scholarly journals Circulation of Non- SARS-CoV-2 Respiratory Pathogens and Coinfection with SARS-CoV-2 Amid the COVID-19 Pandemic

2021 ◽  
Author(s):  
Katharine Uhteg ◽  
Adannaya Amadi ◽  
Michael Forman ◽  
Heba H Mostafa
Keyword(s):  
Retrospective Analysis ◽  
Standard Of Care ◽  
Respiratory Pathogen ◽  
Respiratory Pathogens ◽  
Diagnostic Laboratory ◽  
Viral Pathogens ◽  
Symptomatic Disease ◽  
Pathogen Testing

Abstract Background Our understanding of the co-circulation of infrequently targeted respiratory pathogens and their contribution to symptoms during the COVID-19 pandemic is currently limited. This research aims at 1) understanding the epidemiology of respiratory pathogens since the start of the pandemic, 2) assessing the contribution of non-SARS-CoV-2/influenza/RSV respiratory pathogens to symptoms, and 3) evaluating coinfection rates in SARS-CoV-2 positive patients, both vaccinated and unvaccinated. Methods Retrospective analysis of respiratory pathogens identified by the Johns Hopkins Diagnostic Laboratory between December 2019 and October 2021 was performed. In addition, we assessed the contribution of respiratory pathogens other than SARS-CoV-2 to symptomatic disease by re-testing two cohorts of specimens that were 1) collected from symptomatic patients and 2) received limited respiratory pathogen testing. The first cohort was patients tested negative by the standard of care SARS-CoV-2/influenza/RSV testing. The second was a cohort of SARS-CoV-2 positive symptomatic fully COVID-19 immunized and unimmunized patients. Results Between December 2019 and October 2021, a total of 11,806, 62,829, and 579,666 specimens were tested for an extended respiratory panel, influenza/RSV/with or without SARS-CoV-2 panel, or SARS-CoV-2, respectively. Positivity rates of different targets differed between different months and were impacted by the COVID-19 pandemic. The SARS-CoV-2 negative cohort had 8.5% positivity for other respiratory pathogens that included primarily enterovirus/rhinovirus (5.8%). In the SARS-CoV-2 positive cohort, no other respiratory pathogens were detected. Conclusions The COVID-19 pandemic impacted the circulation of certain respiratory pathogens. Other respiratory viral pathogens were associated with symptomatic infections; however, coinfections with SARS-CoV-2 were highly uncommon.

scholarly journals Broad respiratory testing to identify SARS-CoV-2 viral co-circulation and inform diagnostic stewardship in the COVID-19 pandemic

2020 ◽  
Author(s):  
Natalie C. Marshall ◽  
Ruwandi M. Kariyawasam ◽  
Nathan Zelyas ◽  
Mathew A. Diggle
Keyword(s):  
Public Health ◽  
Respiratory Viruses ◽  
Cross Reactivity ◽  
Respiratory Pathogen ◽  
Health Concern ◽  
Respiratory Pathogens ◽  
Public Health Importance ◽  
Clinical Laboratories ◽  
Pathogen Testing ◽  
Virus Testing

