# bib

id: cord-312522-mymgnf8z
title: Rapid molecular detection of macrolide resistance
author: Nelson, Megan M.
date: 2019-02-12
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url: https://doi.org/10.1186/s12879-019-3762-4
doi: 10.1186/s12879-019-3762-4
summary:
  METHODS: We use Recombinase Polymerase Assay (RPA) to detect the antimicrobial resistance gene mef(A) from raw lysates without nucleic acid purification. We show that detection of mef(A) accurately predicts real antimicrobial resistance assessed by traditional culture methods, and that the assay is robust to high levels of spiked-in non-specific nucleic acid contaminant. In this study, we developed and tested a novel RPA assay for the detection of the Macrolide Efflux A, or mef(A) gene, an efflux pump rendering host bacteria resistant to 14-and 15-membered macrolide antibiotics (including erythromycin A and azithromycin) [33, 34] . Our RPA assay uncovered an unexpected occurrence of the mef(A) gene within commensal Streptococcus salivarius strain, and subsequent laboratory testing confirmed that this strain has genuine antimicrobial resistance. To assess assay sensitivity we ran a serial dilution of DNA derived from mef(A)-positive Streptococcus pyogenes serotype M6 strain MGAS10394 [39] and found that confident detection was around 2000 genome copies (Fig. 1b) .

abstract:
  BACKGROUND: Emerging antimicrobial resistance is a significant threat to human health. However, methods for rapidly diagnosing antimicrobial resistance generally require multi-day culture-based assays. Macrolide efflux gene A, mef(A), provides resistance against erythromycin and azithromycin and is known to be laterally transferred among a wide range of bacterial species. METHODS: We use Recombinase Polymerase Assay (RPA) to detect the antimicrobial resistance gene mef(A) from raw lysates without nucleic acid purification. To validate these results we performed broth dilution assays to assess antimicrobial resistance to erythromycin and ampicillin (a negative control). RESULTS: We validate the detection of mef(A) in raw lysates of Streptococcus pyogenes, S. pneumoniae, S. salivarius, and Enterococcus faecium bacterial lysates within 7–10 min of assay time. We show that detection of mef(A) accurately predicts real antimicrobial resistance assessed by traditional culture methods, and that the assay is robust to high levels of spiked-in non-specific nucleic acid contaminant. The assay was unaffected by single-nucleotide polymorphisms within divergent mef(A) gene sequences, strengthening its utility as a robust diagnostic tool. CONCLUSIONS: This finding opens the door to implementation of rapid genomic diagnostics in a clinical setting, while providing researchers a rapid, cost-effective tool to track antibiotic resistance in both pathogens and commensal strains.


id: cord-312544-vip4jtlv
title: Specific detection of H5N1 avian influenza A virus in field specimens by a one-step RT-PCR assay
author: Ng, Lisa FP
date: 2006-03-02
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url: https://www.ncbi.nlm.nih.gov/pubmed/16512903/
doi: 10.1186/1471-2334-6-40
summary:
  METHODS: A one-step reverse-transcription PCR assay was developed to detect the H5N1 avian influenza A virus. RESULTS: Validation on 145 field specimens from Vietnam and Malaysia showed that the assay was specific without cross reactivity to a number of other infuenza strains as well as human respiratory related pathogens. In this study, we describe the development of a nucleic acid detection test that is rapid, specific and sensitive, thus allowing greatly improved detection of the H5N1 avian influenza A virus. To establish the specificity of the assays for H5N1 subtype detection, we then tested the primers on several known strains of influenza A viruses derived from avian sources (H3N8, H5N3, H7N3 and H9N2). A total of 145 field samples comprising of known and suspect cases from chickens, ducks and muscovies isolated from Vietnam and Malaysia during the 2004 to 2005 outbreak were tested for H5N1 RNA (Table Detection of H5N1 avian influenza A virus by one-step RT-PCR 2).

abstract:
  BACKGROUND: Continuous outbreaks of the highly pathogenic H5N1 avian influenza A in Asia has resulted in an urgent effort to improve current diagnostics to aid containment of the virus and lower the threat of a influenza pandemic. We report here the development of a PCR-based assay that is highly specific for the H5N1 avian influenza A virus. METHODS: A one-step reverse-transcription PCR assay was developed to detect the H5N1 avian influenza A virus. The specificity of the assay was shown by testing sub-types of influenza A virus and other viral and bacterial pathogens; and on field samples. RESULTS: Validation on 145 field specimens from Vietnam and Malaysia showed that the assay was specific without cross reactivity to a number of other infuenza strains as well as human respiratory related pathogens. Detection was 100% from allantoic fluid in H5N1 positive samples, suggesting it to be a reliable sampling source for accurate detection. CONCLUSION: The assay developed from this study indicates that the primers are specific for the H5N1 influenza virus. As shown by the field tested results, this assay would be highly useful as a diagnostic tool to help identify and control influenza epidemics.


id: cord-313054-w90eitw9
author: Mobaraki, Kazhal
date: 2019-04-27
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url: https://www.ncbi.nlm.nih.gov/pubmed/31029095/
doi: 10.1186/s12879-019-3987-2
summary:
  RESULTS: A total of 229 MERS-CoV cases, including 70 deaths (30.5%), were recorded in the disease outbreak news on world health organization website over the study period. Middle East respiratory syndrome coronavirus (MERS-CoV) infection is considered to cause a new viral epidemic [1] , and was first reported in a patient who died from a severe respiratory illness in a hospital in Jeddah, Saudi Arabia, in June 2012 [2, 3] . The occurrence of a large number of MERS-CoV cases and their associated deaths in the world indicate that this disease must be considered as a severe threat to public health [13] because millions of pilgrims from 184 countries converge in Saudi Arabia each year to perform Hajj and Umrah ceremony. Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study

title:
  Current epidemiological status of Middle East respiratory syndrome coronavirus in the world from 1.1.2017 to 17.1.2018: a cross-sectional study

abstract:
  BACKGROUND: Middle East respiratory syndrome coronavirus (MERS-CoV) is considered to be responsible for a new viral epidemic and an emergent threat to global health security. This study describes the current epidemiological status of MERS-CoV in the world. METHODS: Epidemiological analysis was performed on data derived from all MERS-CoV cases recorded in the disease outbreak news on WHO website between 1.1.2017 and 17.1.2018. Demographic and clinical information as well as potential contacts and probable risk factors for mortality were extracted based on laboratory-confirmed MERS-CoV cases. RESULTS: A total of 229 MERS-CoV cases, including 70 deaths (30.5%), were recorded in the disease outbreak news on world health organization website over the study period. Based on available details in this study, the case fatality rate in both genders was 30.5% (70/229) [32.1% (55/171) for males and 25.8% (15/58) for females]. The disease occurrence was higher among men [171 cases (74.7%)] than women [58 cases (25.3%)]. Variables such as comorbidities and exposure to MERS-CoV cases were significantly associated with mortality in people affected with MERS-CoV infections, and adjusted odds ratio estimates were 2.2 (95% CI: 1.16, 7.03) and 2.3 (95% CI: 1.35, 8.20), respectively. All age groups had an equal chance of mortality. CONCLUSIONS: In today’s “global village”, there is probability of MERS-CoV epidemic at any time and in any place without prior notice. Thus, health systems in all countries should implement better triage systems for potentially imported cases of MERS-CoV to prevent large epidemics.


id: cord-313529-xm76ae08
author: Liu, Wen-Kuan
date: 2011-12-14
txt: ./txt/cord-313529-xm76ae08.txt
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url: https://doi.org/10.1186/1471-2334-11-345
doi: 10.1186/1471-2334-11-345
summary:
  title: Detection of human bocavirus from children and adults with acute respiratory tract illness in Guangzhou, southern China Our study is the first to analyze the characteristics of HBoV-positive samples from ARTI patients with a wide age distribution from Guangzhou, southern China. HBoV DNA positive samples were tested for 16 other potential pathogens, including 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 pneumoniae, and Chlamydia pneumoniae by Taqman real-time PCR, in accordance with the manufacturer''s protocol (Guangzhou HuYanSuo Medical Technology Co., Ltd). Our study successfully analyzed the characteristics of HBoV-positive samples from ARTI-infected patients with a wide age distribution from Guangzhou, southern China for the first reported time. Phylogenetic analysis suggested that HBoV-GU338055 from an elderly patient is in a single lineage with other HBoVs. Osterhaus ADME: A newly discovered human pneumovirus isolated from young children with respiratory tract disease

title:
  Detection of human bocavirus from children and adults with acute respiratory tract illness in Guangzhou, southern China

abstract:
  BACKGROUND: Human bocavirus (HBoV) is a newly discovered parvovirus associated with acute respiratory tract illness (ARTI) and gastrointestinal illness. Our study is the first to analyze the characteristics of HBoV-positive samples from ARTI patients with a wide age distribution from Guangzhou, southern China. METHODS: Throat swabs (n=2811) were collected and analyzed from children and adults with ARTI over a 13-month period. The HBoV complete genome from a 60 year-old female patient isolate was also determined. RESULTS: HBoV DNA was detected in 65/2811 (2.3%) samples, of which 61/1797 were from children (<18 years old) and 4/1014 from adults (≥18 years old). Seasonal peaks of 4.8% and 7.7% were detected in May and June, respectively. 28 of 65 (43.1%) HBoV-positive samples were co-detected with 11/16 other potential pathogens. Mycoplasma pneumoniae had the highest frequency of 16.9% (11/65). Upper and lower respiratory tract illness were common symptoms, with 19/65 (29.2%) patients diagnosed with pneumonia by chest radiography. All four adult patients had systemic influenza-like symptoms. Phylogenetic analysis of the complete genome revealed a close relationship with other HBoVs, and a more distant relationship with HBoV2 and HBoV3. CONCLUSIONS: HBoV was detected from children and adults with ARTI from Guangzhou, southern China. Elderly people were also susceptive to HBoV. A single lineage of HBoV was detected among a wide age distribution of patients with ARTI.


id: cord-314826-usfvulc2
title: Evaluation of bacterial co-infections of the respiratory tract in COVID-19 patients admitted to ICU
author: Sharifipour, Ehsan
date: 2020-09-01
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url: https://www.ncbi.nlm.nih.gov/pubmed/32873235/
doi: 10.1186/s12879-020-05374-z
summary:
  In total, all patients were found positive for bacterial infections, including seventeen Acinetobacter baumannii (90%) and two Staphylococcus aureus (10%) strains. Although COVID-19 associated deaths have mainly occurred in the elderly with serious underlying diseases [3] , nosocomial pneumonia (NP) in intensive care units remains a major risk factor for the patients and the health of patients, especially when intubated, may deteriorate in the presence of lower respiratory tract infections. Some studies have shown that viral agents such as influenza viruses can be associated with secondary bacterial pneumonia that might occur throughout hospitalization and lead to the death of individuals with or without preexisting respiratory diseases [8] . Therefore, our aim was to evaluate secondary bacterial infections and their antibiotic resistance in COVID-19 positive patients admitted to ICUs in Qom, the first city in Iran to report COVID-19 disease [14] . However, further work is required to investigate whether there are increased mortality rates associated with patients co-infected with COVID-19 and antibiotic-resistant bacteria.

abstract:
  BACKGROUND: COVID-19 is known as a new viral infection. Viral-bacterial co-infections are one of the biggest medical concerns, resulting in increased mortality rates. To date, few studies have investigated bacterial superinfections in COVID-19 patients. Hence, we designed the current study on COVID-19 patients admitted to ICUs. METHODS: Nineteen patients admitted to our ICUs were enrolled in this study. To detect COVID-19, reverse transcription real-time polymerase chain reaction was performed. Endotracheal aspirate samples were also collected and cultured on different media to support the growth of the bacteria. After incubation, formed colonies on the media were identified using Gram staining and other biochemical tests. Antimicrobial susceptibility testing was carried out based on the CLSI recommendations. RESULTS: Of nineteen COVID-19 patients, 11 (58%) patients were male and 8 (42%) were female, with a mean age of ~ 67 years old. The average ICU length of stay was ~ 15 days and at the end of the study, 18 cases (95%) expired and only was 1 case (5%) discharged. In total, all patients were found positive for bacterial infections, including seventeen Acinetobacter baumannii (90%) and two Staphylococcus aureus (10%) strains. There was no difference in the bacteria species detected in any of the sampling points. Seventeen of 17 strains of Acinetobacter baumannii were resistant to the evaluated antibiotics. No metallo-beta-lactamases -producing Acinetobacter baumannii strain was found. One of the Staphylococcus aureus isolates was detected as methicillin-resistant Staphylococcus aureus and isolated from the patient who died, while another Staphylococcus aureus strain was susceptible to tested drugs and identified as methicillin-sensitive Staphylococcus aureus. CONCLUSIONS: Our findings emphasize the concern of superinfection in COVID-19 patients due to Acinetobacter baumannii and Staphylococcus aureus. Consequently, it is important to pay attention to bacterial co-infections in critical patients positive for COVID-19.


id: cord-315866-6vcts4w3
author: Chan, KC Allen
date: 2005-04-09
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url: https://www.ncbi.nlm.nih.gov/pubmed/15819995/
doi: 10.1186/1471-2334-5-26
summary:
  title: Absence of association between angiotensin converting enzyme polymorphism and development of adult respiratory distress syndrome in patients with severe acute respiratory syndrome: a case control study Thus, we have investigated the association between ACE insertion/deletion (I/D) polymorphism and the progression to ARDS or requirement of intensive care in SARS patients. RESULTS: There is no significant difference in the genotypic distributions and the allelic frequencies of the ACE I/D polymorphism between the SARS patients and the healthy control subjects. Therefore, in this study, we investigated the association of the ACE insertion/deletion (I/D) polymorphism of the 287 bp Alu repeat to the susceptibility to SARS and the development of adult respiratory distress syndrome (ARDS) with a larger population. The genotypic distributions and allelic frequencies of ACE I/D polymorphism in the SARS patients and control subjects are shown in table 2.

title:
  Absence of association between angiotensin converting enzyme polymorphism and development of adult respiratory distress syndrome in patients with severe acute respiratory syndrome: a case control study

abstract:
  BACKGROUND: It has been postulated that genetic predisposition may influence the susceptibility to SARS-coronavirus infection and disease outcomes. A recent study has suggested that the deletion allele (D allele) of the angiotensin converting enzyme (ACE) gene is associated with hypoxemia in SARS patients. Moreover, the ACE D allele has been shown to be more prevalent in patients suffering from adult respiratory distress syndrome (ARDS) in a previous study. Thus, we have investigated the association between ACE insertion/deletion (I/D) polymorphism and the progression to ARDS or requirement of intensive care in SARS patients. METHOD: One hundred and forty genetically unrelated Chinese SARS patients and 326 healthy volunteers were recruited. The ACE I/D genotypes were determined by polymerase chain reaction and agarose gel electrophoresis. RESULTS: There is no significant difference in the genotypic distributions and the allelic frequencies of the ACE I/D polymorphism between the SARS patients and the healthy control subjects. Moreover, there is also no evidence that ACE I/D polymorphism is associated with the progression to ARDS or the requirement of intensive care in the SARS patients. In multivariate logistic analysis, age is the only factor associated with the development of ARDS while age and male sex are independent factors associated with the requirement of intensive care. CONCLUSION: The ACE I/D polymorphism is not directly related to increased susceptibility to SARS-coronavirus infection and is not associated with poor outcomes after SARS-coronavirus infection.


id: cord-316245-n6tmn4ph
author: Cui, Binglin
date: 2015-03-13
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url: https://www.ncbi.nlm.nih.gov/pubmed/25884513/
doi: 10.1186/s12879-015-0863-6
summary:
  METHODS: Paired nasal/throat-flocked swabs collected from 1,074 children with ARIs, who visited outpatient walk-in clinics in a tertiary hospital between December 2010 and November 2011, were examined for fourteen respiratory viruses influenza viruses (FluA, FluB), respiratory syncytial viruses (RSV A and B), human coronaviruses (hCoV: 229E, OC43, HKU1, NL63), human metapneumoviruses (hMPV A and B), parainfluenza viruses (PIV1-4), human rhinoviruses (HRV A, B, C), enteroviruses (EV), adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV) by multiplex real-time PCR. Multiplex real-time PCR was performed using Roche, Lightcycler 480 II (Roche Diagnostics, Penzberg, Germany) to identify the following 14 respiratory viruses: influenza A (FluA), influenza B (FluB), respiratory syncytial viruses A and B (RSV), human coronaviruses 229E, OC43, HKU1 and NL63 (hCoV), human metapneumoviruses A and B (hMPV), human parainfluenza virus types 1, 2 , 3, and 4 (PIV1, PIV2, PIV3, and PIV4), human rhinoviruses A, B, and C (HRV), human enteroviruses (EV), human adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV).

