44%) were admitted to an intensive care unit and 10 (14.7%) died. The median age of patients was 41 years (range, 18-66), and only one patient was over 65 years of age. The male to female ratio was 2.78:1 (50:18). Of the 68 patients, 23 (34%) had at least one underlying medical condition, 9 (13%) had a cigarette index ≥400 and 22 (32%) were obese. All patients underwent chest radiography on admission and the findings were consistent with pneumonia in all cases. All patients were treated with oseltamivir and treatment was initiated at a median time of seven days after the onset of illness. The laboratory test results indicated lymphopenia, hypoproteinemia and elevated lactic dehydrogenase and C reactive protein levels. Of the 68 patients, 33 (52%) showed a reduction in CD4 T cell counts. Of the 58 patients who survived, 31 (53%) had lymphopenia and 27 recovered from this condition after five days. Of the 10 patients who died, nine (90%) had lymphopenia and only two patients recovered from this condition after five days. Obesity and recovery from lymphopenia after five days were factors associated with death, as determined by multivariate logistic-regression analysis (obesity, odds ratio = 23.06; lymphocytopenia reversion, odds ration = 28.69). CONCLUSIONS: During the evaluation period in Shenyang, China, 2009 H1N1 influenza caused severe illness requiring hospitalization in 68 patients, 10 (14.7%) of which died. Many of these patients were considered healthy adults and few were elderly (65 years or older). Obesity and lymphopenia, which was not restored after five days of treatment, were factors associated with poor outcomes of 2009 H1N1 influenza infection.


id: cord-300116-r93w4jm3
title: Profiling bacterial community in upper respiratory tracts
author: Yi, Hana
date: 2014-11-13
url: https://doi.org/10.1186/s12879-014-0583-3
doi: 10.1186/s12879-014-0583-3
abstract:
  BACKGROUND: Infection by pathogenic viruses results in rapid epithelial damage and significantly impacts on the condition of the upper respiratory tract, thus the effects of viral infection may induce changes in microbiota. Thus, we aimed to define the healthy microbiota and the viral pathogen-affected microbiota in the upper respiratory tract. In addition, any association between the type of viral agent and the resultant microbiota profile was assessed. METHODS: We analyzed the upper respiratory tract bacterial content of 57 healthy asymptomatic people (17 health-care workers and 40 community people) and 59 patients acutely infected with influenza, parainfluenza, rhino, respiratory syncytial, corona, adeno, or metapneumo viruses using culture-independent pyrosequencing. RESULTS: The healthy subjects harbored primarily Streptococcus, whereas the patients showed an enrichment of Haemophilus or Moraxella. Quantifying the similarities between bacterial populations by using Fast UniFrac analysis indicated that bacterial profiles were apparently divisible into 6 oropharyngeal types in the tested subjects. The oropharyngeal types were not associated with the type of viruses, but were rather linked to the age of the subjects. Moraxella nonliquefaciens exhibited unprecedentedly high abundance in young subjects aged <6 years. The genome of M. nonliquefaciens was found to encode various proteins that may play roles in pathogenesis. CONCLUSIONS: This study identified 6 oropharyngeal microbiome types. No virus-specific bacterial profile was discovered, but comparative analysis of healthy adults and patients identified a bacterium specific to young patients, M. nonliquefaciens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-014-0583-3) contains supplementary material, which is available to authorized users.


id: cord-300230-a3jk6w90
author: Ding, Ji-Guang
date: 2009-07-25
txt: ./txt/cord-300230-a3jk6w90.txt
cache: ./cache/cord-300230-a3jk6w90.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/19630992/
doi: 10.1186/1471-2334-9-115
summary:
  RESULTS: Among 1980 patients admitted over the period of time, the overall patient nosocomial infection rate was 26.8% or 51.0 per 1000 patient days., Lower respiratory tract infections (LRTI) accounted for most of the infections (68.4%), followed by urinary tract infections (UTI, 15.9%), bloodstream (BSI, 5.9%), and gastrointestinal tract (GI, 2.5%) infections. In conclusion, there was a high and relatively stable rate of nosocomial infections in the ICU of a tertiary hospital in China through year 2003-2007, with some differences in the distribution of the infection sites, and pathogen and antibiotic susceptibility profiles from those reported in the Western countries. In conclusion, there was a high and relatively stable rate of nosocomial infections in the ICU of a tertiary hospital in China through year 2003-2007, with some differences in the distribution of the infection sites, and pathogen and antibiotic susceptibility profiles from those reported in the Western countries.