Abstract Background: SARS-CoV-2 infection can present with a broad clinical differential that includes many other respiratory viruses; therefore, accurate tests are crucial to distinguish true COVID-19 cases from pathogens that do not require urgent public health interventions. Co-circulation of other respiratory viruses is largely unknown during the COVID-19 pandemic but would inform strategies to rapidly and accurately test patients with respiratory symptoms.Methods: This study retrospectively examined 298,415 respiratory specimens collected from symptomatic patients for SARS-CoV-2 testing in the three months since COVID-19 was initially documented in the province of Alberta, Canada. By focusing on 52,285 specimens that were also tested with the Luminex Respiratory Pathogen Panel for 17 other pathogens, this study examines the prevalence of 18 potentially co-circulating pathogens and their relative rates in prior years versus since COVID-19 emerged, including four endemic coronaviruses. Results: SARS-CoV-2 was identified in 2.2% of specimens. Parallel broad multiplex testing detected additional pathogens in only 3.4% of these specimens: significantly less than in SARS-CoV-2-negative specimens (p < 0.0001), suggesting very low rates of SARS-CoV-2 co-infection. Furthermore, the overall co-infection rate was significantly lower among specimens with SARS-CoV-2 detected (p < 0.0001). Finally, less than 0.005% of all specimens tested positive for both SARS-CoV-2 and any of the four endemic coronaviruses tested, strongly suggesting neither co-infection nor cross-reactivity between these coronaviruses. Conclusions: Broad respiratory pathogen testing rarely detected additional pathogens in SARS-CoV-2-positive specimens. While helpful to understand co-circulation of respiratory viruses causing similar symptoms as COVID-19, ultimately these broad tests were resource-intensive and inflexible in a time when clinical laboratories face unprecedented demand for respiratory virus testing, with further increases expected during influenza season. A transition from broad, multiplex tests toward streamlined diagnostic algorithms targeting respiratory pathogens of public health concern could simultaneously reduce the overall burden on clinical laboratories while prioritizing testing of pathogens of public health importance. This is particularly valuable with ongoing strains on testing resources, exacerbated during influenza seasons.

scholarly journals Broad respiratory testing to identify SARS-CoV-2 viral co-circulation and inform diagnostic stewardship in the COVID-19 pandemic

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Natalie C. Marshall ◽  
Ruwandi M. Kariyawasam ◽  
Nathan Zelyas ◽  
Jamil N. Kanji ◽  
Mathew A. Diggle
Keyword(s):  
Public Health ◽  
Respiratory Viruses ◽  
Cross Reactivity ◽  
Respiratory Pathogen ◽  
Health Concern ◽  
Respiratory Pathogens ◽  
Public Health Importance ◽  
Clinical Laboratories ◽  
Pathogen Testing ◽  
Virus Testing

Abstract Background SARS-CoV-2 infection can present with a broad clinical differential that includes many other respiratory viruses; therefore, accurate tests are crucial to distinguish true COVID-19 cases from pathogens that do not require urgent public health interventions. Co-circulation of other respiratory viruses is largely unknown during the COVID-19 pandemic but would inform strategies to rapidly and accurately test patients with respiratory symptoms. Methods This study retrospectively examined 298,415 respiratory specimens collected from symptomatic patients for SARS-CoV-2 testing in the three months since COVID-19 was initially documented in the province of Alberta, Canada (March-May, 2020). By focusing on 52,285 specimens that were also tested with the Luminex Respiratory Pathogen Panel for 17 other pathogens, this study examines the prevalence of 18 potentially co-circulating pathogens and their relative rates in prior years versus since COVID-19 emerged, including four endemic coronaviruses. Results SARS-CoV-2 was identified in 2.2% of all specimens. Parallel broad multiplex testing detected additional pathogens in only 3.4% of these SARS-CoV-2-positive specimens: significantly less than in SARS-CoV-2-negative specimens (p < 0.0001), suggesting very low rates of SARS-CoV-2 co-infection. Furthermore, the overall co-infection rate was significantly lower among specimens with SARS-CoV-2 detected (p < 0.0001). Finally, less than 0.005% of all specimens tested positive for both SARS-CoV-2 and any of the four endemic coronaviruses tested, strongly suggesting neither co-infection nor cross-reactivity between these coronaviruses. Conclusions Broad respiratory pathogen testing rarely detected additional pathogens in SARS-CoV-2-positive specimens. While helpful to understand co-circulation of respiratory viruses causing similar symptoms as COVID-19, ultimately these broad tests were resource-intensive and inflexible in a time when clinical laboratories face unprecedented demand for respiratory virus testing, with further increases expected during influenza season. A transition from broad, multiplex tests toward streamlined diagnostic algorithms targeting respiratory pathogens of public health concern could simultaneously reduce the overall burden on clinical laboratories while prioritizing testing of pathogens of public health importance. This is particularly valuable with ongoing strains on testing resources, exacerbated during influenza seasons.