title:
  Viral aetiology of acute respiratory infections among children and associated meteorological factors in southern China

abstract:
  BACKGROUND: Acute respiratory infections (ARIs) are common in children and mostly caused by viruses, but the significance of the detection of multiple viruses in ARIs is unclear. This study investigated 14 respiratory viruses in ARIs among children and associated meteorological factors in Shantou, southern China. METHODS: Paired nasal/throat-flocked swabs collected from 1,074 children with ARIs, who visited outpatient walk-in clinics in a tertiary hospital between December 2010 and November 2011, were examined for fourteen respiratory viruses - influenza viruses (FluA, FluB), respiratory syncytial viruses (RSV A and B), human coronaviruses (hCoV: 229E, OC43, HKU1, NL63), human metapneumoviruses (hMPV A and B), parainfluenza viruses (PIV1-4), human rhinoviruses (HRV A, B, C), enteroviruses (EV), adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV) - by multiplex real-time PCR. RESULTS: We identified at least one virus in 82.3% (884/1,074) and multiple viruses in 38.6% (415/1,074) of patients. EV and HRV were the most frequently detected single viruses (42.3%, 374/884 and 39.9%, 353/884 respectively) and co-detected pair (23.1%, 96/415). Overlapping seasonal trends of viruses were recorded over the year, with dual peaks for EV and single peaks for the others. By logistic regression analysis, EV was positively associated with the average temperature and humidity, hCoV, and PIV4, but negatively with HRV, PIV3, and hBoV. HRV was inversely associated with EV and PIV3. CONCLUSIONS: This study reports high viral detection and co-detection rates in pediatric ARI cases mainly due to EV and HRV. Many viruses circulated throughout the year with similar seasonal trends in association with temperature, humidity, and wind velocity. Statistically significant associations were present among the viruses. Understanding the polyviral etiology and viral interactions in the cases with multiple viruses warrants further studies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-015-0863-6) contains supplementary material, which is available to authorized users.


id: cord-316493-wszoi6p2
author: Zhou, Weimin
date: 2013-09-16
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url: https://www.ncbi.nlm.nih.gov/pubmed/24040960/
doi: 10.1186/1471-2334-13-433
summary:
  BACKGROUND: Non-severe acute respiratory syndrome (non-SARS)-related human coronaviruses (HCoVs), including HCoV-229E, -HKU1, -NL63, and -OC43, have been detected in respiratory tract samples from children and adults. An S-protein-based indirect immunofluorescence assay (IFA) was then developed to detect anti-S IgG and IgM for the four individual HCoVs and applied to serum samples from a general asymptomatic population (218 children and 576 adults) in Beijing. To expand the epidemiological knowledge of four non-SARS-related endemic HCoVs in China, we expressed S proteins in a eukaryotic system and established an IFA for the detection of IgG or IgM antibodies against these four viruses. Our results showed that the S-based IFA enabled specific detection of IgG or IgM to four individual HCoVs. Using IFA, we investigated the natural seroprevalence of four non-SARS-related HCoVs in blood samples from a general population that comprised a variety of age groups.

title:
  First infection by all four non-severe acute respiratory syndrome human coronaviruses takes place during childhood

abstract:
  BACKGROUND: Non-severe acute respiratory syndrome (non-SARS)-related human coronaviruses (HCoVs), including HCoV-229E, -HKU1, -NL63, and -OC43, have been detected in respiratory tract samples from children and adults. However, the natural prevalence of antibodies against these viruses in serum among population is unknown. METHODS: To measure antibodies to the spike (S) protein of the four common non-SARS HCoVs, recombinant S proteins of the four HCoVs were expressed and characterised in 293 T cell. An S-protein-based indirect immunofluorescence assay (IFA) was then developed to detect anti-S IgG and IgM for the four individual HCoVs and applied to serum samples from a general asymptomatic population (218 children and 576 adults) in Beijing. RESULTS: Of 794 blood samples tested, only 29 (3.65%) were negative for anti-S IgG. The seropositivity of the four anti-S IgG antibodies was >70% within the general population. The majority of seroconversions to four-HCoV positivity first occurred in children. Both S-IgG and S-IgM antibodies were detectable among children and increased with age, reaching a plateau at 6 years of age. However, no anti-S IgM was detected in healthy adults. CONCLUSION: Large proportions of children and adults in Beijing have evidence of anti-S IgG against four the HCoVs, and first infections by all four non-SARS HCoVs takes place during childhood.


id: cord-318057-xagh68jc
author: Gunson, Rory N
date: 2011-07-13
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url: https://doi.org/10.1186/1471-2334-11-192
doi: 10.1186/1471-2334-11-192
summary:
  All were from patients clinically diagnosed as having H1N1/2009 (based on accepted criteria) and all were given a full respiratory screen using real time reverse transcriptase polymerase chain reaction (rtRT-PCR) assays. During April-July 2009 all respiratory samples submitted from patients with a clinical diagnosis of H1N1/2009 (as stated on the specimen request form), were initially tested using a universal influenza A real time rtRT-PCR assay and a H1N1/2009 specific real time rtRT-PCR assay [7] . To determine which respiratory pathogens had been misdiagnosed as H1N1/2009, we examined the results of 3247 samples which had been given a full respiratory screen during the period April-July 2009. Examination of the detection rate over the four-month period shows that respiratory pathogens were detected in 27.9% of all samples submitted (95% confidence interval, 26.3-29.5%) ( Table 4 ).

title:
  During the summer 2009 outbreak of "swine flu" in Scotland what respiratory pathogens were diagnosed as H1N1/2009?

abstract:
  BACKGROUND: During the April-July 2009 outbreak of H1N1/2009 in scotland the West of Scotland Specialist Virology Centre (WoSSVC) in Glasgow tested > 16 000 clinical samples for H1N1/2009. Most were from patients clinically diagnosed with H1N1/2009. Out of these, 9% were positive. This study sought to determine what respiratory pathogens were misdiagnosed as cases of H1N1/2009 during this time. METHODS: We examined the results from 3247 samples which were sent to the laboratory during April-July 2009. All were from patients clinically diagnosed as having H1N1/2009 (based on accepted criteria) and all were given a full respiratory screen using real time reverse transcriptase polymerase chain reaction (rtRT-PCR) assays. RESULTS: In total, respiratory pathogens were detected in 27.9% (95% confidence interval, 26.3-29.5%) of the samples submitted. Numerous pathogens were detected, the most common of which were rhinovirus (8.9% (95% confidence interval, 7.9-9.9%)), parainfluenza 1 (1.9% (95% confidence interval, 1.4-2.4%)) and 3 (4.1% (95% confidence interval, 3.3-4.9%)), and adenovirus ((3.5% (95% confidence interval, 2.9-4.2%)). CONCLUSIONS: This study highlights the problems of using a clinical algorithm to detect H1N1/2009. Clinicians frequently misdiagnosed common respiratory pathogens as H1N1/2009 during the spring/summer outbreak in Scotland. Many undesirable consequences would have resulted, relating to treatment, infection control, and public health surveillance.


id: cord-318340-hptjqmrl
author: Xiang, Nijuan
date: 2019-09-03
txt: ./txt/cord-318340-hptjqmrl.txt
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url: https://doi.org/10.1186/s12879-019-4345-0
doi: 10.1186/s12879-019-4345-0
summary:
  We reviewed medical records for documented exposure history associated with respiratory infectious diseases, collected throat samples that were tested for seasonal and avian influenza, and interviewed clinicians regarding reasons for reporting or not reporting PUE cases. If a case is reported to the PUE system, the local center for disease control and prevention (CDC) will conduct a field investigation, collect respiratory specimens and send them to a national influenza surveillance network laboratory for testing of avian influenza viruses and, if associated with clusters of respiratory disease or relevant travel history, testing of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV). For patients with illnesses meeting the PUE case definition, the surveillance officer used a standard questionnaire to collect information from the hospital information system related to demographics and, if available, epidemiological risk factors, including exposures to poultry, patients with similar symptoms, and travel history.

title:
  Lessons from an active surveillance pilot to assess the pneumonia of unknown etiology surveillance system in China, 2016: the need to increase clinician participation in the detection and reporting of emerging respiratory infectious diseases

abstract:
  BACKGROUND: We sought to assess reporting in China’s Pneumonia of Unknown Etiology (PUE) passive surveillance system for emerging respiratory infections and to identify ways to improve the PUE surveillance system’s detection of respiratory infections of public health significance. METHODS: From February 29–May 29, 2016, we actively identified and enrolled patients in two hospitals with acute respiratory infections (ARI) that met all PUE case criteria. We reviewed medical records for documented exposure history associated with respiratory infectious diseases, collected throat samples that were tested for seasonal and avian influenza, and interviewed clinicians regarding reasons for reporting or not reporting PUE cases. We described and analyzed the proportion of PUE cases reported and clinician awareness of and practices related to the PUE system. RESULTS: Of 2619 ARI admissions in two hospitals, 335(13%) met the PUE case definition; none were reported. Of 311 specimens tested, 18(6%) were seasonal influenza virus-positive; none were avian influenza-positive. < 10% PUE case medical records documented whether or not there were exposures to animals or others with respiratory illness. Most commonly cited reasons for not reporting cases were no awareness of the PUE system (76%) and not understanding the case definition (53%). CONCLUSIONS: Most clinicians have limited awareness of and are not reporting to the PUE system. Exposures related to respiratory infections are rarely documented in medical records. Increasing clinicians’ awareness of the PUE system and including relevant exposure items in standard medical records may increase reporting. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-019-4345-0) contains supplementary material, which is available to authorized users.


id: cord-318984-8m9ygzn5
author: Chen, Yin-Yin
date: 2012-09-10
txt: ./txt/cord-318984-8m9ygzn5.txt
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url: https://www.ncbi.nlm.nih.gov/pubmed/22963041/
doi: 10.1186/1471-2334-12-209
summary:
  We examined the rates of DAI by antimicrobial-resistant pathogens, and 30–day and in–hospital mortality in the intensive care unit (ICU). Decreased susceptibility of both gram-positive and gram-negative microbes to antibiotics has been well described in several surveillance studies over the past decade, and increases in the rate of bloodstream infection caused by multi-drug resistant (MDR) gramnegative bacteria have been reported to be 16-fold [5, [8] [9] [10] [11] . In this study, prospective surveillance was conducted to determine the DAI rate and prevalence of antibiotic-resistant isolates at an adult medical-surgical ICU (MS ICU). Our aim was to analyze the secular trend of incidence for different types of DAIs, determine the common pathogens involved, and determine the rates of antimicrobial resistance and overall 30-day and in-hospital mortality during the period 2000-2008. The involved patient demographic information, the dates and sites of infection, device-utilization (DU) ratio, pathogens, antimicrobial susceptibilities, invasive procedures, and overall 30-day mortality and in-hospital crude mortality were recorded.

title:
  Surveillance on secular trends of incidence and mortality for device–associated infection in the intensive care unit setting at a tertiary medical center in Taiwan, 2000–2008: A retrospective observational study

abstract:
  BACKGROUND: Device–associated infection (DAI) plays an important part in nosocomial infection. Active surveillance and infection control are needed to disclose the specific situation in each hospital and to cope with this problem effectively. We examined the rates of DAI by antimicrobial-resistant pathogens, and 30–day and in–hospital mortality in the intensive care unit (ICU). METHODS: Prospective surveillance was conducted in a mixed medical and surgical ICU at a major teaching hospital from 2000 through 2008. Trend analysis was performed and logistic regression was used to assess prognostic factors of mortality. RESULTS: The overall rate of DAIs was 3.03 episodes per 1000 device–days. The most common DAI type was catheter–associated urinary tract infection (3.76 per 1000 urinary catheter–days). There was a decrease in DAI rates in 2005 and rates of ventilator–associated pneumonia (VAP, 3.18 per 1000 ventilator–days) have remained low since then (p < 0.001). The crude rates of 30–day (33.6%) and in–hospital (52.3%) mortality, as well as infection by antibiotic-resistant VAP pathogens also decreased. The most common antimicrobial-resistant pathogens were methicillin–resistant Staphylococcus aureus (94.9%) and imipenem–resistant Acinetobacter baumannii (p < 0.001), which also increased at the most rapid rate. The rate of antimicrobial resistance among Enterobacteriaceae also increased significantly (p < 0.05). After controlling for potentially confounding factors, the DAI was an independent prognostic factor for both 30–day mortality (OR 2.51, 95% confidence interval [CI] 1.99–3.17, p = 0.001) and in–hospital mortality (OR 3.61, 95% CI 2.10–3.25, p < 0.001). CONCLUSIONS: The decrease in the rate of DAI and infection by resistant bacteria on the impact of severe acute respiratory syndrome can be attributed to active infection control and improved adherence after 2003.


id: cord-319504-jb455t9p
author: Suess, Thorsten
date: 2012-01-26
txt: ./txt/cord-319504-jb455t9p.txt
cache: ./cache/cord-319504-jb455t9p.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-12-26
doi: 10.1186/1471-2334-12-26
summary:
  BACKGROUND: Previous controlled studies on the effect of non-pharmaceutical interventions (NPI) namely the use of facemasks and intensified hand hygiene in preventing household transmission of influenza have not produced definitive results. When analysing only households where intervention was implemented within 36 h after symptom onset of the index case, secondary infection in the pooled M and MH groups was significantly lower compared to the control group (adjusted odds ratio 0.16, 95% CI, 0.03-0.92). Since 2006, the World Health Organisation (WHO) and other organisations have highlighted the need for controlled trials to assist in formulating recommendations on the use of non-pharmaceutical interventions (NPI)such as facemasks or hand hygiene measures -as options to prevent influenza transmission, particularly in households [1, 2] . In intention-to-treat analysis, none of the four household based trials was able to show significant reductions in secondary attack rates (SAR) when comparing intervention to control groups.

title:
  The role of facemasks and hand hygiene in the prevention of influenza transmission in households: results from a cluster randomised trial; Berlin, Germany, 2009-2011

abstract:
  BACKGROUND: Previous controlled studies on the effect of non-pharmaceutical interventions (NPI) - namely the use of facemasks and intensified hand hygiene - in preventing household transmission of influenza have not produced definitive results. We aimed to investigate efficacy, acceptability, and tolerability of NPI in households with influenza index patients. METHODS: We conducted a cluster randomized controlled trial during the pandemic season 2009/10 and the ensuing influenza season 2010/11. We included households with an influenza positive index case in the absence of further respiratory illness within the preceding 14 days. Study arms were wearing a facemask and practicing intensified hand hygiene (MH group), wearing facemasks only (M group) and none of the two (control group). Main outcome measure was laboratory confirmed influenza infection in a household contact. We used daily questionnaires to examine adherence and tolerability of the interventions. RESULTS: We recruited 84 households (30 control, 26 M and 28 MH households) with 82, 69 and 67 household contacts, respectively. In 2009/10 all 41 index cases had a influenza A (H1N1) pdm09 infection, in 2010/11 24 had an A (H1N1) pdm09 and 20 had a B infection. The total secondary attack rate was 16% (35/218). In intention-to-treat analysis there was no statistically significant effect of the M and MH interventions on secondary infections. When analysing only households where intervention was implemented within 36 h after symptom onset of the index case, secondary infection in the pooled M and MH groups was significantly lower compared to the control group (adjusted odds ratio 0.16, 95% CI, 0.03-0.92). In a per-protocol analysis odds ratios were significantly reduced among participants of the M group (adjusted odds ratio, 0.30, 95% CI, 0.10-0.94). With the exception of MH index cases in 2010/11 adherence was good for adults and children, contacts and index cases. CONCLUSIONS: Results suggest that household transmission of influenza can be reduced by the use of NPI, such as facemasks and intensified hand hygiene, when implemented early and used diligently. Concerns about acceptability and tolerability of the interventions should not be a reason against their recommendation. TRIAL REGISTRATION: The study was registered with ClinicalTrials.gov (Identifier NCT00833885).


id: cord-320808-taj5swwc
author: Lu, Guilan
date: 2020-07-23
url: https://www.ncbi.nlm.nih.gov/pubmed/32703176/
doi: 10.1186/s12879-020-05258-2
title:
  An outbreak of acute respiratory infection at a training base in Beijing, China due to human adenovirus type B55

abstract:
  BACKGROUND: Twelve students experienced symptoms of acute respiratory infection (ARI) at a training base in Beijing from August 26 to August 30, 2015. We investigated the cause of this ARI outbreak. METHODS: In partnership with the local center for disease control, we collected a total of twelve pharyngeal swab specimens as well as demographic information for the affected patients. We used multiplex real-time PCR to screen for sixteen common respiratory viruses in these samples. To isolate HAdV, we inoculated Hep-2 cells with the human adenovirus (HAdV)-positive samples and then carried out sequencing and phylogenetic analysis of the hexon, fiber, and penton genes of the isolated adenoviruses. In addition, we analyzed the entire genome of one strain isolated from the index case to identify single-nucleotide substitutions. RESULTS: We identified ten HAdV-positive students using multiplex real-time PCR. None of the students were co-infected with other viruses. We successfully isolated seven HAdV strains from the pharyngeal swab specimens. The coding sequences of the hexon, fiber, and penton genes of these seven HAdV strains were identical, suggesting that they represented seven strains from a single virus clone. One HAdV isolate obtained from the index case, BJDX-01-2015, was selected for whole genome analysis. From this isolate, we obtained a 34,774-nucleotide sequence. The genome of BJDX-01-2015 clustered with HAdV-B55 in phylogenetic analyses and had 99.97% identity with human adenovirus 55 isolate HAdV-B/CHN/BJ01/2011/55 (GenBank accession no. JX491639). CONCLUSIONS: We identified HAdV-B55 as the strain associated with the August 2015 ARI outbreak at a training base in Beijing. This was the first reported outbreak in Beijing due to HAdV-B55. Continuous surveillance of respiratory adenoviruses is urgently needed to understand the epidemiological and evolutionary features of HAdV-B55, and an epidemiological modeling approach may provide further insights into this emerging public health threat. Furthermore, the clinical laboratory data from this outbreak provides important reference for the clinical diagnosis and may ultimately aid in informing the development of strategies to control and prevent respiratory tract infections caused by HAdV-B55.


