cord-000364-ikq38rm1	2011	Lung computer tomography (CT) on admission revealed pronounced diffuse bilateral interstitial infiltrates with pulmonary oedema, dependant atelectasis, and moderate pleural effusions (Fig. 1 ) which were later drained (>800 ml). Hantavirus infection was verified with the detection of PUUV RNA in plasma (630,000 copies/ml) on the day of admission, while IgM and IgG were negative. Consecutive plasma samples were analysed for PUUV RNA with declining viral copy numbers until negative 16 days post onset of Fig. 1 Chest CT-scans of two European patients with hantavirus pulmonary syndrome. Concerning the cases of European hantavirus infection in our present report, there was only mild or no renal impairment at the time of admission, whereas the respiratory involvement was early and severe, consistent with acute respiratory distress syndrome (ARDS), fulfilling criteria of HPS according to CDC case definition [19] .
cord-004967-4523cwwi	2013	This study is to evaluate the efficacy of bacteria killing nanotechnology Bio-Kil on reducing bacterial counts in an intensive care unit (ICU). In this study, we analyzed whether Bio-Kil when applied to different materials in the ICU, such as sheets, bedding, and clothing, desktops and the surfaces of instruments and equipment, reduces or eliminates bacteria in the environment, on the surfaces of surrounding items, and in the air. Routine textile washing and replacement as well as infection control practices for nurses, physicians, visitors, and disinfection of environments and instruments in these two rooms were performed according to hospital regulations. Bacterial culture results for patients admitted to the rooms during the study period Bacteria grown from textiles, the environment, and air samples were not identified to the species level and testing of susceptibility to antimicrobial agents was not performed. In conclusion, we found that Bio-Kil nanotechnology can significantly reduce the bacterial burden in the environment (textiles, environmental surfaces, and air) and the bacterial density of microbial infections or colonization among patients in the ICU.
cord-005057-deq5tv1d	1990	Herpes simplex virus (HSV) isolates derived from the central nervous system of ten patients with HSV-1-induced encephalitis, one patient with multiple sclerosis, and 14 patients with HSV-2-induced meningitis were investigated for neurovirulence by assaying the LD(50) after nose and intracerebral (i.c.) inoculation of mice. Vahlne t Herpes simplex virus (HSV) isolates derived from the central nervous system of ten patients with HSV-l-induced encephalitis, one patient with multiple sclerosis, and 14 patients with HSV-2-induced meningitis were investigated for neurovirnlence by assaying the LDs0 after nose and intracerebrai (i.c.) inoculation of mice. No correlation between high neurovirulence (defined as low LDs0 for both routes of infection) and replication in cell cultures of neuronal and non-neuronal cell lines was found, but the weakly neuruvirulent HSV-1 strain isolated from a patient with multiple sclerosis gave low replication yields.
cord-006174-xrhqisii	2016	In the present study, we assessed whether the IFITM3 rs12252-C allele is associated with susceptibility to and severity of influenza virus infection (IVI) among a white Spanish population. We performed a case-control genetic association study aimed to analyze the role of the IFITM3 rs12252 polymorphism in the susceptibility and severity of IVI. When the different groups of patients were compared according to severity of infection (development of PVP, ARDS or acute respiratory failure, need of ICU admission or hospital mortality), no significant associations were found (data not shown). [9] found three homozygous individuals for the variant rs12252-C among 53 patients from the United Kingdom hospitalized with influenza (89.5 % H1N1pdm), resulting in a significant overrepresentation when compared with Europeans. These studies suggested that homozygosity for the IFITM3 rs12252-C allele was associated with a populationattributable risk for severe influenza of 5.4 % in Northern Europeans and 54.3 % for severe H1N1pdm infection in Chinese [9, 12] .
cord-006302-pnnkfid0	2017	We studied the follow-up changes of circulating vasoactive peptides and cytokines until the improvement or the worsening of a patient and progression into specific organ dysfunctions. In a prospective study, concentrations of tumor necrosis factor-alpha (TNFα), interleukin (IL)-6, IL-8, IL-10, interferon-gamma (IFNγ), endocan and angiopoietin-2 (Ang-2) were measured in serum by an enzyme immunoassay in 175 patients at baseline; this was repeated within 24 h upon progression into new organ dysfunction (n = 141) or improvement (n = 34). Our aims were to monitor the changes of circulating levels of pro-inflammatory and antiinflammatory cytokines and of vasoactive peptides of critically ill patients at well-defined time-points of the clinical course and to understand how these changes mediate progression to organ dysfunction in an individualized way. When pair-wise comparisons between baseline and follow-up measurements were done within the subgroups of patients developing new organ dysfunctions, it was found that the only parameters significantly changing were endocan and Ang-2.
cord-006308-s5le8ugm	2007	The purpose of this study was to compare the risk factors, clinical manifestations, and outcome of candidemia in immunocompromised (IC) and nonimmunocompromised (NIC) critically ill patients. No study to date has been specifically designed to compare risk factors, manifestations, and outcome of candidemia in IC and NIC critically ill patients. Thus, we performed the present study to assess possible clinically significant differences between IC and NIC patients with candidemia receiving care in the ICU setting. The investigational work-up for invasive candidiasis in our patients (other than blood cultures, esophageal endoscopy, and oral scrapings) included (a) identification of predisposing factors, (b) surveillance cultures to detect possible colonization, (c) eye exam, and (d) CT scans of the suspected site of infection. The NIC patients in our study developed candidemia during their ICU hospitalization, and none manifested esophageal candidiasis, although one developed oral thrush.