scholarly journals An algorithmic approach to the use of rapid molecular diagnostics for SARS-CoV-2, influenza viruses, and other respiratory pathogens during an unprecedented respiratory season

2021 ◽  
Vol 156 (Supplement_1) ◽  
pp. S130-S130
Author(s):  
A S Maris ◽  
L Tao ◽  
C W Stratton ◽  
R M Humphries ◽  
J E Schmitz
Keyword(s):  
Point Of Care ◽  
Random Access ◽  
Access Point ◽  
Clinical Situation ◽  
Influenza Viruses ◽  
Respiratory Pathogen ◽  
Respiratory Pathogens ◽  
Test Volume ◽  
Dumpster Diving ◽  
Pathogen Testing

Abstract Introduction/Objective The COVID-19 pandemic exacerbated deficiencies of testing personnel, reagents, supplies and disposables, instruments, and automation in many clinical laboratories. Upon entering respiratory season, a strategy was warranted to optimize laboratory resources when supplies were already limited and expected respiratory season test volume was unknown. An algorithm was devised to prioritize test ordering and TAT based on patient clinical scenario. Methods/Case Report The institutional respiratory season SARS-CoV-2 algorithm was constructed by a multidisciplinary team including infectious disease, infection prevention, laboratory, and IT/LIS leadership. CDC guidance on influenza testing was incorporated. Antigen-based testing was discontinued; only molecular amplification- based platforms with FDA EUA were utilized. Platforms had a range of TAT (20 minutes to 8 hours) and included fully- automated high throughput, rapid random access, point-of-care, and CDC SARS-CoV-2 assays. Test bundles included SARS-CoV-2 (monoplex), or SARS-CoV-2 + fluA&B (triplex), or SARS-CoV-2 + respiratory pathogen panel (multiplex RPP; includes 22 targets, including flu A&B). Results (if a Case Study enter NA) Key factors in the algorithm included whether the patient was outpatient or inpatient, hospital employee or not, symptomatic or not, immunocompetent or immunocompromised, and whether a concurrent order for other respiratory pathogens was included or not. Clinician responses for these factors determined the type of swab collected (wet swab in VTM or dry swab) and how quickly the TAT was indicated for a given patient using a colored-dot sticker system. Priority TAT in decreasing order was symptomatic inpatients, asymptomatic pre- procedure patients, asymptomatic admissions, symptomatic employees, and symptomatic outpatients. Conclusion An algorithm for respiratory pathogen testing during an unprecedented respiratory season prioritizes result TAT to an individual patient’s clinical situation while maximizing laboratory stewardship by eliminating redundant influenza testing and requiring ‘all upfront’ orders to avoid add-on orders that require ‘dumpster diving’ for samples. Limitations include inherent differences in sensitivity, LOD, and specificity when multiple different platforms are utilized to detect the same analytes.

scholarly journals Repeat Molecular Testing for Respiratory Pathogens: Diagnostic Gain or Diminishing Returns?

2020 ◽  
Vol 5 (5) ◽  
pp. 897-907
Author(s):  
Abraham J Qavi ◽  
Allison McMullen ◽  
Carey-Ann D Burnham ◽  
Neil W Anderson
Keyword(s):  
Influenza A ◽  
Nucleic Acid Amplification ◽  
Respiratory Pathogen ◽  
Molecular Testing ◽  
Respiratory Pathogens ◽  
Upper Respiratory Tract ◽  
Repeat Testing ◽  
Syncytial Virus ◽  
Pathogen Testing ◽  
Tract Infections