id: cord-320928-flsaa1wx
author: Aldohyan, Meshal
date: 2019-03-21
txt: ./txt/cord-320928-flsaa1wx.txt
cache: ./cache/cord-320928-flsaa1wx.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-019-3898-2
doi: 10.1186/s12879-019-3898-2
summary:
  This study evaluated the perceived effectiveness of MERS-CoV educational programs and knowledge transfer among primary care HCWs at a hospital in Saudi Arabia that witnessed the largest outbreak of confirmed MERS-CoV cases in this country. CONCLUSIONS: A negative perception of the effectiveness of MERS-CoV knowledge transfer was associated with poorer knowledge and was more prevalent among male HCWs, physicians/pharmacists and less experienced HCWs. Hospitals should always refer to efficient knowledge sharing and educational strategies that render beneficial outcomes to patients, HCWs, and the public community. Therefore, there was an emerging need to evaluate the perceived effectiveness of MERS-CoV educational programs and knowledge transfer from the HCW''s perspective, in a setting that witnessed the largest outbreak of confirmed MERS-CoV cases in Saudi Arabia. This explains why HCWs with less work experience (< 5 years) had significantly more negative perceptions of knowledge transfer and the perceived effectiveness of MERS-CoV educational programs.

title:
  The perceived effectiveness of MERS-CoV educational programs and knowledge transfer among primary healthcare workers: a cross-sectional survey

abstract:
  BACKGROUND: Knowledge transfer of Middle East respiratory syndrome coronavirus (MERS-CoV) involves the dissemination of created/acquired information on MERS-CoV in hospitals, making this information accessible to all healthcare workers (HCWs). This study evaluated the perceived effectiveness of MERS-CoV educational programs and knowledge transfer among primary care HCWs at a hospital in Saudi Arabia that witnessed the largest outbreak of confirmed MERS-CoV cases in this country. METHODS: A survey was distributed among primary care HCWs at five clinics in Saudi Arabia in 2016. Those with non-direct patient care responsibilities were excluded. Their knowledge was evaluated against facts published by Mayo Clinic Foundation, and its percentage mean score (PMS) ± standard deviation was calculated. HCWs’ perceived effectiveness of educational programs and knowledge transfer was classified as negative or positive. RESULTS: Sample comprised of 404 HCWs, of which 64% were females and 36% were males. Almost 26% were ≤ 30 years old, and 42% had > 10 years of work experience. Almost 46.5% were nurses, 23.0% physicians, 18.1% were pharmacists, and 12.4% were technical staff. PMS for knowledge was 71.1 ± 19.4. The prevalence of negative perceptions towards educational programs was 22.5% and of knowledge transfer was 20.8%. Older(> 40 years of age) and more experienced(> 10 years) HCWs had the highest PMS for knowledge(73.4 ± 18.9,P = 0.005 and 76.9 ± 15.7,P < 0.001 respectively). Negative perceptions of educational programs (49.4 ± 20.7; P < 0.001) and knowledge transfer (46.0 ± 19.7; P = 0.001) were associated with a lower knowledge PMS. Males were 2.4[95% confidence interval 1.4–4.2] times and 2.0[1.1–3.5] times more likely to have negative perceptions of educational programs and knowledge transfer (adjusted (adj.)P = 0.001 and adj. P = 0.023, respectively). Physicians/pharmacists were 1.8[1.03–3.11] and 2.8[1.6–5.0] times more likely to have negative perceptions of both outcomes (adj. P = 0.038 and adj. P = 0.001, respectively). Less experienced HCWs were 2.1[1.3–3.5] times and 4.9[2.6–9.2] times more likely to exhibit negative perceptions of the two outcomes (adj. P < 0.001 each). CONCLUSIONS: A negative perception of the effectiveness of MERS-CoV knowledge transfer was associated with poorer knowledge and was more prevalent among male HCWs, physicians/pharmacists and less experienced HCWs. Hospitals should always refer to efficient knowledge sharing and educational strategies that render beneficial outcomes to patients, HCWs, and the public community. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-019-3898-2) contains supplementary material, which is available to authorized users.


id: cord-321235-h3w8827o
title: Pooling for SARS-CoV-2 control in care institutions
author: Cabrera Alvargonzalez, Jorge Julio
date: 2020-10-12
url: https://www.ncbi.nlm.nih.gov/pubmed/33046011/
doi: 10.1186/s12879-020-05446-0
abstract:
  BACKGROUND: Workers and residents in Care Homes are considered at special risk for the acquisition of SARS-CoV-2 infection, due to the infectivity and high mortality rate in the case of residents, compared to other containment areas. The role of presymptomatic people in transmission has been shown to be important and the early detection of these people is critical for the control of new outbreaks. Pooling strategies have proven to preserve SARS-CoV-2 testing resources. The aims of the present study, based in our local experience, were (a) to describe SARS-CoV-2 prevalence in institutionalized people in Galicia (Spain) during the Coronavirus pandemic and (b) to evaluate the expected performance of a pooling strategy using RT-PCR for the next rounds of screening of institutionalized people. METHODS: A total of 25,386 Nasopharyngeal swab samples from the total of the residents and workers at Care Homes in Galicia (March to May 2020) were individually tested using RT-PCR. Prevalence and quantification cycle (Cq) value distribution of positives was calculated. Besides, 26 pools of 20 samples and 14 pools of 5 samples were tested using RT-PCR as well (1 positive/pool). Pooling proof of concept was performed in two populations with 1.7 and 2% prevalence. RESULTS: Distribution of SARS-CoV-2 infection at Care Homes was uneven (0–60%). As the virus circulation global rate was low in our area (3.32%), the number of people at risk of acquiring the infection continues to be very high. In this work, we have successfully demonstrated that pooling of different groups of samples at low prevalence clusters, can be done with a small average delay on Cq values (5 and 2.85 cycles for pools of 20 and 5 samples, respectively). CONCLUSIONS: A new screening system with guaranteed protection is required for small clusters, previously covered with individual testing. Our proposal for Care Homes, once prevalence zero is achieved, would include successive rounds of testing using a pooling solution for transmission control preserving testing resources. Scale-up of this method may be of utility to confront larger clusters to avoid the viral circulation and keeping them operative.


id: cord-321549-r7bmtloy
title: Scent dog identification of samples from COVID-19 patients – a pilot study
author: Jendrny, Paula
date: 2020-07-23
txt: ./txt/cord-321549-r7bmtloy.txt
cache: ./cache/cord-321549-r7bmtloy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32703188/
doi: 10.1186/s12879-020-05281-3
summary:
  METHODS: Eight detection dogs were trained for 1 week to detect saliva or tracheobronchial secretions of SARS-CoV-2 infected patients in a randomised, double-blinded and controlled study. CONCLUSIONS: These preliminary findings indicate that trained detection dogs can identify respiratory secretion samples from hospitalised and clinically diseased SARS-CoV-2 infected individuals by discriminating between samples from SARS-CoV-2 infected patients and negative controls. As dogs can be trained quickly, the aim of the present study was to test the concept of using dogs reliably and in real-time to discriminate between samples of SARS-CoV-2 infected patients and non-infected controls. The individuals were only tested for SARS-CoV-2 virus and therefore one cannot exclude that a former infection, especially with another human coronavirus like HCoV-OC43 resulted in false positive indications of the dogs and that cross detection occurred. Detection dogs were able to discriminate respiratory secretions of infected SARS-CoV-2 individuals from those of healthy controls with high rates of sensitivity and specificity.

abstract:
  BACKGROUND: As the COVID-19 pandemic continues to spread, early, ideally real-time, identification of SARS-CoV-2 infected individuals is pivotal in interrupting infection chains. Volatile organic compounds produced during respiratory infections can cause specific scent imprints, which can be detected by trained dogs with a high rate of precision. METHODS: Eight detection dogs were trained for 1 week to detect saliva or tracheobronchial secretions of SARS-CoV-2 infected patients in a randomised, double-blinded and controlled study. RESULTS: The dogs were able to discriminate between samples of infected (positive) and non-infected (negative) individuals with average diagnostic sensitivity of 82.63% (95% confidence interval [CI]: 82.02–83.24%) and specificity of 96.35% (95% CI: 96.31–96.39%). During the presentation of 1012 randomised samples, the dogs achieved an overall average detection rate of 94% (±3.4%) with 157 correct indications of positive, 792 correct rejections of negative, 33 incorrect indications of negative or incorrect rejections of 30 positive sample presentations. CONCLUSIONS: These preliminary findings indicate that trained detection dogs can identify respiratory secretion samples from hospitalised and clinically diseased SARS-CoV-2 infected individuals by discriminating between samples from SARS-CoV-2 infected patients and negative controls. This data may form the basis for the reliable screening method of SARS-CoV-2 infected people.


id: cord-321704-jozrgcq3
author: Tan, Xin Quan
date: 2014-04-15
url: https://www.ncbi.nlm.nih.gov/pubmed/24735158/
doi: 10.1186/1471-2334-14-204
title:
  Respiratory viral pathogens among Singapore military servicemen 2009 – 2012: epidemiology and clinical characteristics

abstract:
  BACKGROUND: Few studies have comprehensively described tropical respiratory disease surveillance in military populations. There is also a lack of studies comparing clinical characteristics of the non-influenza pathogens with influenza and amongst themselves. METHODS: From May 2009 through October 2012, 7733 consenting cases of febrile respiratory illness (FRI) (temperature [greater than or equal to]37.5degreesC with cough or sorethroat) and controls in the Singapore military had clinical data and nasal washes collected prospectively. Nasal washes underwent multiplex PCR, and the analysis was limited to viral mono-infections. RESULTS: 49% of cases tested positive for at least one virus, of whom 10% had multiple infections. 53% of the FRI cases fulfilled the definition of influenza-like illness (ILI), of whom 52% were positive for at least one virus. The most frequent etiologies for mono-infections among FRI cases were Influenza A(H1N1)pdm09 (13%), Influenza B (13%) and coxsackevirus (9%). The sensitivity, specificity, positive predictive value and negative predictive value of ILI for influenza among FRI cases were 72%, 48%, 40% and 69% respectively. On logistic regression, there were marked differences in the prevalence of different symptoms and signs between viruses with fever more prevalent amongst influenza and adenovirus infections than other viruses. CONCLUSION: There are multiple viral etiologies for FRI and ILI with differing clinical symptoms in the Singapore military. Influenza and coxsackevirus were the most common etiology for FRI, while influenza and adenoviruses displayed the most febrile symptoms. Further studies should explore these differences and possible interventions.


id: cord-321848-qys8r6jo
author: Liu, Nan
date: 2014-03-04
txt: ./txt/cord-321848-qys8r6jo.txt
cache: ./cache/cord-321848-qys8r6jo.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-14-123
doi: 10.1186/1471-2334-14-123
summary:
  BACKGROUND: To analyze the epidemiological characteristics and pathogenic molecular characteristics of an hand, foot, and mouth disease (HFMD) outbreak caused by enterovirus 71 in Linyi City, Shandong Province, China during November 30 to December 28, 2010. Complete sequence analyses of enterovirus 71 strains from fatal and non-fatal cases of the hand, foot and mouth disease outbreak in Identification of enterovirus 71 isolates from an outbreak of hand, foot and mouth disease (HFMD) with fatal cases of encephalomyelitis in Malaysia Outbreak of central nervous system disease associated with hand, foot, and mouth disease in Japan during the summer of 2000: detection and molecular epidemiology of enterovirus 71 An outbreak of hand, foot, and mouth disease associated with subgenotype C4 of human enterovirus 71 in Shandong China An atypical winter outbreak of hand, foot, and mouth disease associated with human enterovirus 71

title:
  An atypical winter outbreak of hand, foot, and mouth disease associated with human enterovirus 71, 2010

abstract:
  BACKGROUND: To analyze the epidemiological characteristics and pathogenic molecular characteristics of an hand, foot, and mouth disease (HFMD) outbreak caused by enterovirus 71 in Linyi City, Shandong Province, China during November 30 to December 28, 2010. METHODS: One hundred and seventy three stool specimens and 40 throat samples were collected from 173 hospitalized cases. Epidemiologic and clinical investigations, laboratory testing, and genetic analyses were performed to identify the causal pathogen of the outbreak. RESULTS: Among the 173 cases reported in December 2010, the male–female ratio was 1.88: 1; 23 cases (13.3%) were severe. The majority of patients were children aged < 5 years (95.4%). Some patients developed respiratory symptoms including runny nose (38.2%), cough (20.2%), and sore throat (14.5%). One hundred and thirty eight EV71 positive cases were identified based on real time reverse-transcription PCR detection and 107 isolates were sequenced with the VP1 region. Phylogenetic analysis of full-length VP1 sequences of 107 Linyi EV71 isolates showed that they belonged to the C4a cluster of the C4 subgenotype and were divided into 3 lineages (Lineage I, II and III). The two amino acid substitutions (Gly and Gln for Glu) at position 145 within the VP1 region are more likely to appear in EV71 isolates from severe cases (52.2%) than those recovered from mild cases (8.3%). CONCLUSION: This outbreak of HMFD was caused by EV71 in an atypical winter. EV71 strains associated with this outbreak represented three separate chains of transmission. Substitution at amino acid position 145 of the VP1 region of EV71 might be an important virulence marker for severe cases. These findings suggest that continued surveillance for EV71 variants has the potential to greatly impact HFMD prevention and control.


id: cord-322202-n6qe38bh
author: Saiki-Macedo, Stephanie
date: 2019-01-21
txt: ./txt/cord-322202-n6qe38bh.txt
cache: ./cache/cord-322202-n6qe38bh.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-019-3671-6
doi: 10.1186/s12879-019-3671-6
summary:
  In a previous study we conducted on children under 1-year-old with a probable diagnosis of Pertussis from 5 Peruvian hospitals, we reported a prevalence of 39.54% pertussis cases [14] . The main objective of this study was to detect the presence of 8 respiratory viruses (Influenza-A, Influenza-B, RSV-A, RSV-B, Adenovirus, Parainfluenza-1, Parainfluenza-2 and Parainfluenza-3) and atypical bacteria (Mycoplasma pneumoniae, Chlamydia pneumonia), via Polymerase Chain Reaction in samples from Peruvian children under 5 years-old previously analyzed for B. Demonstrating the high prevalence of these atypical bacteria among Peruvian children with ARIs. Our results from this current study also make noteworthy that clinical manifestations by Mycoplasma pneumoniae and Flu-B, ADV, or B. Surprisingly, in this study, we have observed 58% of coinfections in our samples, again being the viral-bacterial association the most frequent and the most commonly detected coinfection involving Bordetella pertussis-ADV and Mycoplasma pneumoniae-ADV with frequencies of 12.2 and 6.5%, respectively.

title:
  Identfication of viral and bacterial etiologic agents of the pertussis-like syndrome in children under 5 years old hospitalized

abstract:
  BACKGROUND: Acute respiratory infections (ARIs) represent an important cause of morbidity and mortality in children, remaining a major public health concern, especially affecting children under 5 years old from low-income countries. Unfortunately, information regarding their epidemiology is still limited in Peru. METHODS: A secondary data analysis was performed from a previous cross-sectional study conducted in children with a probable diagnosis of Pertussis from January 2010 to July 2012. All samples were analyzed via Polymerase Chain Reaction (PCR) for the following etiologies: Influenza-A, Influenza-B, RSV-A, RSV-B, Adenovirus, Parainfluenza 1 virus, Parainfluenza 2 virus, Parainfluenza 3 virus, Mycoplasma pneumoniae and Chlamydia pneumoniae. RESULTS: A total of 288 patients were included. The most common pathogen isolated was Adenovirus (49%), followed by Bordetella pertussis (41%) from our previous investigation, the most prevelant microorganisms were Mycoplasma pneumonia (26%) and Influenza-B (19.8%). Coinfections were reported in 58% of samples and the most common association was found between B. pertussis and Adenovirus (12.2%). CONCLUSIONS: There was a high prevalence of Adenovirus, Mycoplasma pneumoniae and other etiologies in patients with a probable diagnosis of pertussis. Despite the presence of persistent cough lasting at least two weeks and other clinical characteristics highly suspicious of pertussis, secondary etiologies should be considered in children under 5 years-old in order to give a proper treatment. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-019-3671-6) contains supplementary material, which is available to authorized users.