title:
  Retrospective analysis of nosocomial infections in the intensive care unit of a tertiary hospital in China during 2003 and 2007

abstract:
  BACKGROUND: Nosocomial infections are a major threat to patients in the intensive care unit (ICU). Limited data exist on the epidemiology of ICU-acquired infections in China. This retrospective study was carried out to determine the current status of nosocomial infection in China. METHODS: A retrospective review of nococomial infections in the ICU of a tertiary hospital in East China between 2003 and 2007 was performed. Nosocomial infections were defined according to the definitions of Centers for Disease Control and Prevention. The overall patient nosocomial infection rate, the incidence density rate of nosocomial infections, the excess length of stay, and distribution of nosocomial infection sites were determined. Then, pathogen and antimicrobial susceptibility profiles were further investigated. RESULTS: Among 1980 patients admitted over the period of time, the overall patient nosocomial infection rate was 26.8% or 51.0 per 1000 patient days., Lower respiratory tract infections (LRTI) accounted for most of the infections (68.4%), followed by urinary tract infections (UTI, 15.9%), bloodstream (BSI, 5.9%), and gastrointestinal tract (GI, 2.5%) infections. There was no significant change in LRTI, UTI and BSI infection rates during the 5 years. However, GI rate was significantly decreased from 5.5% in 2003 to 0.4% in 2007. In addition, A. baumannii, C. albicans and S. epidermidis were the most frequent pathogens isolated in patients with LRTIs, UTIs and BSIs, respectively. The rates of isolates resistant to commonly used antibiotics ranged from 24.0% to 93.1%. CONCLUSION: There was a high and relatively stable rate of nosocomial infections in the ICU of a tertiary hospital in China through year 2003–2007, with some differences in the distribution of the infection sites, and pathogen and antibiotic susceptibility profiles from those reported from the Western countries. Guidelines for surveillance and prevention of nosocomial infections must be implemented in order to reduce the rate.


id: cord-301393-d1duepnb
author: Wolfensberger, Aline
date: 2020-08-17
txt: ./txt/cord-301393-d1duepnb.txt
cache: ./cache/cord-301393-d1duepnb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32807090/
doi: 10.1186/s12879-020-05271-5
summary:
  title: Implementation and evaluation of a care bundle for prevention of non-ventilator-associated hospital-acquired pneumonia (nvHAP) – a mixed-methods study protocol for a hybrid type 2 effectiveness-implementation trial A longitudinal, qualitative study and formative evaluation based on interviews, focus groups, and observations identifies supporting or hindering factors for implementation success in participating departments dynamically over time. DISCUSSION: This comprehensive hybrid mixed-methods study is designed to both, measure the effectiveness of a new nvHAP prevention bundle and multifaceted implementation strategy, while also providing insights into how and why it worked or failed. This comprehensive type 2 hybrid effectivenessimplementation study aims to assess the effectiveness and success factors of both, a new prevention bundle against nvHAP and a specifically designed departmentbased multifaceted implementation strategy in a medical and surgical patient population.

title:
  Implementation and evaluation of a care bundle for prevention of non-ventilator-associated hospital-acquired pneumonia (nvHAP) – a mixed-methods study protocol for a hybrid type 2 effectiveness-implementation trial

abstract:
  BACKGROUND: Hospital acquired pneumonia (HAP) is divided in two distinct groups, ventilator-associated pneumonia (VAP) and non-ventilator-associated HAP (nvHAP). Although nvHAP occurs more frequently than VAP and results in similar mortality and costs, prevention guidelines and prevention focus almost exclusively on VAP. Scientific evidence about nvHAP prevention and its implementation is scarce. Therefore, we designed a mixed-methods hybrid type 2 effectiveness-implementation study to investigate both the effectiveness and implementation of a newly developed nvHAP prevention bundle. METHODS: This single-centre project at the 950-bed University Hospital Zurich (UHZ) will engage the wards of nine departments with substantial nvHAP rates. The nvHAP bundle consists of five primary prevention measures: 1) oral care, 2) prevention of dysphagia-related aspiration, 3) mobilization, 4) stopping unnecessary proton pump inhibitors, and, 5) respiratory therapy. Implementation includes the engagement of department-level implementation teams, who sustain the ‘core’ intervention components of education, training, and environmental restructuring and tailor the implementation strategy to local needs. Both effectiveness and implementation outcomes will be assessed using mixed-methods. As a primary outcome, nvHAP incidence rates will be analysed by Poisson regression models to compare incidence rates before, during, and after the implementation phases (on the hospital and department level). Additionally, the association between process indicators and nvHAP incidence rates will be analysed using longitudinal Poisson regression models. A longitudinal, qualitative study and formative evaluation based on interviews, focus groups, and observations identifies supporting or hindering factors for implementation success in participating departments dynamically over time. This accumulating implementation experience will be constantly fed back to the implementation teams and thus, represents an active implementation element. DISCUSSION: This comprehensive hybrid mixed-methods study is designed to both, measure the effectiveness of a new nvHAP prevention bundle and multifaceted implementation strategy, while also providing insights into how and why it worked or failed. The results of this study may contribute substantially to advancing knowledge and patient safety in the area of a rediscovered healthcare-associated infection - nvHAP. TRIAL REGISTRATION: ClinicalTrials.gov: NCT03361085. Registered December 2017.