Abstract Background Upper respiratory tract infections are common, and the ability to accurately and rapidly diagnose the causative pathogen has important implications for patient management. Methods We evaluated the test-ordering practices for 2 commonly utilized nucleic acid amplification tests (NAATs) for the detection of respiratory pathogens: the Xpert Flu Assay for influenza A/B (Flu assay) and the Biofire FilmArray respiratory panel assay (RP assay), which detects 20 different targets. Our study examined repeat testing; that is, testing within 7 days from an initial test. Results Our study found that repeat testing is common for each of the individual assays: 3.0% of all Flu assays and 10.0% of all RP assays were repeat testing. Of repeat testing, 8/293 (2.7%) of repeat Flu assays and 75/1257 (6.0%) of RP assays resulted diagnostic gains, i.e., new detections. However, for the RP assay, these new detections were not always clinically actionable. The most frequently discrepant organisms were rhinovirus/enterovirus (28/102, 27.5%), followed by respiratory syncytial virus (12/102, 11.8%) and coronavirus OC43 (11/102, 10.8%). Furthermore, there were 3,336 instances in which a patient was tested using both a Flu assay and RP assay, of which only 44 (1.3%) had discrepant influenza results. Conclusions Our findings suggest opportunities exist to better guide ordering practices for respiratory pathogen testing, including limiting repeat testing, with the goal of optimization of clinical yield, and diagnostic stewardship.

scholarly journals Evaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance Study

2020 ◽  
Author(s):  
Ashley E. Kim ◽  
Elisabeth Brandstetter ◽  
Naomi Wilcox ◽  
Jessica Heimonen ◽  
Chelsey Graham ◽  
...  
Keyword(s):  
Online Survey ◽  
Respiratory Infections ◽  
Cross Sectional Study ◽  
Respiratory Pathogen ◽  
Respiratory Pathogens ◽  
Sample Collection ◽  
Community Based ◽  
Cross Sectional ◽  
Home Based ◽  
Pathogen Screening

AbstractIntroductionWhile influenza and other respiratory pathogens cause significant morbidity and mortality, the community-based burden of these infections remains incompletely understood. The development of novel methods to detect respiratory infections is essential for mitigating epidemics and developing pandemic-preparedness infrastructure.MethodsFrom October 2019 to March 2020, we conducted a home-based cross-sectional study in the greater Seattle area, utilizing electronic consent and data collection instruments. Participants received nasal swab collection kits via rapid delivery within 24 hours of self-reporting respiratory symptoms. Samples were returned to the laboratory and were screened for 26 respiratory pathogens and a human marker. Participant data were recorded via online survey at the time of sample collection and one week later.ResultsOf the 4,572 consented participants, 4,359 (95.3%) received a home swab kit, and 3,648 (83.7%) returned a nasal specimen for respiratory pathogen screening. The 3,638 testable samples had a mean RNase P CRT value of 19.0 (SD: 3.4) and 1,232 (33.9%) samples had positive results for one or more pathogens, including 645 (17.7%) influenza-positive specimens. Among the testable samples, the median time between shipment of the home swab kit and completion of laboratory testing was 8 days [IQR: 7.0-14.0].DiscussionHome-based surveillance using online participant enrollment and specimen self-collection is a feasible method for community-level monitoring of influenza and other respiratory pathogens, which can readily be adapted for use during pandemics.

scholarly journals Seattle Flu Study - Swab and Send: Study Protocol for At-Home Surveillance Methods to Estimate the Burden of Respiratory Pathogens on a City-Wide Scale

2020 ◽  
Author(s):  
Ashley E. Kim ◽  
Elisabeth Brandstetter ◽  
Chelsey Graham ◽  
Jessica Heimonen ◽  
Audrey Osterbind ◽  
...  
Keyword(s):  
Metropolitan Area ◽  
Nasal Swab ◽  
Community Dwelling ◽  
Self Report ◽  
Respiratory Pathogen ◽  
List Type ◽  
Respiratory Pathogens ◽  
Sample Collection ◽  
Cross Sectional ◽  
Home Based