cord-006325-3no74e74	2018	A more severe outcome was observed for RSV-bacteria-associated pneumonia compared with RSV pneumonia: length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). In conclusion, we did not observe major differences in the epidemiology of bacterial superinfections in RSV-positive pneumonia compared to reports on post-influenza pneumonia. RSV and bacteria coinfection was statistically associated with a more severe outcome than RSV-positive pneumonia as length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). It is probably due to the systematic testing strategy associated to a Species distribution of pathogenic bacteria involved in RSV-positive pneumonia (CAP) and hospital-acquired pneumonia (HAP) sampling bias toward influenza-like illness. Clinical characteristics and outcome of respiratory syncytial virus infection among adults hospitalized with influenza-like illness in France
cord-006335-j74hnoag	2011	The Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA, propose a total of eight distinctive clinical criteria for its "Hantavirus Pulmonary Syndrome Case Report Form" [9] : (1) fever, (2) thrombocytopaenia, )3) elevated haematocrit (Hct), (4) elevated serum creatinine, (5) left shift leukocytosis with a high percentage of "atypical lymphocytes", (6) need for supplemental oxygen, (7) need for intubation (and mechanical ventilation), and (8) chest Rx showing unexplained bilateral infiltrates or being suggestive of acute respiratory distress syndrome (ARDS). The first isolation in Europe of a murine HTNV-like hantavirus (in hindsight, probably DOBV) and dated 1986, was from the urine of a 21-year-old Greek soldier, infected during manoeuvres in Porogia (northern Greece) and suffering from acute pulmonary oedema, and later from acute renal failure (ARF), prompting both life-saving ventilation and acute dialysis [17] .
cord-006344-de4dhv4b	2006	title: Corticosteroids combined with continuous veno-venous hemodiafiltration for treatment of hantavirus pulmonary syndrome caused by Puumala virus infection Reported here are two cases of hantavirus pulmonary syndrome caused by Puumala virus infection, which rapidly resolved after initiation of corticosteroid treatment combined with continuous veno-venous hemodiafiltration. We describe two cases of PUU-associated HPS, in which administration of intravenous corticosteroids combined with continuous veno-venous hemodiafiltration (CVVHDF) was followed by rapid clinical improvement. On day 5 POS the lung infiltrates had increased considerably (Fig. 3a,b) , and the patient required continuous ventilation with a positive airway pressure mask. We describe two cases of PUU-infected patients who presented with both renal and respiratory failure requiring renal replacement therapy and mechanical ventilation. High levels of cytokineproducing cells in the lung tissues of patients with fatal hantavirus pulmonary syndrome High levels of viremia in patients with the Hantavirus pulmonary syndrome
cord-006448-elfroq6f	2007	We report a case of severe adenovirus pneumonia in a young immunocompetent male who presented with sudden onset respiratory distress that progressed rapidly to respiratory failure and made a successful recovery on supportive measures. Systematic review of the literature identified 14 cases of severe adenovirus pneumonia (defined as respiratory failure requiring ventilatory support at any point during the course of illness) in otherwise healthy immunocompetent adults both in epidemic and community settings. We report a case of severe adenovirus pneumonia in a previously healthy immunocompetent male who presented to us with rapidly developing respiratory failure and made a successful recovery on supportive measures. We defined severe adenovirus pneumonia if associated with respiratory failure requiring ventilatory support at any point during the course of illness and immunocompetent adults as individuals with no acquired or congenital immunodeficiency state with or without associated premorbid conditions.
cord-006450-si5168pb	2012	The variables associated with positive viral tests on univariate analysis were immunosuppression [human immunodeficiency virus (HIV), corticosteroids >10 mg/day for ≥3 weeks, or other immunosuppressive therapy], ground-glass attenuations on computed tomography (CT) scanning, late-onset ventilator-associated pneumonia (VAP), and durations of (i) hospital stay, (ii) intensive care unit (ICU) stay, and (iii) mechanical ventilation before BAL (p < 0.01 for each comparison). The variables significantly associated with positive viral tests on univariate analysis were immunosuppression (i.e., HIV infection, corticosteroids >10 mg/day for ≥3 weeks, and/or other immunosuppressive therapy), ground-glass attenuations on chest CT scans, late-onset ventilator-associated pneumonia (VAP), and durations of (i) hospital stay, (ii) ICU stay, and (iii) mechanical ventilation before BAL was performed (p<0.01 for each comparison). This advocates for the systematic use of PCR techniques for viral tests in BALF, in accordance with previous studies [27, 28] , in the situations where viruses may reasonably be suspected (i.e., acute lower tract respiratory disease in immunocompromised patients and/or patients with unexplained bilateral ground-glass attenuations on CT scan).
cord-006478-qkw1ik4e	1999	title: High-Frequency Transduction of Antibiotic Resistance in Pseudomonas aeruginosa by a Wild-Type Bacteriophage with Restricted Specificity for Recipient Strains Bartoníková Antibiotic resistance can be transferred among strains of Pseudomonas aeruginosa by conjugation [1] , transduction by wild-type phages as well as by generalised transducing phages, such as F-116 or G-101 [2] [3] [4] [5] , or by transposition of integrons [6] . In contrast to other wild-type phages isolated from multiple-drug-resistant nosocomial strains of Pseudomonas aeruginosa [3, 5, 9] , the phage lysate of Pseudomonas aeruginosa 103 showed a lytic reaction when added, in dilution of up to 10 -12 , to the recipient strain Pseudomonas aeruginosa PAO 1670 (Figure 1 ) but not to the other strains. Transduction of antibiotic resistance including imipenem resistance in nosocomial Pseudomonas aeruginosa strains by wild-type phages Transduction of imipenem resistance by wild-type bacteriophages from three Pseudomonas aeruginosa strains from a single clinical source
cord-006490-jo8dhtb0	2013	All positive Pj qPCR [targeting the major surface glycoprotein (MSG) gene] obtained in respiratory samples from immunocompromised patients presenting pneumonia at the Grenoble University Hospital, France, were collected between August 2009 and April 2011. qPCR targeting the MSG gene can be helpful to discriminate PCP from Pj colonization in immunocompromised patients, using two cut-off values, with a gray zone between them. The aim of this study was to use Pj real-time quantitative PCR (qPCR) in order to differentiate PCP and Pj colonization in immunocompromised patients. A receiver operating characteristic (ROC) curve for copy numbers was constructed and used to define cut-off values in order to discriminate the definite and probable PCP groups from the colonized group (possible PCP group and other diagnosis). In conclusion, our study shows that our qPCR targeting the MSG gene in respiratory samples can help discriminate PCP from pneumonia with Pj colonization in immunocompromised patients, using two cut-off values of 3,160 and 31,600 copies/ml, with a gray zone between them.