id: cord-302393-hrz3bypr
author: Omrani, Ali S.
date: 2020-10-19
txt: ./txt/cord-302393-hrz3bypr.txt
cache: ./cache/cord-302393-hrz3bypr.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-020-05511-8
doi: 10.1186/s12879-020-05511-8
summary:
  Multivariable logistic regression showed that older age [adjusted odds ratio (aOR) 1.041, 95% confidence interval (CI) 1.022–1.061 per year increase; P < 0.001], male sex (aOR 4.375, 95% CI 1.964–9.744; P < 0.001), diabetes (aOR 1.698, 95% CI 1.050–2.746; P 0.031), chronic kidney disease (aOR 3.590, 95% CI 1.596–8.079, P 0.002), and higher BMI (aOR 1.067, 95% CI 1.027–1.108 per unit increase; P 0.001), were all independently associated with increased risk of ICU admission. In this study, we describe 60-day outcomes of a nationwide COVID-19 cohort from Qatar, and explore patient characteristics associated with the need for admission to an intensive care unit (ICU). In the multivariable logistic regression, we found that older age, male sex, co-existing diabetes or chronic kidney disease, and higher BMI were all independently associated with increased risk of need for ICU admission ( Table 2) .

title:
  The first consecutive 5000 patients with Coronavirus Disease 2019 from Qatar; a nation-wide cohort study

abstract:
  BACKGROUND: There are limited data on Coronavirus Disease 2019 (COVID-19) outcomes at a national level, and none after 60 days of follow up. The aim of this study was to describe national, 60-day all-cause mortality associated with COVID-19, and to identify risk factors associated with admission to an intensive care unit (ICU). METHODS: This was a retrospective cohort study including the first consecutive 5000 patients with COVID-19 in Qatar who completed 60 days of follow up by June 17, 2020. The primary outcome was all-cause mortality at 60 days after COVID-19 diagnosis. In addition, we explored risk factors for admission to ICU. RESULTS: Included patients were diagnosed with COVID-19 between February 28 and April 17, 2020. The majority (4436, 88.7%) were males and the median age was 35 years [interquartile range (IQR) 28–43]. By 60 days after COVID-19 diagnosis, 14 patients (0.28%) had died, 10 (0.2%) were still in hospital, and two (0.04%) were still in ICU. Fatal COVID-19 cases had a median age of 59.5 years (IQR 55.8–68), and were mostly males (13, 92.9%). All included pregnant women (26, 0.5%), children (131, 2.6%), and healthcare workers (135, 2.7%) were alive and not hospitalized at the end of follow up. A total of 1424 patients (28.5%) required hospitalization, out of which 108 (7.6%) were admitted to ICU. Most frequent co-morbidities in hospitalized adults were diabetes (23.2%), and hypertension (20.7%). Multivariable logistic regression showed that older age [adjusted odds ratio (aOR) 1.041, 95% confidence interval (CI) 1.022–1.061 per year increase; P < 0.001], male sex (aOR 4.375, 95% CI 1.964–9.744; P < 0.001), diabetes (aOR 1.698, 95% CI 1.050–2.746; P 0.031), chronic kidney disease (aOR 3.590, 95% CI 1.596–8.079, P 0.002), and higher BMI (aOR 1.067, 95% CI 1.027–1.108 per unit increase; P 0.001), were all independently associated with increased risk of ICU admission. CONCLUSIONS: In a relatively younger national cohort with a low co-morbidity burden, COVID-19 was associated with low all-cause mortality. Independent risk factors for ICU admission included older age, male sex, higher BMI, and co-existing diabetes or chronic kidney disease. SUPPLEMENTARY INFORMATION: Supplementary information accompanies this paper at 10.1186/s12879-020-05511-8.