id: cord-324638-gwd8qin6
author: Chiu, Rossa WK
date: 2006-02-09
txt: ./txt/cord-324638-gwd8qin6.txt
cache: ./cache/cord-324638-gwd8qin6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16466582/
doi: 10.1186/1471-2334-6-20
summary:
  We developed a modified protocol in compliance with the recommended biosafety guidelines from the World Health Organization based on the use of the MagNA Pure total nucleic acid large volume isolation kit for the extraction of SARS-coronavirus RNA. The main objective of this study was to compare the resultant analytical sensitivity and quantitative performance of the serum SARS-CoV RNA test when either the manual or automated extraction protocol was used. The modified large volume protocol with the external lysis step was further compared with the external lysis protocol of the total nucleic acid isolation kit using a transport medium mixture containing 10 6 copies/mL of inactivated SARS-CoV. Serially diluted inactivated SARS-CoV isolate in transport medium was extracted by both the column-based manual method and the MagNA Pure LC instrument using the modified large volume protocol with external lysis.

title:
  Automated extraction protocol for quantification of SARS-Coronavirus RNA in serum: an evaluation study

abstract:
  BACKGROUND: We have previously developed a test for the diagnosis and prognostic assessment of the severe acute respiratory syndrome (SARS) based on the detection of the SARS-coronavirus RNA in serum by real-time quantitative reverse transcriptase polymerase chain reaction (RT-PCR). In this study, we evaluated the feasibility of automating the serum RNA extraction procedure in order to increase the throughput of the assay. METHODS: An automated nucleic acid extraction platform using the MagNA Pure LC instrument (Roche Diagnostics) was evaluated. We developed a modified protocol in compliance with the recommended biosafety guidelines from the World Health Organization based on the use of the MagNA Pure total nucleic acid large volume isolation kit for the extraction of SARS-coronavirus RNA. The modified protocol was compared with a column-based extraction kit (QIAamp viral RNA mini kit, Qiagen) for quantitative performance, analytical sensitivity and precision. RESULTS: The newly developed automated protocol was shown to be free from carry-over contamination and have comparable performance with other standard protocols and kits designed for the MagNA Pure LC instrument. However, the automated method was found to be less sensitive, less precise and led to consistently lower serum SARS-coronavirus concentrations when compared with the column-based extraction method. CONCLUSION: As the diagnostic efficiency and prognostic value of the serum SARS-CoV RNA RT-PCR test is critically associated with the analytical sensitivity and quantitative performance contributed both by the RNA extraction and RT-PCR components of the test, we recommend the use of the column-based manual RNA extraction method.


id: cord-324880-s1oqkqef
title: A fatal case associated with respiratory syncytial virus infection in a young child
author: Xu, Lili
date: 2018-05-11
txt: ./txt/cord-324880-s1oqkqef.txt
cache: ./cache/cord-324880-s1oqkqef.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29751747/
doi: 10.1186/s12879-018-3123-8
summary:
  RSV-related encephalitis with acute encephalopathic symptoms such as seizure, severe sequelae and even death following RSV infection in children without underlying disease has sporadically been reported [5] . In this report, we present the case of a 2-year-old girl who was not born prematurely and had no underlying disease whose sudden death may have been related to an RSV infection identified by conventional methods and metagenomic analyses. Viral antigen detection based on both an immunofluorescence assay and the Luminex xTAG respiratory viral panel assay was positive for RSV in the patient''s nasopharyngeal aspirates (which were collected on 14 Nov, the 5th day of disease onset and the 2nd day of admission) and negative for adenovirus, influenza A and B viruses, parainfluenza virus 1-4, human metapneumovirus, enteroviruses and rhinoviruses, human coronavirus HKU1, 229E, NL63 and OC43, and human bocavirus. reported that influenza virus RNA was detected in the CSF of 71.4% (5/7) of patients who developed influenza-associated acute encephalopathy/encephalitis [17] .

abstract:
  BACKGROUND: Respiratory syncytial virus (RSV) is the most common viral cause of pediatric bronchiolitis and pneumonia worldwide. Risk factors for high mortality and prolonged morbidity after RSV infection include premature birth, bronchopulmonary dysplasia, congenital heart disease, and Down syndrome. However, some previously healthy, full-term children who are infected with RSV also require hospitalization and even experience severe sequelae or death. CASE PRESENTATION: In this report, we present the case of an RSV-associated death of a child who was born at full-term and developed normally up to the age of 2 years old. Cardiopulmonary arrest occurred within 3 days after the onset of symptoms, which included cough and high fever. Complete brain edema was prominent, and encephalopathy was developing. Viral antigen detection and microbiome analyses of oral swab and nasopharyngeal aspirate specimens verified an RSV infection, while bacterial culture of blood specimens yielded negative results. The RSV strain detected in this patient was subtyped as RSVB9, and no mutation was found in the six antigenic sites for targeted drugs or vaccines. CONCLUSIONS: The patient had a severe infection associated with RSV, which was very likely the cause of her central nervous system infection and acute neurological complications.


id: cord-324942-zfvzxlj7
author: Yu, Jianxing
date: 2018-02-08
url: https://doi.org/10.1186/s12879-018-2982-3
doi: 10.1186/s12879-018-2982-3
title:
  Comparison of the prevalence of respiratory viruses in patients with acute respiratory infections at different hospital settings in North China, 2012–2015

abstract:
  BACKGROUND: Acute respiratory infections (ARIs) are a great public health challenge globally. The prevalence of respiratory viruses in patients with ARIs attending at different hospital settings is fully undetermined. METHODS: Laboratory-based surveillance for ARIs was conducted at inpatient and outpatient settings of 11 hospitals in North China. The first 2–5 patients with ARIs were recruited in each hospital weekly from 2012 through 2015. The presence of respiratory viruses was screened by PCR assays. The prevalence of respiratory viruses was determined and compared between patients at different hospital settings. RESULTS: A total of 3487 hospitalized cases and 6437 outpatients/Emergency Department (ED) patients were enrolled. The most commonly detected viruses in the hospitalized cases were respiratory syncytial virus (RSV, 33.3%) in children less than two years old, adenoviruses (13.0%) in patients 15–34 years old, and influenza viruses (IFVs, 9.6%) in patients ≥65 years. IFVs were the most common virus in outpatient/ED patients across all age groups (22.7%). After controlling for the confounders caused by other viruses and covariates, adenoviruses (adjusted odds ratio [aOR]: 3.97, 99% confidence interval [99% CI]: 2.19–7.20) and RSV (aOR: 2.04, 99% CI: 1.34–3.11) were independently associated with increased hospitalization in children, as well as adenoviruses in adults (aOR: 2.14, 99% CI: 1.19–3.85). Additionally, co-infection of RSV with IFVs was associated with increased hospitalization in children (aOR: 12.20, 99% CI: 2.65–56.18). CONCLUSIONS: A substantial proportion of ARIs was associated with respiratory viruses in North China. RSV, adenoviruses, and co-infection of RSV and IFVs were more frequent in hospitalized children (or adenoviruses in adults), which might predict the severity of ARIs. Attending clinicians should be more vigilant of these infections. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-2982-3) contains supplementary material, which is available to authorized users.


id: cord-325635-don9qjpz
title: Respiratory virus surveillance in hospitalised pneumonia patients on the Thailand-Myanmar border
author: Turner, Paul
date: 2013-09-16
txt: ./txt/cord-325635-don9qjpz.txt
cache: ./cache/cord-325635-don9qjpz.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-13-434
doi: 10.1186/1471-2334-13-434
summary:
  Using global population data for 2005, for children under the age of five years, it was estimated that RSV was responsible for over 30 million episodes of lower respiratory tract infections (LRTI), with~3 million of these requiring hospital admission, and 66,000-199,000 deaths [7] . In 2007, the US Centers for Disease Control and Prevention (CDC) and the Shoklo Malaria Research Unit (SMRU) established a respiratory virus surveillance programme in the Burmese refugee population living in Maela camp, Northwest Thailand. Laboratory-enhanced surveillance has documented the contribution of respiratory viruses to 708 hospitalised clinical pneumonia episodes occurring in a crowded refugee camp on the Thailand-Myanmar border during April 2009 to September 2011. The results are broadly consistent with a similar surveillance programme conducted in two Kenyan refugee camps [22] , where 51.3% patients with severe acute respiratory infection (SARI) had at least one of adenovirus, hMPV, influenza A/B, parainfluenza virus 1-3, or RSV detected.

abstract:
  BACKGROUND: Pneumonia is a significant cause of morbidity and mortality in the developing world. Viruses contribute significantly to pneumonia burden, although data for low-income and tropical countries are scarce. The aim of this laboratory-enhanced, hospital-based surveillance was to characterise the epidemiology of respiratory virus infections among refugees living on the Thailand-Myanmar border. METHODS: Maela camp provides shelter for ~45,000 refugees. Inside the camp, a humanitarian organisation provides free hospital care in a 158-bed inpatient department (IPD). Between 1st April 2009 and 30th September 2011, all patients admitted to the IPD with a clinical diagnosis of pneumonia were invited to participate. Clinical symptoms and signs were recorded and a nasopharyngeal aspirate (NPA) collected. NPAs were tested for adenoviruses, human metapneumovirus (hMPV), influenza A & B, and RSV by PCR. RESULTS: Seven hundred eight patient episodes (698 patients) diagnosed as pneumonia during the enhanced surveillance period were included in this analysis. The median patient age was 1 year (range: < 1-70), and 90.4% were aged < 5 years. At least one virus was detected in 53.7% (380/708) of episodes. Virus detection was more common in children aged < 5 years old (<1 year: OR 2.0, 95% CI 1.2-3.4, p = 0.01; 1-4 years: OR 1.4, 95% CI 0.8-2.3, p = 0.2). RSV was detected in 176/708 (24.9%); an adenovirus in 133/708 (18.8%); an influenza virus in 68/708 (9.6%); and hMPV in 33/708 (4.7%). Twenty-eight episodes of multiple viral infections were identified, most commonly adenovirus plus another virus. RSV was more likely to be detected in children <5 years (OR 12.3, 95% CI 3.0-50.8, p = 0.001) and influenza viruses in patients ≥5 years (OR 2.8, 95% CI 1.5-5.4, p = 0.002). IPD treatment was documented in 702/708 cases; all but one patient received antimicrobials, most commonly a beta-lactam (amoxicillin/ampicillin +/−gentamicin in 664/701, 94.7%). CONCLUSIONS: Viral nucleic acid was identified in the nasopharynx in half the patients admitted with clinically diagnosed pneumonia. Development of immunisations targeting common respiratory viruses is likely to reduce the incidence of pneumonia in children living refugee camps and similar settings.


id: cord-326632-botshfa1
author: Abolfotouh, Mostafa A.
date: 2020-09-29
txt: ./txt/cord-326632-botshfa1.txt
cache: ./cache/cord-326632-botshfa1.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-020-05443-3
doi: 10.1186/s12879-020-05443-3
summary:
  METHODS: In a cross-sectional study, HCWs at three tertiary hospitals in Saudi Arabia were surveyed via email with an anonymous link, by a concern scale about Covid-19 pandemic during 15–30 April, 2020. Predictors of high concern scores were; HCWs of Saudi nationality (p < 0.001), younger age (p = 0.003), undergraduate education (p = 0.044), living with others (p = 0.003) working in the western region (p = 0.003) and direct contact with patients (p = 0.018). In multiple regression analysis ( Table 4) , predictors of high concern scores were; HCWs of younger age (p = 0.003), Saudi nationality (p < 0.001), undergraduate education (p = 0.044), and those working in the western region (p = 0.003), living with others (p = 0.003) and in direct contact with patients (p = 0.018).

title:
  Perception and attitude of healthcare workers in Saudi Arabia with regard to Covid-19 pandemic and potential associated predictors

abstract:
  BACKGROUND: Healthcare workers (HCWs) face considerable mental and physical stress caring for patients with Covid-19. They are at higher risk of acquiring and transmitting this virus. This study aims to assess perception and attitude of HCWs in Saudi Arabia with regard to Covid-19, and to identify potential associated predictors. METHODS: In a cross-sectional study, HCWs at three tertiary hospitals in Saudi Arabia were surveyed via email with an anonymous link, by a concern scale about Covid-19 pandemic during 15–30 April, 2020. Concerns of disease severity, governmental efforts to contain it and disease outcomes were assessed using 32 concern statements in five distinct domains. Multiple regression analysis was used to identify predictors of high concern scores. RESULTS: A total of 844 HCW responded to the survey. Their average age was 40.4 ± 9.5 years, 40.3% were nurses, 58.2% had direct patient contact, and 77.3% were living with others. The majority of participants (72.1%) had overall concern scores of 55 or less out of a maximum score of 96 points, with an overall mean score of 48.5 ± 12.8 reflecting moderate level of concern. Three-fourth of respondents felt at risk of contracting Covid-19 infection at work, 69.1% felt threatened if a colleague contracted Covid-19, 69.9% felt obliged to care for patients infected with Covid-19 while 27.7% did not feel safe at work using the standard precautions available. Nearly all HCWs believed that the government should isolate patients with Covid-19 in specialized hospitals (92.9%), agreed with travel restriction to and/or from areas affected by Covid-19 (94.7%) and felt safe the government implemented curfew and movement restriction periods (93.6%). Predictors of high concern scores were; HCWs of Saudi nationality (p < 0.001), younger age (p = 0.003), undergraduate education (p = 0.044), living with others (p = 0.003) working in the western region (p = 0.003) and direct contact with patients (p = 0.018). CONCLUSIONS: This study highlights the high concern among HCWs about Covid-19 and identifies the predictors of those with highest concern levels. To minimize the potential negative impact of those concerns on the performance of HCWs during pandemics, measures are necessary to enhance their protection and to minimize the psychological effect of the perceived risk of infection.


id: cord-327961-ysatxwph
author: Wang, Le
date: 2019-11-12
txt: ./txt/cord-327961-ysatxwph.txt
cache: ./cache/cord-327961-ysatxwph.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31718584/
doi: 10.1186/s12879-019-4616-9
summary:
  BACKGROUND: Among pediatric patients hospitalized for Mycoplasma pneumoniae pneumonia (MPP), the risk factors for 90-day readmission after discharge is undefined. CONCLUSIONS: Readmission after MPP are common and is related to patients'' age, body temperature and influenza A coinfection during initial hospital stay, indicating potential targets could be noticed to reduce the rehospitalization after pediatric MPP. A promising approach to resolve this problem is to narrow down study sample according to the pathogenic or clinical features, such as Mycoplasma pneumoniae pneumonia (MPP), which accounts for up to 40% pediatric CAP [12] , and its diagnosis is based on etiology and clinical evidence, thereby elevating the power to detect readmission risk factors associated with the current acute infections. Our aims were to (1) describe the incidence and type of readmission after MPP discharge, (2) investigate the differences between patients with and without readmission at the initial hospital stay, (3) examine the risk factors for 90-day pneumonia-related rehospitalization.

title:
  Risk factors of 90-day rehospitalization following discharge of pediatric patients hospitalized with mycoplasma Pneumoniae pneumonia

abstract:
  BACKGROUND: Among pediatric patients hospitalized for Mycoplasma pneumoniae pneumonia (MPP), the risk factors for 90-day readmission after discharge is undefined. METHODS: We conducted a retrospective observational study of patients <14 years of age who were discharged with a diagnosis of MPP between January 2016 and February 2017. We collected clinical, laboratory and radiographic variables at the time of initial admission. We assessed pneumonia-related readmission within 90-day after discharge. Risk factors independently associated with rehospitalization were identified using multiple logistic regression models. RESULTS: Of the 424 MPP hospitalizations, 48 (11.3%) were readmitted within 90 days and were mainly diagnosed with pneumonia. Patients with younger age or coinfection with influenza A were more likely to be readmitted. In addition, compared with children without readmission, the readmission ones showed different clinical and laboratory characteristics at the index hospital admission. Multiple logistic regression analysis identified age (OR 0.815, 95%CI 0.706–0.940) and body temperature (OR 0.659, 95%CI 0.518–0.839) were significantly associated with lower risk of 90-day readmission. Coinfection with influenza was independently associated with a greater likelihood of 90-day readmission (OR 4.746, 95%CI 1.191–18.913). CONCLUSIONS: Readmission after MPP are common and is related to patients’ age, body temperature and influenza A coinfection during initial hospital stay, indicating potential targets could be noticed to reduce the rehospitalization after pediatric MPP.


id: cord-328040-5qd05e4r
author: Zhao, Xin-Ying
date: 2020-04-29
txt: ./txt/cord-328040-5qd05e4r.txt
cache: ./cache/cord-328040-5qd05e4r.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32345226/
doi: 10.1186/s12879-020-05010-w
summary:
  title: Clinical characteristics of patients with 2019 coronavirus disease in a non-Wuhan area of Hubei Province, China: a retrospective study Since December 2019, several cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection were first reported the virus has caused an outbreak in a short time by human-to-human transmission throughout China, especially in Hubei Province. A considerable proportion of COVID-19 patients develop severe pneumonia, pulmonary edema, acute respiratory distress syndrome, and even multiple organ failure within a short time. Patients suspected of having COVID-19 were admitted and quarantined, and throat swab samples were collected and tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by quantitative polymerase chain reaction assay (qPCR). Clinical data [age, previous chronic disease, epidemiological history, symptoms, vital signs, computed tomography (CT) images, virus load, laboratory tests, complications, and treatment process] of the 91 patients involved in this study were collected.