cord-006517-845w9r6l	2017	The aim of the present study was to assess the frequency and clinical impact of hematological abnormalities in the range of those accepted by the Histyocite Society for the suspicion of HPS [19] in patients who were admitted to the hospital with a confirmed influenza virus infection. In Beutel''s study of 25 critically ill patients with influenza A (H1N1) pdm09 virus associated hemophagocytic syndrome, the absence of steroid therapy in the early phase of the infection might have contributed to the high incidence of HPS (9 out of 25 patients) and the rather poor outcomes [18] . Significant hematological abnormalities are frequently seen in patients with influenza virus infection who required hospital admission and are associated with a poor outcome.
cord-006561-w4s0k75p	2015	Comorbidity was defined as the presence of one of the following chronic conditions: immunocompromise (defined as primary immunodeficiency or secondary immunodeficiency due to splenectomy, haematological malignancy, autoimmune disorder, chemotherapy or radiotherapy within 4 weeks prior to admission), diabetes mellitus (defined as receiving any oral or subcutaneous therapy for diabetes mellitus), COPD (defined as the presence of airflow limitation due to chronic bronchitis or emphysema), current smoker (any number of cigarettes/day), heart disease (defined as prior elective or emergency percutaneous coronary intervention or coronary artery bypass grafting, or New York Heart Association classes III or IV symptoms of heart failure), liver disease (defined as biopsy-proven cirrhosis or past medical history of complications of portal hypertension, including upper gastro-intestinal bleeding, encephalopathy, spontaneous bacterial peritonitis or more Fig. 1 The standard curve for Streptococcus pneumoniae (NCTC 12977 strain) was generated by plotting the mean of at least four samples of each ten-fold dilution (log 10 CFU/ml) against the corresponding fluorescence rate (FR).
cord-006581-f957o5z3	2013	The most important pathogens are Hantaan virus and Seoul virus in the Far East (>90 % of worldwide infections), Puumala virus (PUUV) and Dobrava-Belgrade virus in Europe and Russia, and, finally, Sin Nombre virus and Andes virus in the Americas [1, 2] Until recently, two clinical syndromes were classically described: hantavirus (cardio-)pulmonary syndrome (HPS or HCPS) described since 1994 in the Americas [4] and hemorrhagic fever with renal syndrome (HFRS) or its milder form nephropathia epidemica (NE), known in Eurasia since the early 1930s. The history of our patient fulfills most of the eight clinical findings specified in the "Hantavirus Pulmonary Syndrome Case Report Form", as issued by the Centers for Disease Control and Prevention (CDC), Atlanta, GA [13] : (1) fever, (2) thrombocytopenia, (3) elevated hematocrit, (4) elevated serum creatinine, (5) left shift leukocytosis with "atypical lymphocytes", (6) need for supplemental oxygen, (7) need for intubation (and mechanical ventilation), and (8) chest radiograph showing unexplained bilateral infiltrates or being suggestive of adult respiratory distress syndrome (ARDS).
cord-006714-q7wy76e2	2012	Our study supports the hypothesis that combination short-term antibiotherapy with an aminoglycoside for ICU-acquired bacteraemias could increase survival. Meta-analysis failed to demonstrate improved outcomes in patients treated with antibiotic combinations over those receiving monotherapy [1] [2] [3] [4] and resulted in a decreased use of combination therapy. We performed a retrospective study to evaluate the impact of AGs in antimicrobial combination on ICU-acquired bacteraemia in our universityaffiliated ICU [8] [9] [10] [11] . The aim of the study was to evaluate the impact of AGs in antibiotic combination on the outcome of patients with ICU-acquired bacteraemia. We found a survival benefit with the use of combination therapy with AGs for ICU-acquired bacteraemias. In the ICU, inadequate empirical antibiotic therapy is associated with an increased mortality risk in patients with ventilator-associated pneumonia and bacteraemia. Our study suggests that short-term combination beta-lactams plus AGs therapy in intensive care unit (ICU)-acquired bacteraemia could reduce mortality.
cord-006766-u31go6xi	2011	The aim of this study was to assess the cerebrovascular CO 2 R measured by TCD using the breath-holding method in patients with inflammatory central nervous system (CNS) diseases. The following parameters were recorded in a database: age, gender, physical and neurological signs, mechanical ventilation (MV), cerebrospinal fluid (CSF) characteristics, microbiological findings in CSF and blood, mean arterial pressure (MAP), Glasgow Coma Scale (GCS) score, Glasgow Outcome Scale (GOS) score, and the mean breath-holding index (BHI m ). Non-bacterial inflammatory CNS disease (NBM) was diagnosed on the basis of present encephalopathy with at least one of the following: fever, seizures, focal neurological findings; pleocytosis with increased protein concentration in the CSF; and a positive CSF or blood culture (fungal meningitis); virus detection by PCR assay in CSF samples; proved intrathecal antibody production and electroencephalographic or neuroimaging findings consistent with encephalitis or acute disseminated encephalomyelitis (ADEM). This prospective study assessed cerebrovascular reactivity (CO 2 R) by TCD using the breath-holding method in patients with inflammatory CNS diseases.
cord-010959-sigw7yxk	2020	Resistance to neuraminidase inhibitors has remained at low levels to date and the majority of resistance is seen in influenza A H1N1 pdm09 infected immunocompromised individuals receiving oseltamivir but is also seen less frequently with influenza A H3N2 and B. This potential for vast genetic variability within influenza viruses and their highly error-prone RNA dependent RNA polymerase does raise concerns regarding the possible emergence of treatment resistant strains and generates further questions regarding their viral fitness and transmissibility as well as which strategies to employ in rapidly identifying and effectively treating these resistance variants. Neuraminidase inhibitor susceptibility testing should be considered particularly in young children and immunocompromised patients being treated with a neuraminidase inhibitor for influenza (especially H1N1 pdm09), who are not responding to treatment and/or have persistently high viral loads (low cycle threshold values using RT-PCR) and/or exposed to a suspected or confirmed resistant case.