id: cord-302833-6kntd89t
author: Radonovich, Lewis J.
date: 2016-06-02
url: https://www.ncbi.nlm.nih.gov/pubmed/27255755/
doi: 10.1186/s12879-016-1494-2
title:
  The Respiratory Protection Effectiveness Clinical Trial (ResPECT): a cluster-randomized comparison of respirator and medical mask effectiveness against respiratory infections in healthcare personnel

abstract:
  BACKGROUND: Although N95 filtering facepiece respirators and medical masks are commonly used for protection against respiratory infections in healthcare settings, more clinical evidence is needed to understand the optimal settings and exposure circumstances for healthcare personnel to use these devices. A lack of clinically germane research has led to equivocal, and occasionally conflicting, healthcare respiratory protection recommendations from public health organizations, professional societies, and experts. METHODS: The Respiratory Protection Effectiveness Clinical Trial (ResPECT) is a prospective comparison of respiratory protective equipment to be conducted at multiple U.S. study sites. Healthcare personnel who work in outpatient settings will be cluster-randomized to wear N95 respirators or medical masks for protection against infections during respiratory virus season. Outcome measures will include laboratory-confirmed viral respiratory infections, acute respiratory illness, and influenza-like illness. Participant exposures to patients, coworkers, and others with symptoms and signs of respiratory infection, both within and beyond the workplace, will be recorded in daily diaries. Adherence to study protocols will be monitored by the study team. DISCUSSION: ResPECT is designed to better understand the extent to which N95s and MMs reduce clinical illness among healthcare personnel. A fully successful study would produce clinically relevant results that help clinician-leaders make reasoned decisions about protection of healthcare personnel against occupationally acquired respiratory infections and prevention of spread within healthcare systems. TRIAL REGISTRATION: The trial is registered at clinicaltrials.gov, number NCT01249625 (11/29/2010).


id: cord-303196-ltmu3ncu
author: Pfitscher, L. C.
date: 2016-05-21
txt: ./txt/cord-303196-ltmu3ncu.txt
cache: ./cache/cord-303196-ltmu3ncu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27207244/
doi: 10.1186/s12879-016-1525-z
summary:
  title: Severe maternal morbidity due to respiratory disease and impact of 2009 H1N1 influenza A pandemic in Brazil: results from a national multicenter cross-sectional study BACKGROUND: The aim of this study was to assess the burden of respiratory disease, considering the influenza A pandemic season (H1N1pdm09), within the Brazilian Network for Surveillance of Severe Maternal Morbidity, and factors associated with worse maternal outcome. In each group, PLTC (less severe cases) and Severe Maternal Outcome (SMO: MNM + MD) cases were compared to evaluate the factors potentially associated with more severe disease, including delay in obstetric care, also using the Prevalence Ratios plus their respective 95 % CI adjusted for the design effect of cluster sampling. Our study presents the burden of severe respiratory diseases among cases of severe maternal morbidity and results of the 2009 H1N1 influenza pandemic, considering 27 referral maternity hospitals in Brazil.

title:
  Severe maternal morbidity due to respiratory disease and impact of 2009 H1N1 influenza A pandemic in Brazil: results from a national multicenter cross-sectional study

abstract:
  BACKGROUND: The aim of this study was to assess the burden of respiratory disease, considering the influenza A pandemic season (H1N1pdm09), within the Brazilian Network for Surveillance of Severe Maternal Morbidity, and factors associated with worse maternal outcome. METHODS: A multicenter cross-sectional study, involving 27 referral maternity hospitals in five Brazilian regions. Cases were identified in a prospective surveillance by using the WHO standardized criteria for potentially life-threatening conditions (PLTC) and maternal near miss (MNM). Women with severe complications from respiratory disease identified as suspected or confirmed cases of H1N1 influenza or respiratory failure were compared to those with other causes of severe morbidity. A review of suspected H1N1 influenza cases classified women as non-tested, tested positive and tested negative, comparing their outcomes. Factors associated with severe maternal outcome (SMO = MNM + MD) were assessed in both groups, in comparison to PLTC, using PR and 95 % CI adjusted for design effect of cluster sampling. RESULTS: Among 9555 cases of severe maternal morbidity, 485 (5 %) had respiratory disease. Respiratory disease occurred in one-quarter of MNM cases and two-thirds of MD. H1N1 virus was suspected in 206 cases with respiratory illness. Around 60 % of these women were tested, yielding 49 confirmed cases. Confirmed H1N1 influenza cases had worse adverse outcomes (MNM:MD ratio < 1 (0.9:1), compared to 12:1 in cases due to other causes), and a mortality index > 50 %, in comparison to 7.4 % in other causes of severe maternal morbidity. Delay in medical care was associated with SMO in all cases considered, with a two-fold increased risk among respiratory disease patients. Perinatal outcome was worse in cases complicated by respiratory disease, with increased prematurity, stillbirth, low birth weight and Apgar score < 7. CONCLUSIONS: Respiratory disease, especially considering the influenza season, is a very severe cause of maternal near miss and death. Increased awareness about this condition, preventive vaccination during pregnancy, early diagnosis and treatment are required to improve maternal health.