title:
  Clinical characteristics of patients with 2019 coronavirus disease in a non-Wuhan area of Hubei Province, China: a retrospective study

abstract:
  BACKGROUND: Since December 2019, the 2019 coronavirus disease (COVID-19) has expanded to cause a worldwide outbreak that more than 600,000 people infected and tens of thousands died. To date, the clinical characteristics of COVID-19 patients in the non-Wuhan areas of Hubei Province in China have not been described. METHODS: We retrospectively analyzed the clinical characteristics and treatment progress of 91 patients diagnosed with COVID-19 in Jingzhou Central Hospital. RESULTS: Of the 91 patients diagnosed with COVID-19, 30 cases (33.0%) were severe and two patients (2.2%) died. The severe disease group tended to be older (50.5 vs. 42.0 years; p = 0.049) and have more chronic disease (40% vs. 14.8%; p = 0.009) relative to mild disease group. Only 73.6% of the patients were quantitative polymerase chain reaction (qPCR)-positive on their first tests, while typical chest computed tomography images were obtained for each patient. The most common complaints were cough (n = 75; 82.4%), fever (n = 59; 64.8%), fatigue (n = 35; 38.5%), and diarrhea (n = 14; 15.4%). Non-respiratory injury was identified by elevated levels of aspartate aminotransferase (n = 18; 19.8%), creatinine (n = 5; 5.5%), and creatine kinase (n = 14; 15.4%) in laboratory tests. Twenty-eight cases (30.8%) suffered non-respiratory injury, including 50% of the critically ill patients and 21.3% of the mild patients. CONCLUSIONS: Overall, the mortality rate of patients in Jingzhou was lower than that of Wuhan. Importantly, we found liver, kidney, digestive tract, and heart injuries in COVID-19 cases besides respiratory problems. Combining chest computed tomography images with the qPCR analysis of throat swab samples can improve the accuracy of COVID-19 diagnosis.


id: cord-328501-mbwgi56x
author: Pang, Junxiong
date: 2015-07-25
url: https://www.ncbi.nlm.nih.gov/pubmed/26208494/
doi: 10.1186/s12879-015-1024-7
title:
  Risk factors for febrile respiratory illness and mono-viral infections in a semi-closed military environment: a case-control study

abstract:
  BACKGROUND: Febrile respiratory illness (FRI) results in substantial burden in semi-closed environments. Tackling risk factors may reduce transmission and infection. However, risk factors involved in one setting may not be generalizable in all settings due to differences in climate, residential environment, population genetic and cultural backgrounds. This study aims to identify risk factors of FRI and mono-viral infections in a tropical military environment. METHODS: From year 2009 to 2012, military personnel with temperature ≥37.5 °C, cough and/or sore throat, and personnel with no fever or no respiratory symptoms were recruited as cases and controls, respectively. Subjects provided nasal wash specimens and answered a standardized questionnaire. Resplex assays were used to determine the viral etiologies. Descriptive, univariate and multivariate analyses of the variables were performed using appropriate descriptive tests and logistic regression modelling, respectively, with R program. RESULTS: A total of 7,743 FRI cases and 1,247 non-FRI study controls were recruited. Increasing age [adjusted odds ratio (AOR) = 1.03; 95 % confidence interval (CI) = 1.01-1.05], recruit camp (AOR = 4.67; 95 % CI = 3.99-5.46) and smoker (AOR = 1.31; 95 % CI = 1.13-1.52) were independent risk factors of FRI. Malay ethnicity was positively associated with 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. Significant contact risk factors were stay-out personnel with ill household member (AOR = 4.96; 95 % CI = 3.39-7.24), and stay-in personnel with ill bunkmate and household member (AOR = 3.55; 95 % CI = 2.57-4.91). Staying in camp with none ill in bunk and at home was a protective factor against FRI (AOR = 0.80; 95 % CI = 0.64-0.99). These contact risk factors were similarly observed for the five most common viruses detected, namely adenovirus, rhinoviruses, influenza A and B, and coxsackie/echovirus. CONCLUSION: Increasing age, smoker, recruit-camp, stay-out personnel with ill household members and stay-in personnel with ill bunkmates were independent risk factors of FRI in a semi-closed military environment. Early identification and isolation of ill personnel from their bunk may be effective to prevent and reduce transmission and disease burden.


id: cord-328620-d2jrn1ip
author: van Gageldonk-Lafeber, Arianne B
date: 2007-04-27
url: https://www.ncbi.nlm.nih.gov/pubmed/17466060/
doi: 10.1186/1471-2334-7-35
title:
  Risk factors for acute respiratory tract infections in general practitioner patients in The Netherlands: a case-control study

abstract:
  BACKGROUND: Acute respiratory tract infections (ARTI) are an important public health problem. Improved identification of risk factors might enable targeted intervention. Therefore we carried out a case-control study with the aim of identifying environmental risk factors for ARTI consultations in the Dutch general population. METHODS: A subset of patients visiting their GP in the period of 2000–2003 with an ARTI (cases) and age-matched controls (visiting for other complaints) were included in a case-control study. They were asked to complete a questionnaire about potential risk factors. Conditional logistic regression was used to calculate odds ratio's (OR) and 95% confidence intervals (CI) to estimate the independent effect of potential risk factors. RESULTS: A total of 493 matched pairs of case and control subjects were enrolled. Exposure to persons with respiratory complaints, both inside and outside the household, was found to be an independent risk factor for visiting a GP with an ARTI (respectively OR(adj )= 1.9 and OR(adj )= 3.7). Participants exposed to dampness or mould at home (OR(adj)=0.5) were significantly less likely to visit their GP. In accordance with the general risk of consultations for ARTI, participants with a laboratory-confirmed ARTI who were exposed to persons with respiratory complaints outside the household were also significantly more likely to visit their GP (OR(adj)=2.5). CONCLUSION: This study confirmed that heterogeneity in the general population as well as in pathogens causing ARTI makes it complicated to detect associations between potential risk factors and respiratory infections. Whereas it may be difficult to intervene on the risk posed by exposure to persons with respiratory complaints, transmission of ARTI in the general population might be reduced by improved hygienic conditions.


id: cord-329256-7njgmdd1
title: Modeling the variations in pediatric respiratory syncytial virus seasonal epidemics
author: Leecaster, Molly
date: 2011-04-21
url: https://www.ncbi.nlm.nih.gov/pubmed/21510889/
doi: 10.1186/1471-2334-11-105
abstract:
  BACKGROUND: Seasonal respiratory syncytial virus (RSV) epidemics occur annually in temperate climates and result in significant pediatric morbidity and increased health care costs. Although RSV epidemics generally occur between October and April, the size and timing vary across epidemic seasons and are difficult to predict accurately. Prediction of epidemic characteristics would support management of resources and treatment. METHODS: The goals of this research were to examine the empirical relationships among early exponential growth rate, total epidemic size, and timing, and the utility of specific parameters in compartmental models of transmission in accounting for variation among seasonal RSV epidemic curves. RSV testing data from Primary Children's Medical Center were collected on children under two years of age (July 2001-June 2008). Simple linear regression was used explore the relationship between three epidemic characteristics (final epidemic size, days to peak, and epidemic length) and exponential growth calculated from four weeks of daily case data. A compartmental model of transmission was fit to the data and parameter estimated used to help describe the variation among seasonal RSV epidemic curves. RESULTS: The regression results indicated that exponential growth was correlated to epidemic characteristics. The transmission modeling results indicated that start time for the epidemic and the transmission parameter co-varied with the epidemic season. CONCLUSIONS: The conclusions were that exponential growth was somewhat empirically related to seasonal epidemic characteristics and that variation in epidemic start date as well as the transmission parameter over epidemic years could explain variation in seasonal epidemic size. These relationships are useful for public health, health care providers, and infectious disease researchers.


id: cord-330607-zn4urrxc
title: Differential diagnosis for suspected cases of coronavirus disease 2019: a retrospective study
author: Chi, Qiong
date: 2020-09-18
txt: ./txt/cord-330607-zn4urrxc.txt
cache: ./cache/cord-330607-zn4urrxc.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-020-05383-y
doi: 10.1186/s12879-020-05383-y
summary:
  METHODS: Sixty-eight cases of suspected COVID-19 treated in Wenzhou Central Hospital from January 21 to February 20, 2020 were divided into confirmed and COVID-19-negative groups based on the results of real-time reverse transcriptase polymerase chain reaction (RT-PCR) nucleic acid testing of the novel coronavirus in throat swab specimens to compare the clinical symptoms and laboratory and imaging results between the groups. More common chest imaging characteristics of the confirmed COVID-19 cases by high-resolution computed tomography (HRCT) included ground-glass opacities (GGOs), multiple patchy shadows, and consolidation with bilateral involvement than COVID-19-negative group (82.4% vs 31.4%, P = 0.0002; 41.2% vs 17.6% vs P = 0.048; 76.5% vs 43.1%, P = 0.017; respectively). CONCLUSIONS: WBC count inversely correlated with the severity of fever, GGOs, multiple patchy shadows, and consolidation in chest HRCT and clustered infection are common but not specific features in the confirmed COVID-19 group.

abstract:
  BACKGROUND: Since December 2019, the coronavirus disease 2019 (COVID-19) has infected more than 12,322,000 people and killed over 556,000 people worldwide. However, Differential diagnosis remains difficult for suspected cases of COVID-19 and need to be improved to reduce misdiagnosis. METHODS: Sixty-eight cases of suspected COVID-19 treated in Wenzhou Central Hospital from January 21 to February 20, 2020 were divided into confirmed and COVID-19-negative groups based on the results of real-time reverse transcriptase polymerase chain reaction (RT-PCR) nucleic acid testing of the novel coronavirus in throat swab specimens to compare the clinical symptoms and laboratory and imaging results between the groups. RESULTS: Among suspected patients, 17 were confirmed to COVID-19-positive group and 51 were distinguished to COVID-19-negative group. Patients with reduced white blood cell (WBC) count were more common in the COVID-19-positive group than in the COVID-19-negative group (29.4% vs 3.9%, P = 0.003). Subsequently, correlation analysis indicated that there was a significant inverse correlation existed between WBC count and temperature in the COVID-19-positive patients (r = − 0.587, P = 0.003), instead of the COVID-19-negative group. But reduced lymphocyte count was no different between the two groups (47.1% vs 25.5%, P = 0.096). More common chest imaging characteristics of the confirmed COVID-19 cases by high-resolution computed tomography (HRCT) included ground-glass opacities (GGOs), multiple patchy shadows, and consolidation with bilateral involvement than COVID-19-negative group (82.4% vs 31.4%, P = 0.0002; 41.2% vs 17.6% vs P = 0.048; 76.5% vs 43.1%, P = 0.017; respectively). The rate of clustered infection was higher in COVID-19-positive group than COVID-19-negative group (64.7% vs 7.8%, P = 0.001). Through multiplex PCR nucleic acid testing, 2 cases of influenza A, 3 cases of influenza B, 2 cases of adenovirus, 2 cases of Chlamydia pneumonia, and 7 cases of Mycoplasma pneumoniae were diagnosed in the COVID-19-negative group. CONCLUSIONS: WBC count inversely correlated with the severity of fever, GGOs, multiple patchy shadows, and consolidation in chest HRCT and clustered infection are common but not specific features in the confirmed COVID-19 group. Multiplex PCR nucleic acid testing helped differential diagnosis for suspected COVID-19 cases.


id: cord-333745-nwnt2tde
author: Wang, Yi
date: 2020-10-12
txt: ./txt/cord-333745-nwnt2tde.txt
cache: ./cache/cord-333745-nwnt2tde.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33046047/
doi: 10.1186/s12879-020-05468-8
summary:
  RESULTS: The study found that fibrinogen (FIB) was increased in 45 (65.2%) patients, and when FIB reached a critical value of 4.805 g/L, the sensitivity and specificity、DA, helping to distinguish general and severe cases, were 100 and 14%、92.9%, respectively, which were significantly better than those for lymphocyte count and myoglobin. In a comparison of patients in Group A with patients in Group B, the lymphocyte count absolute value (L), myoglobin (MB) and fibrinogen of COVID-19 pneumonia patients in Group A were significantly higher than those in Group B, with statistically significant differences (P ≤ 0.001) ( Table 4 ). Laboratory data showed that the WBC, N%, and CRP in Group B COVID-19 pneumonia patients were significantly higher than those of Group A patients, and the differences were statistically significant (P < 0.05).

title:
  Clinical characteristics and laboratory indicator analysis of 67 COVID-19 pneumonia patients in Suzhou, China

abstract:
  BACKGROUND: Sudden exacerbations and respiratory failure are major causes of death in patients with severe coronavirus disease 2019(COVID-19) pneumonia, but indicators for the prediction and treatment of severe patients are still lacking. METHODS: A retrospective analysis of 67 collected cases was conducted and included approximately 67 patients with COVID-19 pneumonia who were admitted to the Suzhou Fifth People’s Hospital from January 1, 2020 to February 8, 2020. The epidemiological, clinical and imaging characteristics as well as laboratory data of the 67 patients were analyzed. RESULTS: The study found that fibrinogen (FIB) was increased in 45 (65.2%) patients, and when FIB reached a critical value of 4.805 g/L, the sensitivity and specificity、DA, helping to distinguish general and severe cases, were 100 and 14%、92.9%, respectively, which were significantly better than those for lymphocyte count and myoglobin. Chest CT images indicated that the cumulative number of lung lobes with lesions in severe patients was significantly higher than that in general patients (P < 0.05), and the cumulative number of lung lobes with lesions was negatively correlated with lymphocyte count and positively correlated with myoglobin and FIB. Our study also found that there was no obvious effect of hormone therapy in patients with severe COVID-19. CONCLUSIONS: Based on the retrospective analysis, FIB was found to be increased in severe patients and was better than lymphocyte count and myoglobin in distinguishing general and severe patients. The study also suggested that hormone treatment has no significant effect on COVID-19.


id: cord-334424-z7ygy25e
author: McCaw, James M
date: 2012-12-11
txt: ./txt/cord-334424-z7ygy25e.txt
cache: ./cache/cord-334424-z7ygy25e.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/23231698/
doi: 10.1186/1471-2334-12-345
summary:
  Table 1 summarizes the descriptive statistics (and logistic model results) associated with presence or absence of transmission in the household for the 177 household ILI events in which the participant was the primary case. In correspondence with the logistic regression model for transmission, we include presence of children in the In a secondary analysis, we considered the influence of prior vaccination on the reported number of secondary household cases among participants testing positive for influenza compared with all other participants. This study, notable in its consideration of a broad range of respiratory pathogens in addition to influenza, demonstrates that household transmission of ILI is most strongly associated with host and demographic factors: female sex and the presence of children within the household (Tables 1 and 2) .

title:
  Household transmission of respiratory viruses – assessment of viral, individual and household characteristics in a population study of healthy Australian adults

abstract:
  BACKGROUND: Household transmission of influenza-like illness (ILI) may vary with viral and demographic characteristics. We examined the effect of these factors in a population-based sample of adults with ILI. METHODS: We conducted a prospective cohort study in community-dwelling Australian adults nested within an influenza vaccine effectiveness trial. On presentation with ILI, participants were swabbed for a range of respiratory viruses and asked to return a questionnaire collecting details of household members with or without similar symptoms. We used logistic and Poisson regression to assess the key characteristics of household transmission. RESULTS: 258 participants from multi-occupancy households experienced 279 ILI episodes and returned a questionnaire. Of these, 183 were the primary case in the household allowing assessment of factors associated with transmission. Transmission was significantly associated in univariate analyses with female sex (27% vs. 13%, risk ratio (RR) = 2.13 (1.08, 4.21)) and the presence of a child in the house (33% vs. 17%, RR = 1.90 (1.11, 3.26)). The secondary household attack proportion (SHAP) was 0.14, higher if influenza was isolated (RR = 2.1 (1.0, 4.5)). Vaccinated participants who nonetheless became infected with influenza had a higher SHAP (Incidence RR = 5.24 (2.17, 12.6)). CONCLUSIONS: The increased SHAP in households of vaccinated participants who nonetheless had confirmed influenza infection supports the hypothesis that in years of vaccine mismatch, not only is influenza vaccine less protective for the vaccine recipient, but that the population’s immunity is also lower.


id: cord-334746-anqvdi2k
author: Fischer, Doris
date: 2019-04-29
txt: ./txt/cord-334746-anqvdi2k.txt
cache: ./cache/cord-334746-anqvdi2k.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-019-3981-8
doi: 10.1186/s12879-019-3981-8
summary:
  BACKGROUND: Overcrowding, reduced nurse to patient ratio, limited distance between incubators and absence of microbiological surveillance have been shown to promote spread of multidrug-resistant gram-negative organisms (MDRGN) in patients with birthweight < 1500 g. Care of MDRGN colonized patient was provided by staff wearing gloves and gowns according to the current recommendations by the Commission for Hospital Hygiene and Infection Prevention of the Robert Koch Institute, Berlin, Germany (KRINKO) [29] . In this study, we implemented the available recommendations concerning neonatal MDRGN transmission into the daily life settings on NIMCU in the scenario of a short-term and high risk overcrowding period. We therefore assume our management consisting of active surveillance, staff training as well as adherence to infection control demands has proven to be a successful procedure to escort through overcrowding period and prevent the spread of multidrug-resistant organisms in hospital setting.