cord-011417-a5q15dq1	2020	Similarly, a strategy using a conjugate MenACWY vaccine targeting 9-month to 4-year-old children to control MenW disease in Chile provided direct protection to the vaccinated group but did not result in a herd immune effect [17] . In European countries, the highest MenB and C disease burden is similarly seen in infants (although the incidence rate reached 5.4/100,000 and 2.1/100,000 infants for MenB and C, respectively, much less when compared with the mean incidence rate of 9.66/100,000 and 6.72/100,000 infants for the corresponding capsular groups in Malta), with children less than 5 years old and adolescents and young adults being more affected than other age groups [1, 31] . Furthermore, a MenB immunization programme consisting of a 2 dose prime and boost MenB infant vaccine schedule in addition to MenB adolescent vaccination at 12 years of age would also be projected to provide direct protection and reduce the incidence of MenB, which is responsible for the highest meningococcal disease burden in Malta.
cord-025861-nsrs6dmc	2020	We aimed to describe prognostic factors for influenza-associated IA (IAA) and poor outcome and mortality in critically ill patients in Switzerland. Aspergillus is a common superinfection in critically ill influenza patients associated with poor outcome and longer duration of organ supportive therapies. Since no data on IAA was available from Switzerland, we retrospectively analysed all patients with severe influenza infection needing treatment in two large Swiss ICUs during the 2017/2018 influenza season with regard to predictors of IAA, mortality and poor outcome. In this retrospective cohort study, sixteen ICUs of tertiary hospitals in Switzerland were asked if they had observed cases of IAA and severe influenza and routinely looked for IAA based on clinical suspicion with galactomannan and fungal cultures in BAL; only two of them met the criteria (Cantonal Hospital of St. Gallen and University Hospital of Geneva). IAA is a severe and relatively frequent complication affecting 11% of patients with influenza treated in two Swiss ICUs. Aspergillus represented the most frequent respiratory co-infection of influenza in this cohort.
cord-028379-ghudhac6	2020	Complement and cytokine levels were measured in serum samples from 20 hospitalized patients with SAB, 20 hospitalized patients with GNB, 10 non-infected hospitalized patients, and 10 community controls. Low C4 and C3 levels were associated with septic shock and 30-day mortality in patients with GNB, and elevated C3 was associated with a desirable outcome defined as absence of (1) septic shock, (2) acute renal failure, and (3) death within 30 days of bacteremia. We evaluated complement and cytokine levels in patients with Staphylococcus aureus and Gram-negative bacteremia as compared to non-bacteremic hospitalized patients and community controls and explored potential associations between levels of these immune components and clinical outcome of the source patients. The BSIR collects and stores both clinical data and biological specimens from non-neutropenic hospitalized patients aged 18 years or older who have culture-confirmed monomicrobial bloodstream infections caused by either Staphylococcus aureus or Gram-negative bacteria.
cord-255785-wqlp6ogb	2019	title: Paramyxoviruses respiratory syncytial virus, parainfluenza virus, and human metapneumovirus infection in pediatric hospitalized patients and climate correlation in a subtropical region of southern China: a 7-year survey To investigate the features of paramyxovirus respiratory syncytial virus (RSV), parainfluenza virus (PIV), and human metapneumovirus (HMPV) infection and determine the effect of meteorological conditions in Guangzhou, a subtropical region of southern China. In this study, we analyzed paramyxovirus infection among children hospitalized with ARI over a 7-year period in Guangzhou, and we collected local meteorological data for climate correlation analysis. In the present study, we sought to analyze the features of paramyxovirus infection and correlation with meteorological conditions in a subtropical region of southern China, by collecting respiratory samples from pediatric patients (≤ 14 years old) hospitalized with ARI in Guangzhou and testing for RSV, PIV, HMPV, and other common respiratory pathogens.
cord-265729-prgj36g0	2014	Due to the lack of confirmatory studies and varied data available, more randomized, double-blind, and placebo-controlled trials in different age populations investigating probiotic dose response, comparing probiotic strains/genera, and elucidating the antiviral effect mechanisms are necessary. Many experimental studies in vitro and in animals show that specific strains of probiotics are capable of providing protection against virus infections by stimulating antiviral, cytokine, and chemokine responses in the respiratory and gastrointestinal epithelial cells or immune cells. Lactobacillus GG in the prevention of gastrointestinal and respiratory tract infections in children who attend day care centers: a randomized, double-blind, placebo-controlled trial Effects of consumption of a fermented dairy product containing the probiotic Lactobacillus casei DN-114 001 on common respiratory and gastrointestinal infections in shift workers in a randomized controlled trial Consumption of a fermented dairy product containing the probiotic Lactobacillus casei DN-114001 reduces the duration of respiratory infections in the elderly in a randomised controlled trial
cord-267533-nmgtan4e	2020	By LASSO and multivariate Cox regression analyses, we observed that delayed hospital admission, subpleural lesion, and high-dose corticosteroid use were independent risk factors of prolonged SARS-CoV-2 RNA detection. The study of Xu and colleagues [5] estimated the risk factors of delayed viral shedding (≥ 15 days after illness onset) and found that male, delayed hospital admission, and invasive mechanical ventilation were positively associated with prolonged SARS-CoV-2 RNA detection duration. Delayed hospital admission, hypokalemia, and subpleural lesion were still the independent risk factors of long-term SARS-CoV-2 RNA detection in multivariate binomial logistic regression analysis with a generalized additive model. LASSO analysis with Cox regression model found six independent risk factors of prolonged SARS-CoV-2 RNA detection duration, including cough, dyspnea, delayed hospital admission, subpleural lesion, the use of methylprednisolone, and the use of thymosin.
cord-268750-kox3uah2	2004	When the operations were performed, the Centers for Disease Control and Prevention (CDC; Atlanta, Ga., USA) had not yet prepared guidelines for the prevention of SARS transmission during Caesarean sections. For the three Caesarean sections performed on mothers with SARS, the number of healthcare workers was limited to a minimum, with only those personnel essential to carry out the operation, neonatal resuscitation, and cleanup being involved (i.e., 2 senior obstetricians, 2 senior neonatologists, 1 senior anaesthetist, 1 theatre assistant, a team of 4 senior midwives, and 2 cleansing staff). The participating HCWs wore appropriate PPE according to the hospital''s guidelines prior to the arrival of the patient from the intensive care unit. In conclusion, the procedures described above were sufficient to prevent our healthcare workers from contracting SARS while performing these very high-risk operations.