id: cord-304718-w469n0o8
title: Lack of association between polymorphisms of MASP2 and susceptibility to SARS coronavirus infection
author: Wang, Yan
date: 2009-05-01
txt: ./txt/cord-304718-w469n0o8.txt
cache: ./cache/cord-304718-w469n0o8.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-9-51
doi: 10.1186/1471-2334-9-51
summary:
  One case-control study has reported an association between susceptibility to SARS and mannan-binding lectin (MBL) in China. As the downstream protein of MBL, variants of the MBL-associated serine protease-2 (MASP2) gene may be associated with SARS coronavirus (SARS-CoV) infection in the same population. RESULTS: There is no significant association between alleles or genotypes of the MASP2 tagSNP and susceptibility to SARS-CoV in both Beijing and Guangzhou populations. A few case-control studies have reported an association between SARS susceptibility and human leucocyte antigen (HLA) and MBL [8] [9] [10] [11] . With regard to SARS-CoV infection, the codon 54 variant of the MBL gene has been shown to be associated with infection susceptibility but not with disease severity [11] . As the downstream protein of MBL, variants of the MASP2 gene may be associated with SARS-CoV infection. Genomic DNA from 30 individuals with SARS was chosen for analysis of MASP2 gene polymorphisms.

abstract:
  BACKGROUND: The pathogenesis of severe acute respiratory disease syndrome (SARS) is not fully understood. One case-control study has reported an association between susceptibility to SARS and mannan-binding lectin (MBL) in China. As the downstream protein of MBL, variants of the MBL-associated serine protease-2 (MASP2) gene may be associated with SARS coronavirus (SARS-CoV) infection in the same population. METHODS: Thirty individuals with SARS were chosen for analysis of MASP2 polymorphisms by means of PCR direct sequencing. Tag single nucleotide polymorphisms (tagSNPs) were chosen using pairwise tagging algorithms. The frequencies of four tag SNPs (rs12711521, rs2261695, rs2273346 and rs7548659) were ascertained in 376 SARS patients and 523 control subjects, using the Beckman SNPstream Ultra High Throughput genotyping platform. RESULTS: There is no significant association between alleles or genotypes of the MASP2 tagSNP and susceptibility to SARS-CoV in both Beijing and Guangzhou populations. Diplotype (rs2273346 and rs12711521)were analyzed for association with susceptibility to SARS, no statistically significant evidence of association was observed. The Beijing and Guangzhou sample groups were homogeneous regarding demographic and genetic parameters, a joined analysis also showed no statistically significant evidence of association. CONCLUSION: Our data do not suggest a role for MASP2 polymorphisms in SARS susceptibility in northern and southern China.


id: cord-306175-p5rtp31m
title: Frequent detection of bocavirus DNA in German children with respiratory tract infections
author: Weissbrich, Benedikt
date: 2006-07-11
txt: ./txt/cord-306175-p5rtp31m.txt
cache: ./cache/cord-306175-p5rtp31m.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16834781/
doi: 10.1186/1471-2334-6-109
summary:
  METHODS: We tested 835 nasopharyngeal aspirates (NPA) obtained between 2002 and 2005 from pediatric in-patients with acute respiratory tract diseases at the University of Würzburg, Germany, for the presence of hBoV DNA. The samples tested for hBoV infection consisted of stored nasopharyngeal aspirates (NPA) that were sent by the University of Würzburg Children''s hospital for screening of respiratory viruses from January 2002 to September 2005. In 34 (39.1 %) of the hBoV positive infants and children, coinfections with other respiratory viruses were present, most frequently with RSV (n = 14) followed by influenza A (n = 9). Clinical data were available for 63 of the 87 hBoV positive NPAs. The patients suffered from upper and/or lower respiratory tract diseases (Table 4) . We found hBoV DNA in 10.3 % of NPA samples obtained from infants and children with respiratory tract diseases during the years 2002 to 2005 in the region of northern Bavaria in Germany.