AbstractIntroductionWhile seasonal influenza and other respiratory pathogens cause significant morbidity and mortality each year, the community-based burden of these infections remains incompletely understood. Understanding the prevalence, epidemiology, and transmission dynamics of respiratory pathogen infections among community-dwelling individuals is essential during pandemic and epidemic settings and for developing pandemic-preparedness infrastructure.Methods and AnalysisWe present the protocol for a novel, city-wide home-based cross-sectional study in the Seattle Metropolitan area, utilizing rapid delivery systems for self-collection of a nasal swab and return to the laboratory for respiratory pathogen testing. All participation takes place electronically, including recruitment, consent, and data collection. Within 48 hours of participants self-reporting respiratory symptoms, a nasal swab kit is delivered to the household via a courier service. Demographic and illness characteristics are collected at the time of sample collection and recovery and behavioral information collected one week later. Specimens are tested in the laboratory for multiple respiratory pathogens, and results are available on a public website for participants.Ethics and DisseminationThe study was approved by the University of Washington Institutional Review Board (Protocol #00006181). Results will be disseminated through peer-reviewed publications, talks at conferences, and on the Study Website (www.seattleflu.org).Article SummaryThe findings of this study will inform whether a home-based approach to city-wide respiratory surveillance is possible in epidemic settingsA key strength of this study is that it is conducted across diverse neighborhoods spanning a major metropolitan areaClinical findings may not be generalizable, as they are reliant on self-report (vaccination status, symptoms, healthcare utilization, etc.)

scholarly journals Evidence to Support Tooth Brushing in Critically Ill Patients

2011 ◽  
Vol 20 (3) ◽  
pp. 242-250 ◽  
Author(s):  
Nancy J. Ames
Keyword(s):  
Critically Ill ◽  
Critically Ill Patients ◽  
Oral Care ◽  
Standard Of Care ◽  
Tooth Brushing ◽  
Oral Microbiome ◽  
Respiratory Pathogens ◽  
Adults And Children ◽  
Critically Ill Adults ◽  
Powered Toothbrush

Tooth brushing in critically ill patients has been advocated by many as a standard of care despite the limited evidence to support this practice. Attention has been focused on oral care as the evidence accumulates to support an association between the bacteria in the oral microbiome and those respiratory pathogens that cause pneumonia. It is plausible to assume that respiratory pathogens originating in the oral cavity are aspirated into the lungs, causing infection. A recent study of the effects of a powered toothbrush on the incidence of ventilator-associated pneumonia was stopped early because of a lack of effect in the treatment group. This review summarizes the evidence that supports the effectiveness of tooth brushing in critically ill adults and children receiving mechanical ventilation. Possible reasons for the lack of benefit of tooth brushing demonstrated in clinical trials are discussed. Recommendations for future trials in critically ill patients are suggested. With increased emphasis being placed on oral care, the evidence that supports this intervention must be evaluated carefully.

Lactobacilli intra-tracheal administration protects from Pseudomonas aeruginosa pulmonary infection in mice – a proof of concept

2019 ◽  
Vol 10 (8) ◽  
pp. 893-900 ◽  
Author(s):  
M.S. Fangous ◽  
Y. Alexandre ◽  
N. Hymery ◽  
S. Gouriou ◽  
D. Arzur ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Murine Model ◽  
Alveolar Epithelial Cell ◽  
A549 Cells ◽  
Respiratory Pathogen ◽  
Public Health Issue ◽  
Epithelial Cell Line ◽  
High Morbidity ◽  
Respiratory Pathogens