cord-269726-z0frgm7s	2020	Criteria for patients'' selection were diagnosis of SARS-CoV-2 infection [5] ; the subsequent meeting of criteria for hospital discharge (improvement of symptoms and two negative swabs collected at least 24 h apart) [4] ; and a positive respiratory sample collected after discharge. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement protocol [8] , a systematic review has been performed concerning the patients with a diagnosis of COVID-19 that, after clinical and virological recovery, presented a new positive respiratory sample (swab, sputum, saliva, tracheal aspirate, or BAL). The patient was discharged in good clinical conditions with indication to repeat quarantine and swab tests that came negative for SARS-CoV-2 (Allplex™ 2019-nCoV Assay) on April 27 and 28 (Fig. 1b) .
cord-271781-cfv0ta10	2020	To date, many studies have discussed that the rationale behind its transmission potential is that viral RNA has unexpectedly been detected in multiple bodily fluids, with some samples having remained positive for extended periods of time. In this evidence-based comprehensive review, we discuss various potential routes of transmission of SARS-CoV-2—respiratory/droplet, indirect, fecal-oral, vertical, sexual, and ocular. Additionally, studies have noted that its fecal-oral transmission potential may lie in the fact that prolonged viral shedding can occur in fecal matter-one case reported an asymptomatic COVID-19 patient experiencing viral detection in the stool for up to 42 days, while nasopharyngeal sampling was negative [31] . To oppose, in a retrospective review of nine COVID-19 pregnant mothers who underwent cesarean section, six patients had samples of amniotic fluid, cord blood, neonatal throat swab, and breastmilk samples tested for SARS-CoV-2, and all were negative [43] .
cord-272943-q09i8fqu	2014	Surprisingly, the use of fluoroquinolones in indications other than bacterial infections has never been exploited, although not only nalidixic acid and its congener chloroquine exerts pleiotropic actions but, e.g., β-lactams and aminoglycosides are characterized by a broad range of biological activities too [47, 48] , so that a multitude of antimicrobial effects would not have been unusual. Fluoroquinolones inhibit not only enzymic activity of viral topoisomerases/helicases, but inhibit in vitro human immunodeficiency virus (HIV) reverse transcriptase as well; complete inhibition was observed at concentrations of ciprofloxacin and ofloxacin of 3 μM and norfloxacin of 1 μM, respectively [71] [72] [73] . Fluoroquinolones like ciprofloxacin, amifloxacin, enoxacin, norfloxacin, ofloxacin, pefloxacin, grepafloxacin, trovafloxacin, and 16 additional commercially available quinolones exhibit marked in vitro activity and in vivo efficacy against Plasmodium spp.
cord-274567-xd37wxxf	2002	title: Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid A quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) method based on TaqMan technology was developed to determine the presence and amount of enterovirus RNA. Amplification of the internal positive control was effective in all but two specimens, confirming the absence of PCR inhibitors and allowing the results of amplification to be validated. Detection of EVs by amplification of viral RNA from CSF using reverse transcriptase-polymerase chain reaction (RT-PCR) assay has already been reported [4, 5, 6 ]. The fluorogenic RT-PCR was applied to detection of EVs in the CSF of 104 patients presenting with signs of meningitis. Amplicor enterovirus polymerase chain reaction in patients with aseptic meningitis: a sensitive test limited by amplification inhibitors Comparison of use of cerebrospinal fluid, serum, and throat swab specimens in diagnosis of enteroviral acute neurological infection by a rapid RNA detection PCR assay
cord-275561-9f1las3y	2015	title: Single nucleotide polymorphisms in immune response genes in acute Q fever cases with differences in self-reported symptoms Single nucleotide polymorphisms (SNPs) in the IFNG (rs2430561/rs1861493), STAT1 (rs1914408), and VDR (rs2228570) genes were determined in 85 patients from the 2007 Dutch acute Q fever outbreak, and a symptom score was calculated. burnetii antigens ≥1:64 (indirect immunofluorescence assay, IFA; Focus Diagnostics, Cypress, CA, USA)], based on available questionnaire data (self-reported symptoms), including no more than one person per household, and giving consent for the investigation of genetic differences. This study investigated the association of four SNPs in several immune response genes with susceptibility to and severity of self-reported symptoms in acute C. In conclusion, a significant difference was found for the IFNG rs1861493 SNP between persons with a mild or more severe presentation of acute Q fever, which was not confirmed in a second study population.
cord-283399-iz4l9i0d	2006	This study was carried out to further the available information on adult cases of human metapneumovirus (hMPV), a recently described cause of respiratory infection. For adults presenting with respiratory symptoms and a background of pre-existing respiratory disease or who are immunocompromised, nucleic acid-based techniques are a cost-effective means of making the viral diagnosis in a clinically relevant time frame. In young children and elderly patients hMPV is most commonly associated with a clinical diagnosis of bronchiolitis or bronchitis, respectively, whereas in middle-aged adults, it may produce an influenza-like illness, which can be complicated by pneumonitis in the presence of immunocompromising factors [5] . This retrospective observational study reviewed all cases of hMPV detected in patients over 18 years of age, from the time the RT-PCR method was adopted in July 2003 through to January 2005.
cord-285757-fiqx4tll	1999	To study whether MxA protein expression is systemically upregulated during rhinovirus infection, blood specimens were collected from 40 patients with common cold and MxA expression in mononuclear cells analyzed by flow cytometry. In conclusion, expression of MxA in blood lymphocytes and an apparently systemic type I interferon response is not induced during rhinovirus infection or during most other cases of common cold in young adult patients. In the present study, the induction of a systemic IFN response as reflected by the expression of MxA protein in blood lymphocytes of patients with rhinovirus infection was examined. Our data suggests that type I IFN production in serum is not comparable to that seen in most other respiratory viral infections in vivo, since the rhinovirus-positive patients had only low or no expression of the MxA protein and no IFN-a/b was detectable in serum samples.