abstract:
  BACKGROUND: In a substantial proportion of respiratory tract diseases of suspected infectious origin, the etiology is unknown. Some of these cases may be caused by the recently described human bocavirus (hBoV). The aim of this study was to investigate the frequency and the potential clinical relevance of hBoV in pediatric patients. METHODS: We tested 835 nasopharyngeal aspirates (NPA) obtained between 2002 and 2005 from pediatric in-patients with acute respiratory tract diseases at the University of Würzburg, Germany, for the presence of hBoV DNA. The specificity of positive PCR reactions was confirmed by sequencing. RESULTS: HBoV DNA was found in 87 (10.3 %) of the NPAs. The median age of the infants and children with hBoV infection was 1.8 years (mean age 2.0 years; range 18 days – 8 years). Infections with hBoV were found year-round, though most occurred in the winter months. Coinfections were found in 34 (39.1 %) of the hBoV positive samples. RSV, influenza A, and adenoviruses were most frequently detected as coinfecting agents. Sequence determination of the PCR products in the NP-1 region revealed high identity (99 %) between the nucleotide sequences obtained in different years and in comparison to the Swedish viruses ST1 and ST2. An association of hBoV with a distinct respiratory tract manifestation was not apparent. CONCLUSION: HBoV is frequently found in NPAs of hospitalized infants and children with acute respiratory tract diseases. Proving the clinical relevance of hBoV is challenging, because application of some of Koch's revised postulates is not possible. Because of the high rate of coinfections with hBoV and other respiratory tract pathogens, an association between hBoV and respiratory tract diseases remains unproven.


id: cord-307307-b5yl88mh
author: Lau, Joseph TF
date: 2010-05-28
txt: ./txt/cord-307307-b5yl88mh.txt
cache: ./cache/cord-307307-b5yl88mh.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-10-139
doi: 10.1186/1471-2334-10-139
summary:
  This study investigated whether the general population in Hong Kong avoided visiting different places (going out, visiting crowded places and visiting hospitals) and assessed some negative psychological responses to H1N1, including whether people were much worried about contracting H1N1 and their level of emotional distress (panicking, depression or emotional disturbance) due to H1N1. Factors in association with the outcome variables on avoidance behaviors and negative psychological responses were investigated, including variables such as socio-demographic characteristics, confirmed knowledge and unconfirmed beliefs about modes of H1N1 transmission, evaluation towards governmental preparedness/ performance, perceived availability of treatment, and risk perception (perceived severity and susceptibility related to H1N1). Females, older respondents, those with >= 1 unconfirmed beliefs about modes of H1N1 transmission, those who knew that H1N1 could be transmitted ''via droplets'', ''bodily contact with infected person'' or ''touching contaminated objects'', those who were very worried that either they or their family members would contract H1N1, those expressing emotional distress (in panic or feeling very depressed or being highly emotionally disturbed due to H1N1) were more likely than others to avoid visiting crowded places (multivariate OR = 1.42 to 3.90, p < .05; Table 4 ).

title:
  Avoidance behaviors and negative psychological responses in the general population in the initial stage of the H1N1 pandemic in Hong Kong

abstract:
  BACKGROUND: During the SARS pandemic in Hong Kong, panic and worry were prevalent in the community and the general public avoided staying in public areas. Such avoidance behaviors could greatly impact daily routines of the community and the local economy. This study examined the prevalence of the avoidance behaviors (i.e. avoiding going out, visiting crowded places and visiting hospitals) and negative psychological responses of the general population in Hong Kong at the initial stage of the H1N1 epidemic. METHODS: A sample of 999 respondents was recruited in a population-based survey. Using random telephone numbers, respondents completed a structured questionnaire by telephone interviews at the 'pre-community spread phase' of the H1N1 epidemic in Hong Kong. RESULTS: This study found that 76.5% of the respondents currently avoided going out or visiting crowded places or hospitals, whilst 15% felt much worried about contracting H1N1 and 6% showed signs of emotional distress. Females, older respondents, those having unconfirmed beliefs about modes of transmissions, and those feeling worried and emotionally distressed due to H1N1 outbreak were more likely than others to adopt some avoidance behaviors. Those who perceived high severity and susceptibility of getting H1N1 and doubted the adequacy of governmental preparedness were more likely than others to feel emotionally distressed. CONCLUSIONS: The prevalence of avoidance behaviors was very high. Cognitions, including unconfirmed beliefs about modes of transmission, perceived severity and susceptibility were associated with some of the avoidance behaviors and emotional distress variables. Public health education should therefore provide clear messages to rectify relevant perceptions.