title:
  Overcrowding in a neonatal intermediate care unit: impact on the incidence of multidrug-resistant gram-negative organisms

abstract:
  BACKGROUND: Overcrowding, reduced nurse to patient ratio, limited distance between incubators and absence of microbiological surveillance have been shown to promote spread of multidrug-resistant gram-negative organisms (MDRGN) in patients with birthweight < 1500 g. Patients > 1500 g treated on an intermediate care unit are unrepresented in recent literature. We therefore intended to present data obtained from a short-term overcrowded neonatal intermediate care unit (NIMCU) at a level III (international categorization) perinatal center at University Hospital Frankfurt, Germany. METHODS: During a 25 day overcrowding (OV) and 28 day post-overcrowding period (POST-OV) on NIMCU, epidemiological data obtained from continuously hold microbiological surveillance were investigated and compared to the last 12 months of ward-regular bed occupancy preceding OV (PRAE-OV). RESULTS: During OV, the number of patients simultaneously treated at the NIMCU increased from 18 to 22, resulting in a reduced bed-to-bed space. Nurse: patient ratio was 4:22 during OV compared to 3:18 during PRAE-OV. Cumulative incidence of MDRGN was 4.7% in OV and 2.4% POST-OV compared to 4.8% to PRAE-OV, respectively, without any significant variations. During OV and POST-OV, septic episodes due to MDRGN were not observed. In one case, potential nosocomial transmission of Enterobacter cloacae resistant to Piperacillin and 3rd/4th generation cephalosporins was observed. CONCLUSIONS: Prevention of nosocomial spread of MDRGN in an overcrowded NIMCU is based on staff’s diligent training and adequate staffing. Concise microbiological surveillance should be guaranteed to escort through overcrowding periods. In our setting, impact of bed-to-bed distance on MDRGN transmission seemed to be less strong.


id: cord-336663-fawcn6em
author: Liu, Chunyan
date: 2015-10-01
txt: ./txt/cord-336663-fawcn6em.txt
cache: ./cache/cord-336663-fawcn6em.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26429778/
doi: 10.1186/s12879-015-1126-2
summary:
  Here, HAdV types are characterized in children in the Beijing area with acute lower respiratory tract infections (ALRTIs) and the clinical features and laboratory findings of hospitalized HAdV-infected cases are described. However, because most clinical laboratories do not type the isolates, there is little published information about epidemiologic and clinical features of HAdV infections by type in children with ALRTIs. To identify HAdV types and species in children with ALRTIs in Beijing area and to characterize clinical features and laboratory findings of hospitalized HAdVinfected cases, respiratory specimens were collected from hospital-admitted pediatric patients with ALRTIs and typed HAdV positive samples using PCR and sequencing. This may also suggest that schoolage children are exposed to the most common endemic types of HAdV early in life, thereby establishing a protective immunity resulting only in mild clinical symptoms, such that upper respiratory tract infection does not require care in an emergency department or hospital in this age group.

title:
  Adenovirus infection in children with acute lower respiratory tract infections in Beijing, China, 2007 to 2012

abstract:
  BACKGROUND: Human adenoviruses (HAdV) play a significant role in pediatric respiratory tract infections. To date, over 60 types of HAdV have been identified. Here, HAdV types are characterized in children in the Beijing area with acute lower respiratory tract infections (ALRTIs) and the clinical features and laboratory findings of hospitalized HAdV-infected cases are described. METHODS: Respiratory specimens were collected from pediatric patients with ALRTIs in the emergency department or from those admitted to Beijing Children’s Hospital between March 2007 and December 2012. Infections with common respiratory viruses were determined by PCR or RT-PCR. HAdV positive samples were further typed by PCR and sequencing. RESULTS: Among 3356 patients with ALRTIs, 194 (5.8 %) were found to have HAdV infection. HAdV infection was primarily confined to children (88.35 %) less than 5 years of age. A total of 11 different types of HAdV were detected throughout the study period, with HAdV-B7 (49.0 %) and HAdV-B3 (26.3 %) as the most prevalent types, followed by HAdV-C2 (7.7 %) and HAdVC1 (4.6 %). Newly emerging and re-emergent types or variants, HAdV-B55 (n = 5), HAdV-C57 (n = 3), and HAdV-B14p1 (n = 1), were identified. Results also included the reported first case of co-infection with HAdV-C2 and HAdV-C57. Clinical entities of patients with single HAdV infection (n = 49) were similar to those with mixed HAdV/respiratory syncytial virus (RSV) infections (n = 41). Patients with HAdV-B7 infection had longer duration of fever and higher serum levels of muscle enzymes than HAdV-B3-infected patients. CONCLUSIONS: During the study period, HAdV-B7 and HAdV-B3 were the predominant types identified in pediatric ALRTIs. HAdV-B7 infection tends to have more severe clinical consequences. The presence of newly emerging types or variants and co-infection with different types of HAdV highlights the need for constant and close surveillance of HAdV infection.


id: cord-336975-28mtmw2z
author: Sadeghi, Christine D
date: 2011-02-07
txt: ./txt/cord-336975-28mtmw2z.txt
cache: ./cache/cord-336975-28mtmw2z.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/21299840/
doi: 10.1186/1471-2334-11-41
summary:
  PCR-based studies have suggested the important role of respiratory picornaviruses (rhinovirus and enterovirus) as a leading cause of lower respiratory tract infections in children [5] , in particular wheezing illnesses such as bronchiolitis [6, 7] , wheezy bronchitis [8] and asthma exacerbations [9] , but also pneumonia [2] . In addition, PCR has allowed for the detection of new respiratory viruses, such as hMPV [10] , which has been implicated in upper and lower respiratory tract infections in children [11] [12] [13] . A significant proportion of asymptomatic children test positive by PCR to respiratory viruses [14] [15] [16] , and picornavirus RNA can be detected by PCR up to 5 weeks after an acute infection [17] . In order to determine the value of DFA in conducting epidemiological studies on respiratory viruses now that assays for respiratory picornaviruses and hMPV are available, we retrospectively analysed the results of 12 years of DFA screening of viral pathogens in hospitalized children with respiratory disease.

title:
  Twelve years'' detection of respiratory viruses by immunofluorescence in hospitalised children: impact of the introduction of a new respiratory picornavirus assay

abstract:
  BACKGROUND: Direct immunofluorescence assays (DFA) are a rapid and inexpensive method for the detection of respiratory viruses and may therefore be used for surveillance. Few epidemiological studies have been published based solely on DFA and none included respiratory picornaviruses and human metapneumovirus (hMPV). We wished to evaluate the use of DFA for epidemiological studies with a long-term observation of respiratory viruses that includes both respiratory picornaviruses and hMPV. METHODS: Since 1998 all children hospitalized with respiratory illness at the University Hospital Bern have been screened with DFA for common respiratory viruses including adenovirus, respiratory syncytial virus (RSV), influenza A and B, and parainfluenza virus 1-3. In 2006 assays for respiratory picornaviruses and hMPV were added. Here we describe the epidemiological pattern for these respiratory viruses detected by DFA in 10'629 nasopharyngeal aspirates collected from 8'285 patients during a 12-year period (1998-2010). RESULTS: Addition of assays for respiratory picornaviruses and hMPV raised the proportion of positive DFA results from 35% to 58% (p < 0.0001). Respiratory picornaviruses were the most common viruses detected among patients ≥1 year old. The seasonal patterns and age distribution for the studied viruses agreed well with those reported in the literature. In 2010, an hMPV epidemic of unexpected size was observed. CONCLUSIONS: DFA is a valid, rapid, flexible and inexpensive method. The addition of assays for respiratory picornaviruses and hMPV broadens its range of viral detection. DFA is, even in the "PCR era", a particularly adapted method for the long term surveillance of respiratory viruses in a pediatric population.


id: cord-337028-8fh4pe3i
author: Reyes, Leticia
date: 2009-01-26
url: https://doi.org/10.1186/1471-2334-9-9
doi: 10.1186/1471-2334-9-9
title:
  Different inflammatory responses are associated with Ureaplasma parvum-induced UTI and urolith formation

abstract:
  BACKGROUND: Epidemiologic studies show a strong association between Ureaplasmas and urogenital tract disease in humans. Since healthy humans can be colonized with Ureaplasmas, its role as a pathogen remains controversial. In order to begin to define the role of the host in disease, we developed a rodent model of urinary tract infection (UTI) using Fischer 344 (F344) rats. Animals were inoculated with sterile broth, 10(1), 10(3), 10(5), 10(7), or 10(9 )log CFU of a rat-adapted strain of Ureaplasma parvum. RESULTS: Infected animals exhibited two distinct profiles, asymptomatic UTI and UTI complicated with struvite urolithiasis. Inoculum dose of U. parvum affected the incidence of UTI, and 50% to 57% of animals inoculated with ≥ 10(7 )CFU of U. parvum remained infected (p < 0.04). However, inoculum dose did not influence immune response to U. parvum. Asymptomatic UTI was characterized by a minimal immune response that was predominantly monocytic and lymphocytic, with limited lesions, and elevated urinary levels of IFN-γ, IL-18 and MCP-1 (P ≤ 0.02). UTI complicated with struvite formation was characterized by an exaggerated immune response that was mostly neutrophilic (P ≤ 0.0001), with lesions that showed extensive uroepithelial hyperplasia (P ≤ 0.0001), and a predominance of IL-1α, IL-1β, and GRO/KC in the urine (P ≤ 0.02). Animals with asymptomatic UTI also had a significantly high rate of kidney infection (P ≤ 0.0005). CONCLUSION: Complications associated with U. parvum infection are primarily dependent upon host-specific factors rather than Ureaplasma microbial load. The immune response in F344 rats is similar to that which occurs in humans with ureaplasmal associated disease. Therefore, this model of infection is a useful tool for elucidating U. parvum-host interactions that confer UTI and disease.


id: cord-338054-n2r4pzan
author: Lau, Joseph TF
date: 2007-03-15
txt: ./txt/cord-338054-n2r4pzan.txt
cache: ./cache/cord-338054-n2r4pzan.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17359545/
doi: 10.1186/1471-2334-7-18
summary:
  Respondents were asked how likely they would be to adopt the following preventive behaviors if a local human-to-human H5N1 outbreak (defined as "if 2-3 new human-to-human transmission of H5N1 cases were to be reported in Hong Kong") were to occur: face mask use in public venues, increased frequency of handwashing, avoidance of eating poultry, declaration of influenzalike illness (ILI) symptoms at border health checkpoints, the seeking of medical consultation immediately with the onset of a fever, face mask use in public venues when having ILI symptoms and compliance with any quarantine policies. Respondents were asked about perceptions related to human-to-human H5N1 transmission, including perceived modes of transmission (whether human-to-human transmission of the H5N1 virus could occur via respiratory droplets, bodily contact, contaminated objects, eating well-cooked poultry), perceived susceptibility to H5N1 in different groups of people (self, family members, children, adults, older people, health care workers, food handlers, food vendors and the general public), perceived chance of having a major outbreak in Hong Kong in the next 12 months and perceived efficacy of various prevention measures (quarantine of infected people, face mask use in public venues, frequent handwashing, home disinfection, mass extermination of poultry).

title:
  Anticipated and current preventive behaviors in response to an anticipated human-to-human H5N1 epidemic in the Hong Kong Chinese general population

abstract:
  BACKGROUND: The prevalence of self-reported preventive behaviors in response to an anticipated local human-to-human H5N1 transmission outbreak and factors associated with such behaviors have not been examined. METHODS: A random, anonymous, cross-sectional telephone survey of 503 Hong Kong Chinese adults. RESULTS: The public in Hong Kong is likely to adopt self-protective behaviors (e.g., wearing face mask in public venues (73.8%), increasing the frequency of handwashing (86.7%)) and behaviors that protect others (e.g., wearing face masks when experiencing influenza-like illness (ILI, 92.4%), immediately seeking medical consultation (94.2%), making declarations when crossing the border with ILI (87.1%), complying to quarantine policies (88.3%)). Multivariate analyses indicated that factors related to age, full-time employment, perceived susceptibility, perceived efficacy of preventive measures, perceived higher fatality as compared to SARS, perceived chance of a major local outbreak, and being worried about self/family members contracting the virus were significantly associated with the inclination to adopt self-protective measures. Similar analyses showed that education level, variables related to perceived efficacy, perceived major local outbreak and such were significantly associated with various behaviors directed towards protecting others. CONCLUSION: In the event of a human-to-human H5N1 outbreak, the public in Hong Kong is likely to adopt preventive measures that may help contain the spread of the virus in the community.


id: cord-341347-nzptmdbe
author: Neske, Florian
date: 2010-07-20
url: https://www.ncbi.nlm.nih.gov/pubmed/20646318/
doi: 10.1186/1471-2334-10-215
title:
  High prevalence of antibodies against polyomavirus WU, polyomavirus KI, and human bocavirus in German blood donors

abstract:
  BACKGROUND: DNA of the polyomaviruses WU (WUPyV) and KI (KIPyV) and of human bocavirus (HBoV) has been detected with varying frequency in respiratory tract samples of children. However, only little is known about the humoral immune response against these viruses. Our aim was to establish virus-specific serological assays and to determine the prevalence of immunoglobulin G (IgG) against these three viruses in the general population. METHODS: The capsid proteins VP1 of WUPyV and KIPyV and VP2 of HBoV were cloned into baculovirus vectors and expressed in Sf9 insect cells. IgG antibodies against WUPyV VP1, KIPyV VP1, and HBoV VP2 were determined by immunofluorescence assays in 100 plasma samples of blood donors. RESULTS: The median age of the blood donors was 31 years (range 20 - 66 yrs), 52% were male. 89% of the samples were positive for WUPyV IgG (median age 31 yrs, 49.4% male), 67% were positive for KIPyV IgG (median age 32 yrs, 46.3% male), and 76% were positive for HBoV IgG (median age 32 yrs, 51.3% male). For WUPyV and HBoV, there were no significant differences of the seropositivity rates with respect to age groups or gender. For KIPyV, the seropositivity rate increased significantly from 59% in the age group 20 - 29 years to 100% in the age group > 50 years. CONCLUSIONS: High prevalences of antibodies against WUPyV, KIPyV, and HBoV were found in plasma samples of healthy adults. The results indicate that primary infection with these viruses occurs during childhood or youth. For KIPyV, the seropositivity appears to increase further during adulthood.


id: cord-341818-mm3d4jkh
title: COVID-19 with acute cholecystitis: a case report
author: Ying, Mingliang
date: 2020-06-22
txt: ./txt/cord-341818-mm3d4jkh.txt
cache: ./cache/cord-341818-mm3d4jkh.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-020-05164-7
doi: 10.1186/s12879-020-05164-7
summary:
  CASE PRESENTATION: A case of 68-year-old female with COVID-19 pneumonia who had constant pain in the right upper quadrant of her abdomen during her hospitalization that was finally diagnosed as acute cholecystitis. Ultrasound-guided percutaneous transhepatic gallbladder drainage (PTGD) was performed, and the real-time fluorescence polymerase chain reaction (RT-PCR) COVID-19 nucleic acid assay of the bile was found to be negative. Here, we report a confirmed case of a female with COVID-19 pneumonia who had constant pain in the right upper quadrant of her abdomen during her hospitalization that finally diagnosed as acute cholecystitis. At first, the patient did not show any abdominal symptoms except diarrhea; however, she developed constant pain in the right upper quadrant of her abdomen and Murphy''s sign after 10 days of hospitalization, and her body temperature was elevated to 38.3°C (100.9°F).

abstract:
  BACKGROUND: The 2019 novel coronavirus (COVID-19) presents a major threat to public health and has rapidly spread worldwide since the outbreak in Wuhan, Hubei Province, China in 2019. To date, there have been few reports of the varying degrees of illness caused by the COVID-19. CASE PRESENTATION: A case of 68-year-old female with COVID-19 pneumonia who had constant pain in the right upper quadrant of her abdomen during her hospitalization that was finally diagnosed as acute cholecystitis. Ultrasound-guided percutaneous transhepatic gallbladder drainage (PTGD) was performed, and the real-time fluorescence polymerase chain reaction (RT-PCR) COVID-19 nucleic acid assay of the bile was found to be negative. PTGD, antibacterial and anti-virus combined with interferon inhalation treatment were successful. CONCLUSION: The time course of chest CT findings is typical for COVID-19 pneumonia. PTGD is useful for acute cholecystitis in COVID-19 patients. Acute cholecystitis is likely to be caused by COVID-19 .


id: cord-342210-r8vxz5vu
author: Mukherjee, Pranab K.
date: 2017-01-14
txt: ./txt/cord-342210-r8vxz5vu.txt
cache: ./cache/cord-342210-r8vxz5vu.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-016-2177-8
doi: 10.1186/s12879-016-2177-8
summary:
  We conducted a randomized, double-blinded, placebo-controlled pilot clinical trial to evaluate the safety and efficacy of ARMS-I™ (currently marketed as Halo™) in the prevention of URIs. METHODS: ARMS-I is patented novel formulation for the prevention and treatment of influenza, comprising a broad-spectrum antimicrobial agent (cetylpyridinium chloride, CPC) and components (glycerin and xanthan gum) that form a barrier on the host mucosa, thus preventing viral contact and invasion. The primary objectives were to establish whether ARMS-I decreased the frequency, severity or duration of URIs. Secondary objectives were to evaluate safety, tolerability, rate of virus detection, acceptability and adherence; effect on URI-associated absenteeism and medical visits; and effect of prior influenza vaccination on study outcomes. In the current study, we evaluated the safety and effectiveness of ARMS-I, a novel intra-oral formulation in the prevention of URIs in a randomized, double-blind, placebo-controlled proof-of-concept clinical trial in healthy adults.