cord-286749-si83t03j	2014	title: Epidemic and molecular evolution of human bocavirus in hospitalized children with acute respiratory tract infection Human bocavirus (HBoV) is a novel parvovirus, often associated with respiratory tract diseases in children. This study was aimed to explore the epidemiology pattern and clinical characteristics of HBoV-1 infection in Chinese children, as well as the molecular evolutionary pattern, for HBoV-1, by performing a 4-year laboratory surveillance of ARTI cases. According to our results, the prevalence of HBoV-1 in pediatric ARTI patients is higher than those from other hospital-based studies [2, 6, 21, 22] , whereas it was lower than that previously detected in persistently wheezing children [16] . Human bocavirus in children: mono-detection, high viral load and viraemia are associated with respiratory tract infection Detection and clinical characteristics analysis of human bocavirus 1-3 in children for acute respiratory infection in Lanzhou area
cord-291052-nstfe15a	2020	This manuscript aims to present a treatment algorithm we applied to manage COVID-19 patients admitted to our hospital. We administered hydroxychloroquine plus doxycycline to mild cases (isolated at home) for 3 days and lopinavir plus doxycycline to moderate and severe cases (hospitalized) for 5 days. Second, moderate to severe cases were hospitalized and prescribed with a regimen of lopinavir plus doxycycline plus ceftriaxone for 5 days. We hospitalized moderate to severe cases and administered lopinavir combined with doxycycline and ceftriaxone to 343 patients, among whom 161 had positive PCR test results (161/343, 46.9%). We administered hydroxychloroquine to mild cases isolated at home, lopinavir plus doxycycline to hospitalized moderate to severe cases, and favipiravir in the salvage treatment. We concluded that home isolation of mild cases is an effective means to manage the burden of disease, while lopinavir plus doxycycline is an alternative to current treatment regimens for COVID-19.
cord-293710-f1tzt6jb	2020	SARS-CoV-2 infection is associated with increased risk of thrombosis in severely ill patients but little is known about the risk in outpatients with mild to moderate disease. Studies showed reduced mortality in hospitalized COVID-19 patients treated vs not treated with anticoagulants in patients with a sepsis-induced-coagulopathy (SIC) score ≥ 4 or D-Dimer > 6 times upper limit of normal [4] . We describe a case series of four outpatients with proven SARS-CoV-2 infection who developed pulmonary embolism (PE) with a delay of 2-4 weeks after symptom onset with complete resolution of initial symptoms. The characteristics of outpatients who are suitable for anticoagulation have to be determined.In conclusion, new onset of dyspnea and tachycardia after initial resolution of COVID-19 symptoms ("disease trajectory characterised by two peaks") should raise suspicion of PE and a CT scan should be considered.
cord-294551-s3nsiano	2006	To identify features of the clinical assessment that are useful in SARS diagnosis, the exposure status and the prevalence and timing of symptoms, signs, laboratory and radiographic findings were determined for all adult patients admitted with suspected SARS during the Toronto SARS outbreak. Patients were classified as confirmed SARS if they had a compatible clinical illness (fever or nonproductive cough or dyspnea), an exposure to SARS (direct contact with a known SARS case or travel to a SARS-endemic area or time spent at an institution where SARS transmission was occurring, within 12 days of symptom onset), and a positive microbiological test (positive acute or convalescent serology, or positive PCR from clinical or pathological specimens). Findings associated with a confirmed diagnosis included direct exposure to a known case (OR, 2.34; 95%CI, 1.01-5.40), symptomatic fever as an initial symptom (OR, 5.07; 95%CI, 2.24-11.50), a documented temperature of 38.0°C on admission to hospital (OR, 2.6; 95%CI, 1.14-5.92), and the presence of a pulmonary infiltrate by the time of admission (OR, 2.46; 95%CI, 1.09-5.56).
cord-311207-qkkn0297	2020	Different assays demonstrate 41–45% of diagnostic sensitivities and 91–98% of specificities, with substantial agreement (89.3–91.2%), but a high percentage of weak positive results (13–22%) was observed with ICTs. ICTs performances were comparable to those of automated immunoassays. In COVID-19 confirmed cases (symptomatic patient with SARS-CoV-2 positive molecular detection), date of symptoms onset was used to timing infection at the moment of specimens'' collection. Three stages were identified: early (0-7 days from symptoms onset), intermediate (8China), COVID-19 IgG/IgM Rapid Test Cassette (Zhejiang Orient Gene Biotech Co., Ltd Huzhou, Zhejiang, China), and PRIMA Professional (PRIMA Lab SA, Balerbna, Switzerland) are lateral flow immunochromatographic assays. Sensitivities were assessed on confirmed COVID-19 cases, combining IgG and IgM/IgA positive results, while specificities were estimated on the group of healthy volunteer''s. Compared with the automated immunoassays, the ability of ICTs to detect anti-SARS-CoV-2 IgG was equivalent to that of CLIA-MAGLUMI and better than ELISA-Euroimmun, whose IgG positive rates ranged between 0 and 86% at 14 days after symptoms onset.
cord-314311-xbpb9nfi	2020	In November 2002, a novel betacoronavirus called severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in Guangdong, China, and resulted in more than 8000 infections and 774 deaths in 37 countries. This review makes a comprehensive introduction about this disease, including the genome structure and receptor of SARS-CoV-2, epidemiology, clinical features, diagnosis, treatment, and prognosis of COVID-19. The clinical manifestations of SARS-CoV-2-infected patients ranged from mild non-specific symptoms to severe pneumonia with organ function damage. The COVID-19 patients around the world were diagnosed based on World Health Organization interim guidance [65] , and China updated the novel coronavirus pneumonia diagnosis and treatment program (trial version) (in Chinese) according to epidemic situation and improved awareness of disease. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series
cord-321284-0y69n1ea	2016	title: The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season This study confirms the high rate of detection of viral nucleic acids by multiplex PCR among hospitalized children admitted with SARI, as well as the high rate of co-detection of multiple viruses. Forty healthy age-matched asymptomatic children with no history of a recent respiratory tract infection during the previous 2 weeks, who were not admitted to the hospital, and who do not have any chronic underlying illness were included as a control group. This study confirms the high rate of detection of viral nucleic acids by multiplex PCR) among hospitalized children admitted with severe acute respiratory infection, as well as the high rate of detection of multiple viruses.