id: cord-308655-zntwwqod
author: Dabisch-Ruthe, Mareike
date: 2012-07-24
txt: ./txt/cord-308655-zntwwqod.txt
cache: ./cache/cord-308655-zntwwqod.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/22828244/
doi: 10.1186/1471-2334-12-163
summary:
  title: Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay METHODS: The analytical sensitivity of three multiplex PCR assays, RespiFinder-19, RespiFinder-SMART-22 and xTAG-Respiratory-Virus-Panel-Fast-Assay (RVP), were compared to monoplex real-time PCR with quantified standardized control material. RESULTS: To compare the analytical sensitivity of the multiplex assays, samples were inoculated with 13 different quantified viruses in the range of 10(1) to 10(5) copies/ml. This study presents the first comparison of the analytical sensitivity of three novel multiplex PCR methods, the RespiFinder-19 assay, RespiFinder-SMART(Single tube Multiplex Amplification in Real-Time)-22 assay (both PathoFinder, Maastricht, Netherlands) and the xTAG Respiratory Virus Panel Fast Assay (Abbott Molecular, Wiesbaden, Germany), with quantified virus control material. Previous studies with clinical samples showed that the sensitivity and specificity of the RVP assay was 78.8% and 99.6%, respectively, compared to real-time PCR-methods, that are currently declared as the gold standard [21] .

title:
  Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay

abstract:
  BACKGROUND: A broad spectrum of pathogens is causative for respiratory tract infections, but symptoms are mostly similar. Therefore, the identification of the causative viruses and bacteria is only feasible using multiplex PCR or several monoplex PCR tests in parallel. METHODS: The analytical sensitivity of three multiplex PCR assays, RespiFinder-19, RespiFinder-SMART-22 and xTAG-Respiratory-Virus-Panel-Fast-Assay (RVP), were compared to monoplex real-time PCR with quantified standardized control material. All assays include the most common respiratory pathogens. RESULTS: To compare the analytical sensitivity of the multiplex assays, samples were inoculated with 13 different quantified viruses in the range of 10(1) to 10(5) copies/ml. Concordant results were received for rhinovirus, whereas the RVP detected influenzavirus, RSV and hMPV more frequently in low concentrations. The RespiFinder-19 and the RespiFinder-SMART-22 showed a higher analytical sensitivity for adenoviruses and coronaviruses, whereas the RVP was incapable to detect adenovirus and coronavirus in concentrations of 10(4) copies/ml. The RespiFinder-19 and RespiFinder-SMART-22A did not detect influenzaviruses (10(4) copies/ml) and RSV (10(3) copies/ml). The detection of all 13 viruses in one sample was only achieved using monoplex PCR. To analyze possible competitive amplification reactions between the different viruses, samples were further inoculated with only 4 different viruses in one sample. Compared to the detection of 13 viruses in parallel, only a few differences were found. The incidence of respiratory viruses was compared in tracheal secretion (TS) samples (n = 100) of mechanically ventilated patients in winter (n = 50) and summer (n = 50). In winter, respiratory viruses were detected in 32 TS samples (64%) by RespiFinder-19, whereas the detection rate with RVP was only 22%. The most frequent viruses were adenovirus (32%) and PIV-2 (20%). Multiple infections were detected in 16 TS samples (32%) by RespiFinder-19. Fewer infections were found in summer (RespiFinder-19: 20%; RVP: 6%). All positive results were verified using monoplex PCR. CONCLUSIONS: Multiplex PCR tests have a broad spectrum of pathogens to test at a time. Analysis of multiple inoculated samples revealed a different focus of the detected virus types by the three assays. Analysis of clinical samples showed a high concordance of detected viruses by the RespiFinder-19 compared to monoplex tests.


id: cord-311382-ioemd0ij
title: Recognition of aerosol transmission of infectious agents: a commentary
author: Tellier, Raymond
date: 2019-01-31
txt: ./txt/cord-311382-ioemd0ij.txt
cache: ./cache/cord-311382-ioemd0ij.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-019-3707-y
doi: 10.1186/s12879-019-3707-y
summary:
  For example, when the infectious dose (the number of infectious agents required to cause disease) of an organism is low, and where large numbers of pathogen-laden droplets are produced in crowded conditions with poor ventilation (in hospital waiting rooms, in lecture theatres, on public transport, etc.), explosive outbreaks can still occur, even with pathogens whose airborne transmission capacity is controversial, e.g. the spread of influenza in a grounded plane where multiple secondary cases were observed in the absence of any ventilation [11] . For example, tighter control of the environment may reduce or prevent airborne transmission by: 1) isolating infectious patients in a single-bed, negative pressure isolation room [25] ; 2) controlling environmental relative humidity to reduce airborne influenza survival [59] ; 3) reducing exposure from aerosols produced by patients through coughing, sneezing or breathing with the use of personal protective equipment (wearing a mask) on the patient (to reduce source emission) and/or the healthcare worker (to reduce recipient exposure) [60] ; 4) carefully controlling the use and exposure to any respiratory assist devices (high-flow oxygen masks, nebulizers) by only allowing their use in designated, containment areas or rooms [61] .