title:
  Randomized, double-blind, placebo-controlled clinical trial to assess the safety and effectiveness of a novel dual-action oral topical formulation against upper respiratory infections

abstract:
  BACKGROUND: Current prevention options for upper respiratory infections (URIs) are not optimal. We conducted a randomized, double-blinded, placebo-controlled pilot clinical trial to evaluate the safety and efficacy of ARMS-I™ (currently marketed as Halo™) in the prevention of URIs. METHODS: ARMS-I is patented novel formulation for the prevention and treatment of influenza, comprising a broad-spectrum antimicrobial agent (cetylpyridinium chloride, CPC) and components (glycerin and xanthan gum) that form a barrier on the host mucosa, thus preventing viral contact and invasion. Healthy adults (18–45 years of age) were randomized into ARMS-I or placebo group (50 subjects each). The drug was sprayed intra-orally (3× daily) for 75 days. The primary objectives were to establish whether ARMS-I decreased the frequency, severity or duration of URIs. Secondary objectives were to evaluate safety, tolerability, rate of virus detection, acceptability and adherence; effect on URI-associated absenteeism and medical visits; and effect of prior influenza vaccination on study outcomes. RESULTS: Of the 94 individuals who completed the study (placebo: n = 44, ARMS-I: n = 50), six presented with confirmed URI (placebo: 4, ARMS-I: 2), representing a 55% relative reduction, albeit this was statistically not significant). Influenza, coronavirus or rhinovirus were detected in three participants; all in the placebo group. Moreover, frequency of post-treatment exit visits was reduced by 55% in ARMS-I compared to the placebo group (N = 4 and 2, respectively). Fever was reported only in the placebo group. ARMS-I significantly reduced the frequency and severity of cough and sore throat, and duration of cough (P ≤ .019 for all comparisons). ARMS-I was safe, well tolerated, had high acceptability and high adherence to medication use. Medical visits occurred only in the placebo group while absenteeism did not differ between the two arms. Prior influenza vaccination had no effect on study outcome. CONCLUSIONS: This randomized proof-of-concept clinical trial demonstrated that ARMS-I tended to provide protection against URIs in the enrolled study participants, while reducing severity and duration of cough and sore throat. A clinical trial with a larger number of study participants is warranted. TRIAL REGISTRATION: ClinicalTrials.gov NCT02644135 (retrospectively registered). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-016-2177-8) contains supplementary material, which is available to authorized users.


id: cord-342250-x5bzrpcu
author: Faires, Meredith C
date: 2014-07-08
txt: ./txt/cord-342250-x5bzrpcu.txt
cache: ./cache/cord-342250-x5bzrpcu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25005247/
doi: 10.1186/1471-2334-14-375
summary:
  The objectives of this study were to investigate the utility of the temporal scan statistic for detecting MRSA clusters, validate clusters using molecular techniques and hospital records, and determine significant differences in the rate of MRSA cases using regression models. The objectives of this study were to investigate the utility of the temporal scan statistic for detecting MRSA clusters in a community hospital and to validate significant clusters using molecular techniques and hospital records concerning known MRSA outbreaks; and to determine if there were significant differences in the rate of MRSA infection and colonization cases by month, season, and year using regression models. Data pertaining to known MRSA outbreaks that occurred during the study period (e.g., start and end date, ward location, and number of patients involved) were collected from the hospital''s Infection Prevention and Control (IPC) department.

title:
  The use of the temporal scan statistic to detect methicillin-resistant Staphylococcus aureus clusters in a community hospital

abstract:
  BACKGROUND: In healthcare facilities, conventional surveillance techniques using rule-based guidelines may result in under- or over-reporting of methicillin-resistant Staphylococcus aureus (MRSA) outbreaks, as these guidelines are generally unvalidated. The objectives of this study were to investigate the utility of the temporal scan statistic for detecting MRSA clusters, validate clusters using molecular techniques and hospital records, and determine significant differences in the rate of MRSA cases using regression models. METHODS: Patients admitted to a community hospital between August 2006 and February 2011, and identified with MRSA > 48 hours following hospital admission, were included in this study. Between March 2010 and February 2011, MRSA specimens were obtained for spa typing. MRSA clusters were investigated using a retrospective temporal scan statistic. Tests were conducted on a monthly scale and significant clusters were compared to MRSA outbreaks identified by hospital personnel. Associations between the rate of MRSA cases and the variables year, month, and season were investigated using a negative binomial regression model. RESULTS: During the study period, 735 MRSA cases were identified and 167 MRSA isolates were spa typed. Nine different spa types were identified with spa type 2/t002 (88.6%) the most prevalent. The temporal scan statistic identified significant MRSA clusters at the hospital (n = 2), service (n = 16), and ward (n = 10) levels (P ≤ 0.05). Seven clusters were concordant with nine MRSA outbreaks identified by hospital staff. For the remaining clusters, seven events may have been equivalent to true outbreaks and six clusters demonstrated possible transmission events. The regression analysis indicated years 2009–2011, compared to 2006, and months March and April, compared to January, were associated with an increase in the rate of MRSA cases (P ≤ 0.05). CONCLUSIONS: The application of the temporal scan statistic identified several MRSA clusters that were not detected by hospital personnel. The identification of specific years and months with increased MRSA rates may be attributable to several hospital level factors including the presence of other pathogens. Within hospitals, the incorporation of the temporal scan statistic to standard surveillance techniques is a valuable tool for healthcare workers to evaluate surveillance strategies and aid in the identification of MRSA clusters.


id: cord-344770-aoi42xq4
author: Bialasiewicz, Seweryn
date: 2014-05-19
url: https://www.ncbi.nlm.nih.gov/pubmed/24885416/
doi: 10.1186/1471-2334-14-275
title:
  Detection of a divergent Parainfluenza 4 virus in an adult patient with influenza like illness using next-generation sequencing

abstract:
  BACKGROUND: Human Parainfluenza viruses are a common cause of both upper and lower respiratory tract infections, particularly in children. Of the four Parainfluenza virus serotypes, Parainfluenza 4 is least well characterised from both the clinical, epidemiological and genetic perspectives. METHODS: Flocked nose or throat swabs from a previous study investigating viral prevalence in community-based adults suffering from influenza like illness were used as the basis for this study. Samples in which no virus was detected using a 16 viral respiratory pathogen real-time PCR panel were barcoded and pyrosequenced using the Roche 454 GS FLX Titanium chemistry. The sequences were analysed using the VirusHunter bioinformatic pipeline. Sanger sequencing was used to complete the detected Parainfluenza 4 coding region. RESULTS: A variant Parainfluenza 4 subtype b strain (QLD-01) was discovered in an otherwise healthy adult who presented with influenza like illness. Strain QLD-01 shared genomic similarities with both a and b subtypes. The extent of divergence of this genome from the 5 available whole Parainfluenza 4 genomes impacted the predicted binding efficiencies of the majority of published Parainfluenza 4 PCR assays. CONCLUSIONS: These findings further support a possible role for Parainfluenza 4 in the aetiology of adult respiratory disease within the community setting, and highlight the caution needed to be used in designing PCR assays from limited sequence information or in using proprietary commercial PCR assays.


id: cord-345046-str19r9a
author: Al Ghamdi, Mohammed
date: 2016-04-21
url: https://www.ncbi.nlm.nih.gov/pubmed/27097824/
doi: 10.1186/s12879-016-1492-4
title:
  Treatment outcomes for patients with Middle Eastern Respiratory Syndrome Coronavirus (MERS CoV) infection at a coronavirus referral center in the Kingdom of Saudi Arabia

abstract:
  BACKGROUND: Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV) is a poorly understood disease with no known treatments. We describe the clinical features and treatment outcomes of patients with laboratory confirmed MERS-CoV at a regional referral center in the Kingdom of Saudi Arabia. METHODS: In 2014, a retrospective chart review was performed on patients with a laboratory confirmed diagnosis of MERS-CoV to determine clinical and treatment characteristics associated with death. Confounding was evaluated and a multivariate logistic regression was performed to assess the independent effect of treatments administered. RESULTS: Fifty-one patients had an overall mortality of 37 %. Most patients were male (78 %) with a mean age of 54 years. Almost a quarter of the patients were healthcare workers (23.5 %) and 41 % had a known exposure to another person with MERS-CoV. Survival was associated with male gender, working as a healthcare worker, history of hypertension, vomiting on admission, elevated respiratory rate, abnormal lung exam, elevated alanine transaminase (ALT), clearance of MERS-CoV on repeat PCR polymerase chain reaction (PCR) testing, and mycophenolate mofetil treatment. Survival was reduced in the presence of coronary artery disease, hypotension, hypoxemia, CXR (chest X-ray) abnormalities, leukocytosis, creatinine >1 · 5 mg/dL, thrombocytopenia, anemia, and renal failure. In a multivariate analysis of treatments administered, severity of illness was the greatest predictor of reduced survival. CONCLUSIONS: Care for patients with MERS-CoV remains a challenge. In this retrospective cohort, interferon beta and mycophenolate mofetil treatment were predictors of increased survival in the univariate analysis. Severity of illness was the greatest predictor of reduced survival in the multivariate analysis. Larger randomized trials are needed to better evaluate the efficacy of these treatment regimens for MERS-CoV.


id: cord-345854-f0dq94j1
author: Chong, Wai Po
date: 2006-05-04
url: https://www.ncbi.nlm.nih.gov/pubmed/16672072/
doi: 10.1186/1471-2334-6-82
title:
  The interferon gamma gene polymorphism +874 A/T is associated with severe acute respiratory syndrome

abstract:
  BACKGROUND: Cytokines play important roles in antiviral action. We examined whether polymorphisms of IFN-γ,TNF-α and IL-10 affect the susceptibility to and outcome of severe acute respiratory syndrome (SARS). METHODS: A case-control study was carried out in 476 Chinese SARS patients and 449 healthy controls. We tested the polymorphisms of IFN-γ,TNF-α and IL-10 for their associations with SARS. RESULTS: IFN-γ +874A allele was associated with susceptibility to SARS in a dose-dependent manner (P < 0.001). Individuals with IFN-γ +874 AA and AT genotype had a 5.19-fold (95% Confidence Interval [CI], 2.78-9.68) and 2.57-fold (95% CI, 1.35-4.88) increased risk of developing SARS respectively. The polymorphisms of IL-10 and TNF-α were not associated with SARS susceptibility. CONCLUSION: IFN-γ +874A allele was shown to be a risk factor in SARS susceptibility.


id: cord-346669-7n75m669
author: Wang, Shixin
date: 2008-02-29
url: https://doi.org/10.1186/1471-2334-8-27
doi: 10.1186/1471-2334-8-27
title:
  Roles of TNF-α gene polymorphisms in the occurrence and progress of SARS-Cov infection: A case-control study

abstract:
  BACKGROUND: Host genetic factors may play a role in the occurrence and progress of SARS-Cov infection. This study was to investigate the relationship between tumor necrosis factor (TNF)-α gene polymorphisms with the occurrence of SARS-CoV infection and its role in prognosis of patients with lung interstitial fibrosis and femoral head osteonecrosis. METHODS: The association between genetic polymorphisms of TNF-α gene and susceptibility to severe acute respiratory syndromes (SARS) was conducted in a hospital-based case-control study including 75 SARS patients, 41 health care workers and 92 healthy controls. Relationships of TNF-α gene polymorphisms with interstitial lung fibrosis and femoral head osteonecrosis were carried out in two case-case studies in discharged SARS patients. PCR sequencing based typing (PCR-SBT) method was used to determine the polymorphisms of TNF-α gene in locus of the promoter region and univariate logistic analysis was conducted in analyzing the collected data. RESULTS: Compared to TT genotype, the CT genotype at the -204 locus was found associated with a protective effect on SARS with OR(95%CI) of 0.95(0.90–0.99). Also, TT genotype, CT and CC were found associated with a risk effect on femoral head necrosis with ORs(95%CI) of 5.33(1.39–20.45) and 5.67(2.74–11.71), respectively and the glucocorticoid adjusted OR of CT was 5.25(95%CI 1.18–23.46) and the combined (CT and CC) genotype OR was 6.0 (95%CI 1.60–22.55) at -1031 site of TNF-α gene. At the same time, the -863 AC genotype was manifested as another risk effect associated with femoral head necrosis with OR(95%CI) of 6.42(1.53–26.88) and the adjusted OR was 8.40(95%CI 1.76–40.02) in cured SARS patients compared to CC genotype. CONCLUSION: SNPs of TNF-α gene of promoter region may not associate with SARS-CoV infection. And these SNPs may not affect interstitial lung fibrosis in cured SARS patients. However, the -1031CT/CC and -863 AC genotypes may be risk factors of femoral head necrosis in discharged SARS patients.


id: cord-348802-3f8kmw31
author: Tang, Jialiang
date: 2019-01-07
txt: ./txt/cord-348802-3f8kmw31.txt
cache: ./cache/cord-348802-3f8kmw31.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30616564/
doi: 10.1186/s12879-018-3662-z
summary:
  title: Diversity of upper respiratory tract infections and prevalence of Streptococcus pneumoniae colonization among patients with fever and flu-like symptoms METHODS: We performed qualitative real-time PCR tests to detect common upper respiratory tract pathogens including 9 viruses and 3 bacteria in 1221 nasopharyngeal swabs from patients with fever and influenza-like symptoms in a Chinese city. Common upper respiratory tract pathogens other than Flu, such as human rhinovirus (hRV), respiratory syncytial virus (RSV), parainfluenza viruses (PIVs), adenovirus (ADV), human metapneumovirus (hMPV) and bacterial pathogens that are difficult to culture including Mycoplasma penumoniae, Chlamydophila pneumoniae and Bordetella pertussis are generally not tested in China, except for a few high-ranking academic medical centers (facts based on personal observations and communication with colleagues in China). pneumoniae colonization and its relationship with the pathogens causing URTIs may help solve the controversy over using antibiotic prophylaxis to prevent possible secondary lower respiratory tract infections (LRTIs) caused by S.

title:
  Diversity of upper respiratory tract infections and prevalence of Streptococcus pneumoniae colonization among patients with fever and flu-like symptoms

abstract:
  BACKGROUND: Many upper respiratory pathogens cause similar symptoms. In China, routine molecular tests for upper respiratory pathogens are not widely performed and antibiotics abuse in treating upper respiratory tract infections (URTIs) is a major public health concern. METHODS: We performed qualitative real-time PCR tests to detect common upper respiratory tract pathogens including 9 viruses and 3 bacteria in 1221 nasopharyngeal swabs from patients with fever and influenza-like symptoms in a Chinese city. A quantitative real-time PCR was also performed to measure the bacterial density of the colonizing Streptococcus pneumoniae in these samples. RESULTS: We found very diverse pathogens including 81.7% viruses, 11.6% bacteria and 6.7% mixed viruses and bacteria. S. pneumoniae colonization was found in 8.0% of the cases but most of them had low bacterial density (Mean = 3.9 log cfu/ml). We also discovered an increase of S. pneumoniae colonization frequency (but not the density) in patients with detectable upper respiratory tract pathogens, in a pathogen variety-dependent manner. CONCLUSIONS: Our study provided strong evidence against empiric antibiotic use for treating URTIs, and highlighted a strong need for improving the diagnostic capacity for URTIs by using more molecular testing in China.


id: cord-349238-qfvm883x
title: Risk factors for contracting watery diarrhoea in Kadoma City, Zimbabwe, 2011: a case control study
author: Maponga, Brian A
date: 2013-12-02
url: https://doi.org/10.1186/1471-2334-13-567
doi: 10.1186/1471-2334-13-567
abstract:
  BACKGROUND: Kadoma City experienced an increase in watery diarrhoea from 27 cases during week beginning 5(th) September, to 107 cases during week beginning 26(th) September 2011. The weekly diarrhoea cases crossed the threshold action line during week beginning 5(th) September at the children’s clinic in Rimuka Township, and the remaining four clinics reported cases crossing threshold action lines between week beginning 12(th) September and week beginning 26(th) September. Eighty-two percent of the cases were children less than 5 years old. We conducted a case controlstudy to determine risk factorsfor contracting watery diarrhoea in children less than 5 years in Kadoma City. METHODS: An unmatched 1:1 case control study was conducted in Ngezi and Rimuka townships in Kadoma City, Zimbabwe. A case was a child less than 5 years old, who developed acute watery diarrhoea between 5(th) September and 1(st) October 2011. A control was a child less than 5 years old who stayed in the same township and did not suffer from diarrhoea. A structured questionnaire was administered to caregivers of cases and controls.Laboratory water quality tests and stool test results were reviewed.Epi Info™ statistical software was used to analyse data. RESULTS: A total of 109 cases and 109 controls were enrolled. Independent protective factors were: having been exclusively breastfed for six months [AOR = 0.44; 95% CI (0.24-0.82)]; using municipal water [AOR = 0.38; 95% CI (0.18-0.80)]; using aqua tablets, [AOR = 0.49; 95% CI (0.26–0.94)] and; storing water in closed containers, [AOR = 0.24; 95% CI (0.07–0.0.83). The only independent risk factor for contracting watery diarrhoea was hand washing in a single bowl, [AOR = 2.89; 95% CI (1.33–6.28)]. Salmonella, Shigella, Rotavirus, and Enteropathogenic Escherichia coli were isolated in the stool specimens. None of the 33 municipal water samples tested showed contamination with Escherichia coli, whilst 23 of 44 (52%) shallow well water samples and 3 of 15(20%) borehole water samples tested were positive for Escherichia coli. CONCLUSIONS: The outbreak resulted from inadequate clean water and use of contaminated water. Evidence from this study was used to guide public health response to the outbreak.