cord-321455-ooouqna7	2020	In the peripheral blood system of non-severe symptom COVID-19 patients, lymphocytes, eosinophils, basophils, total procollagen type 1 amino-terminal propeptide, osteocalcin N-terminal, thyroid-stimulating hormone, growth hormone, and insulin-like growth factor–binding protein 3 significantly decreased, and total protein, albumin, alanine transaminase, alkaline phosphatase, γ-glutamyl transferase, activated partial thromboplastin time, prothrombin time, fibrinogen, D-dimer, fibrinogen degradation products, human epididymal protein 4, serum ferritin, and C-reactive protein were elevated. In the process of continuous monitoring, the expression of CRE in patients with COVID-19 were significantly lower than those in the controls on the 1st, 4th, and 7th days of admission, and showed an overall downward trend (Fig. 3a) . The expression of Ca 2+ in patients with COVID-19 were significantly lower than those in the controls on the 1st, 4th, 7th and 10th days of admission, and showed an overall upward trend (Fig. 3d ).
cord-323476-rb9n5wc0	2020	title: How are rapid diagnostic tests for infectious diseases used in clinical practice: a global survey by the International Society of Antimicrobial Chemotherapy (ISAC) Novel rapid diagnostic tests (RDTs) offer huge potential to optimise clinical care and improve patient outcomes. An electronic survey was devised by the International Society of Antimicrobial Chemotherapy (ISAC) Rapid Diagnostics and Biomarkers working group focussing on the availability, structure and impact of RDTs around the world. The International Society of Antimicrobial Chemotherapy (ISAC)''s Rapid Diagnostics and Biomarkers Working Group conducted this international survey aiming to identify and highlight some key issues related to RDTs and their impacts in clinical practice and provide a number of key points to consider while adopting a RDT. Our survey highlights the availability of these tests in different resource settings, as well as the current models for governance, quality control and reporting.
cord-325238-2nhade3s	2020	The studied virulence factors include biofilm formation, twitching and swarming motilities, proteolytic enzyme production, and resistance to oxidative stress. The virulence factors were detected in absence and presence of 1 8 MIC of potential QSIs. Assay of biofilm formation, twitching motility, sensitivity to oxidative stress and protease, and gelatinase activity were performed for both P. Among the tested drugs, erythromycin, levamisole, propranolol, and chloroquine showed the highest inhibition of quorum sensing in CV026 as they produced a large clear zone around each well on a purple background (Fig. 1) ; hence, these four drugs were tested in the further experiments. The obtained results revealed that PAO1 biofilm (strong) was markedly inhibited in presence of 1/8 MIC of tested drugs (> 68%); the highest inhibition was observed with erythromycin (82.7%) as shown in Table 2 and Fig. 2a .
cord-335671-j3wrtsxj	2004	title: Similar environmental survival patterns of Streptococcus pyogenes strains of different epidemiologic backgrounds and clinical severity S. pyogenes strains 2, 6 and 8 were isolated from different patients during a hospital outbreak reported previously by Davies et al. It can be seen that from an initial measurement of approximately 10 8 cfu the strains died off rapidly, with the decline ranging from 4 to 7-log 10 cfu during the 14-day dry-out period to counts between 20 and 9,000 cfu. pyogenes strains tested-even our own outbreak strain that had demonstrated MRSAlike spread [4] -contrasts sharply with the prolonged survival of around a year reported previously for epidemic MRSA strains [7] . pyogenes strains in the hospital environment is shorter than the period of 3 months reported by Lidwell and Lowbury [8] , it should be noted that their study measured survival in dust.
cord-336909-nnxa5ant	2020	The aim of this study is to evaluate three immunocromathographic assays (Sienna®, Wondfo® and Prometheus®) for detection of antibodies against SARS-CoV-2 in serum samples, considering RT-qPCR as a reference. RT-qPCR tests presented a high specificity with a low probability of false positive; however, sensitivity relies on different factors as specimen site, method of collection, viral load and time from the onset of symptoms [3, 7] . Detection rate of IgM, IgG and IgM/IgG antibodies against SARS-CoV-2 with the three ICT strip assays in positive and negative RT-PCR patients along three periods of time since the onset of symptoms is shown in Table 3 . Detection rates of total antibodies (IgM/IgG) obtained with Sienna® and Wondfo® by the two groups of patients along the three stages since the symptoms onset are collected in Table 4 . In this study, we have investigated the diagnostic value of detection of SARS-CoV-2 IgM and IgG antibodies in different stages of the disease, using three ICT strip assays, in comparison with RT-qPCR.
cord-338070-y8zi8iz9	2020	This study aimed to explore the effects of PARP-1 inhibitor olaparib on IAV-induced lung injury and the underlying mechanisms. To the expectations, mice in the olaparib group showed higher survival rate compared with that in the IAV group in a dose-dependent manner, indicating that olaparib could powerfully protect against influenza virus challenge in by H&E staining and the quantitative analysis of histological changes in the lung tissues (e) (n = 8 for each group). The detection of cytokine/chemokine in BALF samples at day 6 post-infection showed that IL-6, MCP-1, G-CSF, TNF-α, CXCL1, CXCL10, CCL3, and RANTES were remarkably increased in the IAV group compared with those in the control group, while olaparib treatment significantly reduced the abnormal increased levels of the above cytokine/chemokines, which was similar with the results obtained from lung tissue (Fig. 4a-h) . To explore the mechanisms underlying the protective effect of olaparib against IAV-induced injury to murine lungs, western blot was performed to detect the PARPs, the marker of apoptosis.
cord-344017-qldawc8m	2020	Incorporating an inactivated clinical SARS-CoV-2 isolate as the antigen, the specificity of the assay was measured as 100% for IgA titre ≥ 1:200, 98.6% for IgM titre ≥ 1:200 and 96.3% for IgG titre ≥ 1:100 after testing a series of negative controls. In this study, we are reporting our experience to develop an indirect immunofluorescent assay (IFA) for the detection of anti-SARS-CoV-2 antibodies that we implemented before any other serological test was available in France. ELISA To compare our IFA with commercial ELISA IgG, we randomly selected 70 sera with possible cross-reactivity (including 45 sera with possible nonspecific serological interference and 25 sera from patients diagnosed with common others human coronavirus), 30 sera collected before the pandemic and 100 sera from our cohort of SARS-CoV-2-infected patients among all the sera that we tested by IFA. Some other studies also reported an earlier serological response in severe compared to mild SARS-CoV-2 infection [5, 20, 25] that is consistent with the earlier seroconversion that we found in patients with poor clinical outcome (PClinO).