abstract:
  Although short-range large-droplet transmission is possible for most respiratory infectious agents, deciding on whether the same agent is also airborne has a potentially huge impact on the types (and costs) of infection control interventions that are required. The concept and definition of aerosols is also discussed, as is the concept of large droplet transmission, and airborne transmission which is meant by most authors to be synonymous with aerosol transmission, although some use the term to mean either large droplet or aerosol transmission. However, these terms are often used confusingly when discussing specific infection control interventions for individual pathogens that are accepted to be mostly transmitted by the airborne (aerosol) route (e.g. tuberculosis, measles and chickenpox). It is therefore important to clarify such terminology, where a particular intervention, like the type of personal protective equipment (PPE) to be used, is deemed adequate to intervene for this potential mode of transmission, i.e. at an N95 rather than surgical mask level requirement. With this in mind, this review considers the commonly used term of ‘aerosol transmission’ in the context of some infectious agents that are well-recognized to be transmissible via the airborne route. It also discusses other agents, like influenza virus, where the potential for airborne transmission is much more dependent on various host, viral and environmental factors, and where its potential for aerosol transmission may be underestimated.


id: cord-312222-aw5849rc
author: Österdahl, Marc F.
date: 2020-10-20
txt: ./txt/cord-312222-aw5849rc.txt
cache: ./cache/cord-312222-aw5849rc.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-020-05484-8
doi: 10.1186/s12879-020-05484-8
summary:
  METHODS: This prospective service improvement project piloted an RT-LAMP method on nasal and pharyngeal swabs on 21 residents of a high dependency care home, with two index COVID-19 cases, and compared it to multiplex tandem reverse transcription polymerase chain reaction (RT-PCR). We recorded vital signs of patients to correlate clinical and laboratory information and calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of a single swab using RT-LAMP compared with the current standard, RT-PCR, as per Standards for Reporting Diagnostic Accuracy Studies (STARD) guidelines. Since then, a number [13] of other groups have published high-quality studies demonstrating that RT-LAMP has the potential to replace RT-PCR as a means for detecting SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) within RNA extracted from nose -throat swabs and endotracheal secretions/bronchoalveolar lavage fluid [5, 14, 15] .

title:
  Detecting SARS-CoV-2 at point of care: preliminary data comparing loop-mediated isothermal amplification (LAMP) to polymerase chain reaction (PCR)

abstract:
  BACKGROUND: A cost effective and efficient diagnostic tool for COVID-19 as near to the point of care (PoC) as possible would be a game changer in the current pandemic. We tested reverse transcription loop mediated isothermal amplification (RT-LAMP), a method which can produce results in under 30 min, alongside standard methods in a real-life clinical setting. METHODS: This prospective service improvement project piloted an RT-LAMP method on nasal and pharyngeal swabs on 21 residents of a high dependency care home, with two index COVID-19 cases, and compared it to multiplex tandem reverse transcription polymerase chain reaction (RT-PCR). We recorded vital signs of patients to correlate clinical and laboratory information and calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of a single swab using RT-LAMP compared with the current standard, RT-PCR, as per Standards for Reporting Diagnostic Accuracy Studies (STARD) guidelines. RESULTS: The novel method accurately detected 8/10 RT-PCR positive cases and identified a further 3 positive cases. Eight further cases were negative using both methods. Using repeated RT-PCR as a “gold standard”, the sensitivity and specificity of a single novel test were 80 and 73% respectively. PPV was 73% and NPV was 83%. Incorporating retesting of low signal RT-LAMP positives improved the specificity to 100%. We also speculate that hypothermia may be a significant early clinical sign of COVID-19. CONCLUSIONS: RT-LAMP testing for SARS-CoV-2 was found to be promising, fast and to work equivalently to RT-PCR methods. RT-LAMP has the potential to transform COVID-19 detection, bringing rapid and accurate testing to the PoC. RT-LAMP could be deployed in mobile community testing units, care homes and hospitals to detect disease early and prevent spread.