id: cord-349905-jniqriu6
author: Xu, Xinyin
date: 2020-11-05
txt: ./txt/cord-349905-jniqriu6.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-020-05494-6
doi: 10.1186/s12879-020-05494-6
summary:
  METHODS: The number of confirmed cases, daily growth, incidence and length of time from the first reported case to the end of the local cases (i.e., non-overseas imported cases) were compared by spatial (geographical) and temporal classification and visualization of the development and changes of the epidemic situation by layers through maps. The time of the first confirmed case report in the 21 cities of Sichuan Province mainly came one week after the Wuhan lockdown (January 24-January 31) [17] . In the next four weeks after the Wuhan lockdown, 90% of the cities nationwide were affected, and the number of cases increased by a factor Fig. 3 Time distribution of the number of confirmed cases and counties with the first diagnosed cases in Sichuan Province (mainland cases). Data from various countries were from the WHO COVID-19 Daily Report published since January 21, 7, which also contained the confirmed information of the different provinces in China before the date of March 15.

title:
  Should we remain hopeful? The key 8 weeks: spatiotemporal epidemic characteristics of COVID-19 in Sichuan Province and its comparative analysis with other provinces in China and global epidemic trends

abstract:
  BACKGROUND: The COVID-19 spread worldwide quickly. Exploring the epidemiological characteristics could provide a basis for responding to imported cases abroad and to formulate prevention and control strategies in areas where COVID-19 is still spreading rapidly. METHODS: The number of confirmed cases, daily growth, incidence and length of time from the first reported case to the end of the local cases (i.e., non-overseas imported cases) were compared by spatial (geographical) and temporal classification and visualization of the development and changes of the epidemic situation by layers through maps. RESULTS: In the first wave, a total of 539 cases were reported in Sichuan, with an incidence rate of 0.6462/100,000. The closer to Hubei the population centres were, the more pronounced the epidemic was. The peak in Sichuan Province occurred in the second week. Eight weeks after the Wuhan lockdown, the health crisis had eased. The longest epidemic length at the city level in China (except Wuhan, Taiwan, and Hong Kong) was 53 days, with a median of 23 days. Spatial autocorrelation analysis of China showed positive spatial correlation (Moran’s Index > 0, p < 0.05). Most countries outside China began to experience a rapid rise in infection rates 4 weeks after their first case. Some European countries experienced that rise earlier than the USA. The pandemic in Germany, Spain, Italy, and China took 28, 29, 34, and 18 days, respectively, to reach the peak of daily infections, after their daily increase of up to 20 cases. During this time, countries in the African region and Southeast Asian region were at an early stage of infections, those in the Eastern Mediterranean region and region of the Americas were in a rapid growth phase. CONCLUSIONS: After the closure of the outbreak city, appropriate isolation and control measures in the next 8 weeks were key to control the outbreak, which reduced the peak value and length of the outbreak. Some countries with improved epidemic situations need to develop a continuous “local strategy at entry checkpoints” to to fend off imported COVID-19.


id: cord-350949-ystkjdwk
author: Gao, Yi-jie
date: 2020-08-03
txt: ./txt/cord-350949-ystkjdwk.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-020-05274-2
doi: 10.1186/s12879-020-05274-2
summary:
  The meta-analysis showed the following results: the incidence of severe case or death was 12, 95% CI: 0.03-0.20, I 2 = 0%, P = 0.006; the incidence of fever was 51, 95% CI: 0.35-0.67, I 2 = 89%, P < 0.00001; the incidence of cough was 31, 95% CI: 0.23-0.39, I 2 = 38%, P < 0.00001; the incidence of lymphopenia was 49, 95% CI: 0.29-0.70, I 2 = 83%, P < 0.00001; the incidence of positive CT findings was 71, 95% CI: 0.49-0.93, I 2 = 90%, P < 0.00001; the incidence of coexisting disorders was 33, 95% CI: 0.21-0.44, I 2 = 70%, P < 0.00001; the incidence of preterm labor was 23, 95% CI: 0.14-0.32, I 2 = 21%, P < 0.00001; the incidence of caesarean section was 65, 95% CI: 0.42-0.87, I 2 = 90%, P < 0.00001; the incidence of fetal distress was 29, 95% CI: 0.08-0.49, I 2 = 68%, P = 0.007; the incidence of neonatal asphyxia or neonatal death or stillbirth was 9, 95% CI: − 0.03-0.21, I 2 = 0%, P = 0.14; the incidence of neonatal infection was 12, 95% CI: − 0.01-0.26, I 2 = 0%, P = 0.06; and SARS-CoV-2 testing of breast milk was only mentioned in the study by Chen H (2020.2.12), and the incidence was 0, which cannot be calculated by metaanalysis.

title:
  Clinical features and outcomes of pregnant women with COVID-19: a systematic review and meta-analysis

abstract:
  BACKGROUND: The recent COVID-19 outbreak in Wuhan, China, has quickly spread throughout the world. In this study, we systematically reviewed the clinical features and outcomes of pregnant women with COVID-19. METHODS: PubMed, Web of Science, EMBASE and MEDLINE were searched from January 1, 2020, to April 16, 2020. Case reports and case series of pregnant women infected with SARS-CoV-2 were included. Two reviewers screened 366 studies and 14 studies were included. Four reviewers independently extracted the features from the studies. We used a random-effects model to analyse the incidence (P) and 95% confidence interval (95% CI). Heterogeneity was assessed using the I(2) statistic. RESULTS: The meta-analysis included 236 pregnant women with COVID-19. The results were as follows: positive CT findings (71%; 95% CI, 0.49–0.93), caesarean section (65%; 95% CI, 0.42–0.87), fever (51%; 95% CI, 0.35–0.67), lymphopenia (49%; 95% CI, 0.29–0.70), coexisting disorders (33%; 95% CI, 0.21–0.44), cough (31%; 95% CI, 0.23–0.39), fetal distress (29%; 95% CI, 0.08–0.49), preterm labor (23%; 95% CI, 0.14–0.32), and severe case or death (12%; 95% CI, 0.03–0.20). The subgroup analysis showed that compared with non-pregnant patients, pregnant women with COVID-19 had significantly lower incidences of fever (pregnant women, 51%; non-pregnant patients, 91%; P < 0.00001) and cough (pregnant women, 31%; non-pregnant patients, 67%; P < 0.0001). CONCLUSIONS: The incidences of fever, cough and positive CT findings in pregnant women with COVID-19 are less than those in the normal population with COVID-19, but the rate of preterm labor is higher among pregnant with COVID-19 than among normal pregnant women. There is currently no evidence that COVID-19 can spread through vertical transmission.


id: cord-351126-d6lfktf9
author: Kofman, Aaron D.
date: 2020-09-29
url: https://doi.org/10.1186/s12879-020-05439-z
doi: 10.1186/s12879-020-05439-z
title:
  A young adult with COVID-19 and multisystem inflammatory syndrome in children (MIS-C)-like illness: a case report

abstract:
  BACKGROUND: A healthy 25-year-old woman developed COVID-19 disease with clinical characteristics resembling Multisystem Inflammatory Syndrome in Children (MIS-C), a rare form of COVID-19 described primarily in children under 21 years of age. CASE PRESENTATION: The patient presented with 1 week of weakness, dyspnea, and low-grade fevers, followed by mild cough, sore throat, vomiting, diarrhea, and lymph node swelling. She was otherwise healthy, with no prior medical history. Her hospital course was notable for profound acute kidney injury, leukocytosis, hypotension, and cardiac dysfunction requiring ICU admission and vasopressor support. MIS-C-like illness secondary to COVID-19 was suspected due to physical exam findings of conjunctivitis, mucositis, and shock. She improved following IVIG, aspirin, and supportive care, and was discharged on hospital day 5. CONCLUSION: MIS-C-like illness should be considered in adults presenting with atypical clinical findings and concern for COVID-19. Further research is needed to support the role of IVIG and aspirin in this patient population.


id: cord-354690-ywb9krdp
author: Barr, Margo
date: 2008-09-15
url: https://www.ncbi.nlm.nih.gov/pubmed/18793441/
doi: 10.1186/1471-2334-8-117
title:
  Pandemic influenza in Australia: Using telephone surveys to measure perceptions of threat and willingness to comply

abstract:
  BACKGROUND: Baseline data is necessary for monitoring how a population perceives the threat of pandemic influenza, and perceives how it would behave in the event of pandemic influenza. Our aim was to develop a module of questions for use in telephone health surveys on perceptions of threat of pandemic influenza, and on preparedness to comply with specific public health behaviours in the event of pandemic influenza. METHODS: A module of questions was developed and field tested on 192 adults using the New South Wales Department of Health's in-house Computer Assisted Telephone Interviewing (CATI) facility. The questions were then modified and re field tested on 202 adults. The module was then incorporated into the New South Wales Population Health Survey in the first quarter of 2007. A representative sample of 2,081 adults completed the module. Their responses were weighted against the state population. RESULTS: The reliability of the questions was acceptable with kappa ranging between 0.25 and 0.51. Overall 14.9% of the state population thought pandemic influenza was very or extremely likely to occur; 45.5% were very or extremely concerned that they or their family would be affected by pandemic influenza if it occurred; and 23.8% had made some level of change to the way they live their life because of the possibility of pandemic influenza. In the event of pandemic influenza, the majority of the population were willing to: be vaccinated (75.4%), be isolated (70.2%), and wear a face mask (59.9%). People with higher levels of threat perception are significantly more likely to be willing to comply with specific public health behaviours. CONCLUSION: While only 14.9% of the state population thought pandemic influenza was very or extremely likely to occur, a significantly higher proportion were concerned for self and family should a pandemic actually occur. The baseline data collected in this survey will be useful for monitoring changes over time in the population's perceptions of threat, and preparedness to comply with specific public health behaviours.


id: cord-354827-ipg1vwmv
title: Searching for the elusive typhoid diagnostic
author: Baker, Stephen
date: 2010-03-05
txt: ./txt/cord-354827-ipg1vwmv.txt
cache: ./cache/cord-354827-ipg1vwmv.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/20205702/
doi: 10.1186/1471-2334-10-45
summary:
  Typhoid (enteric) fever is still a common disease in many developing countries but current diagnostic tests are inadequate. Enteric fever is an all encompassing term for the disease caused by several serovars of Salmonella enterica including (S.) Typhi and (S.)Paratyphi A. An additional caveat for an effective and appropriate diagnostic test is the cross section of organisms that can cause a disease syndrome that is, clinically, indistinguishable from typhoid fever. Transcriptional analysis of RNA extracted from the blood of typhoid patients could be performed to identify specific genes, pathways, interactions or transcriptional regulatory hubs that are activated in the host during infection. Quantitative detection of Salmonella enterica serovar Typhi from blood of suspected typhoid fever patients by real-time PCR Enzyme-linked immunosorbent assay for detection of Salmonella typhi Vi antigen in urine from typhoid patients Rapid diagnosis of typhoid fever by enzyme-linked immunosorbent assay detection of Salmonella serotype typhi antigens in urine

abstract:
  Typhoid (enteric) fever is still a common disease in many developing countries but current diagnostic tests are inadequate. Studies on pathogenesis and genomics have provided new insight into the organisms that cause enteric fever. Better understanding of the microorganisms explains, in part, why our current typhoid methodologies are limited in their diagnostic information and why developing new strategies may be a considerable challenge. Here we discuss the current position of typhoid diagnostics, highlight the need for technological improvements and suggest potential ways of advancing this area.


id: cord-355309-nr8fwc8q
title: A super-spreading ewe infects hundreds with Q fever at a farmers'' market in Germany
author: Porten, Klaudia
date: 2006-10-06
txt: ./txt/cord-355309-nr8fwc8q.txt
cache: ./cache/cord-355309-nr8fwc8q.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17026751/
doi: 10.1186/1471-2334-6-147
summary:
  To investigate risk factors for infection we conducted a case control study (cases were Q fever patients, controls were randomly selected Soest citizens) and a cohort study among vendors at the market. To determine the outbreak size we therefore asked local public health departments in Germany to ascertain a possible link to the farmers'' market in Soest for all patients notified with Q-fever. To obtain an independent, second estimate of the proportion of hospitalizations among symptomatic patients beyond that reported through the statutory surveillance system we calculated the proportion of hospitalized patients among those persons fulfilling the clinical case definition (as used in the vendors'' study (s.b.)) identified through random sampling of the Soest population (within CCS2 (s.b.)) as well as in two cohorts (vendors'' study and the 9 sailor friends (see below)).

abstract:
  BACKGROUND: In May 2003 the Soest County Health Department was informed of an unusually large number of patients hospitalized with atypical pneumonia. METHODS: In exploratory interviews patients mentioned having visited a farmers' market where a sheep had lambed. Serologic testing confirmed the diagnosis of Q fever. We asked local health departments in Germany to identiy notified Q fever patients who had visited the farmers market. To investigate risk factors for infection we conducted a case control study (cases were Q fever patients, controls were randomly selected Soest citizens) and a cohort study among vendors at the market. The sheep exhibited at the market, the herd from which it originated as well as sheep from herds held in the vicinity of Soest were tested for Coxiella burnetii (C. burnetii). RESULTS: A total of 299 reported Q fever cases was linked to this outbreak. The mean incubation period was 21 days, with an interquartile range of 16–24 days. The case control study identified close proximity to and stopping for at least a few seconds at the sheep's pen as significant risk factors. Vendors within approximately 6 meters of the sheep's pen were at increased risk for disease compared to those located farther away. Wind played no significant role. The clinical attack rate of adults and children was estimated as 20% and 3%, respectively, 25% of cases were hospitalized. The ewe that had lambed as well as 25% of its herd tested positive for C. burnetii antibodies. CONCLUSION: Due to its size and point source nature this outbreak permitted assessment of fundamental, but seldom studied epidemiological parameters. As a consequence of this outbreak, it was recommended that pregnant sheep not be displayed in public during the 3(rd )trimester and to test animals in petting zoos regularly for C. burnetii.


id: cord-356349-ey5vnddu
author: Fusco, Francesco M
date: 2012-01-28
txt: ./txt/cord-356349-ey5vnddu.txt
cache: ./cache/cord-356349-ey5vnddu.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-12-27
doi: 10.1186/1471-2334-12-27
summary:
  METHODS: The EuroNHID (European Network for Highly Infectious Diseases) project collected data from 41 EDs and MADs in 14 European countries, located in the same facility as a national/regional referral centre for HIDs, using specifically developed checklists, during on-site visits from February to November 2009. CONCLUSIONS: Preparedness level for the safe and appropriate management of HIDs is partially adequate in the surveyed EDs and MADs. Emergency Departments (EDs) and Medical Admission Departments (MADs) are high-risk areas for disease transmission in hospitals, since they are often overcrowded, and potentially infectious patients and susceptible individuals may wait in close proximity for several hours. The Figure 1 shows the level of adequacy of infection control in the surveyed EDs and MADs. The project explored the availability of triage staff specifically trained for the early recognition of suspected HID patients, or alternatively the existence of other procedures for the early identification of these patients, such as a syndromic approach.

title:
  Infection control management of patients with suspected highly infectious diseases in emergency departments: data from a survey in 41 facilities in 14 European countries

abstract:
  BACKGROUND: In Emergency and Medical Admission Departments (EDs and MADs), prompt recognition and appropriate infection control management of patients with Highly Infectious Diseases (HIDs, e.g. Viral Hemorrhagic Fevers and SARS) are fundamental for avoiding nosocomial outbreaks. METHODS: The EuroNHID (European Network for Highly Infectious Diseases) project collected data from 41 EDs and MADs in 14 European countries, located in the same facility as a national/regional referral centre for HIDs, using specifically developed checklists, during on-site visits from February to November 2009. RESULTS: Isolation rooms were available in 34 facilities (82,9%): these rooms had anteroom in 19, dedicated entrance in 15, negative pressure in 17, and HEPA filtration of exhausting air in 12. Only 6 centres (14,6%) had isolation rooms with all characteristics. Personnel trained for the recognition of HIDs was available in 24 facilities; management protocols for HIDs were available in 35. CONCLUSIONS: Preparedness level for the safe and appropriate management of HIDs is partially adequate in the surveyed EDs and MADs.