cord-346726-u7dhbmht	2018	We aimed to describe the potential benefit of new rapid molecular respiratory tests (MRT) in decreasing inappropriate antibiotic use among the inpatients presenting with influenza-like illness (ILI). It is time to increase the awareness about the viral etiology in respiratory tract infections (RTIs) and implement MRT in clinical practice. In adults, influenza virus, rhinovirus, adenovirus, respiratory syncytial virus (RSV), human coronavirus, and parainfluenza virus cause infections with considerable morbidity and mortality [1, 3] , and in infants, RSV is the most common reason for RTIs among hospitalized patients [4] . In this study, we aimed to describe the viral etiology in influenza-like illness (ILI) in children and adults and to show the benefit of new rapid molecular respiratory tests (MRT) in decreasing inappropriate antibiotic use. By using molecular rapid tests (MRT) in our hospital, inappropriate antibiotic use and also duration of inappropriate antibiotic use after the detection of virus was significantly decreased among inpatients.
cord-348840-s8wjg4ar	2017	Microorganisms contaminating such high-touch surfaces include Gram-positive and Gram-negative bacteria, viruses, yeasts and parasites, with improved cleaning and disinfection effectively decreasing the rate of HAIs. Manual and automated surface cleaning strategies used in the control of infectious outbreaks are discussed and current trends concerning the prevention of contamination by the use of antimicrobial surfaces are taken into consideration in this manuscript. Additionally, evidence that hightouch surfaces (HTS) will work as an extra source of microbial pathogens accumulated over the years, e.g., several microorganisms can survive on medical equipment for hours to months, improved cleaning and disinfection of surfaces decrease the rate of HAI, and hospital environmental screening results and the study of clonal outbreaks, all have given support to the role of contaminated HTS in the transmission of pathogens between patients and healthcare personnel [4] . Microbial pathogens most frequently involved in the contamination of hospital environmental surfaces are (methicillinresistant) Staphylococcus aureus (MRSA), vancomycinresistant enterococci (VRE), Clostridium difficile, multidrug resistant Gramme-negative bacilli (such as Pseudomonas, Acinetobacter and Enterobacteriaceae), Norovirus, Coronavirus and Candida species [6] [7] [8] [9] [10] .
cord-349562-ivu632j2	2010	The purpose of this study was to compare the sampling efficacy of rayon swabs and nylon flocked swabs, and of oropharyngeal and nasopharyngeal specimens for the detection of respiratory viruses in elderly patients. Regardless of the sampling site, a calculated 4.8 times higher viral load (95% confidence interval [CI] 1.3–17, p = 0.017) was obtained using the nylon flocked swabs as compared to the rayon swabs. Samples for the diagnosis of a respiratory viral infection can be obtained by swabbing the oropharynx, the nasal cavity, the nasopharynx or alternatively, by nasopharyngeal aspiration (NPA) or nasopharyngeal washings (NPW). The aim of this study was to compare the respective efficacies of rayon swabs and nylon flocked swabs in providing material for direct respiratory virus detection by real-time PCR in adults above 60 years of age. Using monoplex (RSV and human metapneumovirus) or multiplex (influenza A/B, adenovirus/internal control and parainfluenza virus 1-4) PCR methods, the specimens were examined for, in total, nine different respiratory viruses (Table 2) .
cord-350328-wu1ygt6w	2004	The severe acute respiratory syndrome (SARS) is an emerging infection caused by a novel coronavirus which first appeared in southern China at the end of 2002. The severe acute respiratory syndrome (SARS) is a newly recognized coronavirus infection that emerged in southern China [1] with subsequent global spread to 29 countries [2] [3] [4] [5] . The newly infected individuals traveled onward to their homes or next destinations in the USA, Canada, Singapore, Hong Kong and Ireland sparking off epidemics of varying degrees of severity in each of those countries, mainly in hospitals but also in their respective communities. A directive had gone out from the Hong Kong Department of Health on 21 February 2003 to maintain strict infection control with droplet precautions for all cases of "atypical" community-acquired pneumonia because of concerns that highly pathogenic avian influenza might be easily transmissible from person to person. Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts
cord-350807-qdq96723	2020	Samples were tested by PCR for the presence of herpesviruses (HSV-1/-2; VZV; CMV; HHV6; EBV), adenoviruses, bocaviruses, entero-/rhinoviruses (HRV), parechoviruses, coronaviruses, influenza viruses (IV), parainfluenza viruses as well as for pneumoviruses (HMPV and RSV), and atypical bacteria (Mycoplasma pneumoniae, M.p.; Chlamydia pneumoniae, C.p.). Furthermore, particularly transplant patients are at risk for reactivation of diverse herpesviruses (herpes simplex virus-1/-2, HSV-1/-2; varicella zoster virus, VZV; cytomegalovirus, CMV; human herpesvirus 6, HHV-6; Epstein-Barr virus, EBV) [12, 15, [17] [18] [19] [20] . In this monocentric study, genome equivalents of viruses and M.p. were frequently detected in immunocompromised (66.7%) and immunocompetent (69.2%) patients with respiratory symptoms (Table 1) . Same authors indicated a mean age of 1.8 years Table 2 Detection of multiple pathogens in the respiratory tract of the overall study population (a) as well as of immunocompromised (b) and immunocompetent (c) patients.
cord-355450-v3eh1rtk	2020	Influenza and respiratory syncytial virus (RSV) infections are associated with high rate of morbidity, mortality, and an important burden on healthcare systems worldwide, especially among elderly patients [1] [2] [3] [4] [5] [6] . Especially in epidemiological research, oldest-old patients are considered to be a part of the wider age group of the elderly (≥ 65 years old), and there is limited published evidence about predictors of severity of illness and mortality in viral infections, such as caused by influenza and RSV. The aim of this study was to describe the clinical features of an oldest-old population admitted with influenza and/or RSV infections in three southern European hospitals over two consecutive winter seasons and identify predictors of pneumonia, non-invasive ventilation (NIV), and in-hospital death (IHD). Moreover, in our study, hospital-acquired influenza and/or RSV infections were not identified as predictors of pneumonia, use of NIV, and IHD for patients aged 65 years and older, moving away from evidence available so far [9, 10] .