The spreading of antibiotic resistance is a major public health issue, which requires alternative treatments to antibiotics. Lactobacilli have shown abilities to prevent pneumonia in clinical studies when given by oral route, certainly through the gut-lung axis involvement. Rationally, respiratory administration of lactobacilli has been developed and studied in murine model, to prevent from respiratory pathogens. It allows a direct effect of probiotics into the respiratory system. To our knowledge, no study has ever focused on the effect of probiotic intra-respiratory administration to prevent from Pseudomonas aeruginosa (PA) pneumonia, a major respiratory pathogen associated with high morbidity rates. In this study, we evaluated the beneficial activity of three Lactobacillus strains (Lactobacillus fermentum K.C6.3.1E, Lactobacillus zeae Od.76, Lactobacillus paracasei ES.D.88) previously screened by ourselves and known to be particularly efficient in vitro in inhibiting PAO1 virulence factors. Cytotoxic assays in alveolar epithelial cell line A549 were performed, followed by the comparison of two lactobacilli prophylactic protocols (one or two administrations) by intra-tracheal administration in a C57BL/6 murine model of PA pneumonia. A549 cells viability was improved from 23 to 75% when lactobacilli were administered before PAO1 incubation, demonstrating a protective effect (P<0.001). A significant decrease of 2 log of PAO1 was observed 4 h after PAO1 instillation (3×106 cfu/mouse) in both groups receiving lactobacilli (9×106 cfu/mouse) compared to PAO1 group (P<0.05). One single prophylactic administration of lactobacilli significantly decreased the secretion by 50% in bronchoalveolar lavages of interleukin (IL)-6 and tumour necrosis factor-α compared to PAO1. No difference of secretion was observed for the IL-10 secretion, whatever the prophylactic study design. This is the first study highlighting that direct lung administration of Lactobacillus strains protect against PA pneumonia. Next step will be to decipher the mechanisms involved before developing this novel approach for human applications.

Frequency of molecular detection of equine coronavirus in faeces and nasal secretions in 277 horses with acute onset of fever

2019 ◽  
Vol 184 (12) ◽  
pp. 385-385 ◽  
Author(s):  
Nicola Pusterla ◽  
Kaitlyn James ◽  
Samantha Mapes ◽  
Farifield Bain
Keyword(s):  
Clinical Signs ◽  
Acute Onset ◽  
Molecular Diagnostic ◽  
Nasal Discharge ◽  
Respiratory Pathogens ◽  
Sample Collection ◽  
Diagnostic Laboratory ◽  
Study Results ◽  
Streptococcus Equi ◽  
Nasal Secretions

ContextDue to the inconsistent development of enteric signs associated with ECoV infection in adult horses, many practitioners collect nasal secretions rather than feces for the molecular diagnostic work-up of such horses.Main conclusionECoV infection should be considered in horses presenting with acute onset of fever, especially when nasal discharge is absent as one of the cardinal clinical sign.ApproachA total of 277 adult horses with acute onset of fever were enrolled in this study. Feces were tested for ECoV and nasal secretions for common respiratory pathogens (equine herpesvirus (EHV)-1, EHV-4, equine influenza virus (EIV), equine rhinitis viruses (ERVs) and Streptococcus equi ss. equi) and ECoV by qPCR. Each submission was accompanied by a questionnaire requesting information pertaining to signalment, use, recent transportation, number of affected horses on the premise and presence of clinical signs at the time of sample collection.ResultsThe total number of horses testing qPCR-positive for ECoV in feces was 20 (7.2%), 4 of which also tested qPCR-positive for ECoV in nasal secretions. In the same population 9.0% of horses tested qPCR-positive for EHV-4, 6.1% for EIV, 4.3% for Streptococcus equi ss. equi, 3.2% for ERVs and 0.7% for EHV-1. Draft horses, pleasure use, multiple horses affected on a premise and lack of nasal discharge were significantly associated with ECoV qPCR-positive horses.InterpretationThe present study results showed that 7.2% of horses with acute onset of fever tested qPCR-positive for ECoV in feces, highlighting the importance of testing such horses for ECoV in feces. The various prevalence factors associated with ECoV qPCR-positive status likely relate to the high infectious nature of ECoV and breed-specific differences in management and husbandry practices.Significance of findingsECoV infection should be suspected and tested for in horses presenting with acute onset of fever, lethargy and anorexia with no respiratory signs. A two-step approach should be consider in which respiratory secretions and feces should be collected from such horses and submitted to a diagnostic laboratory. If the respiratory secretions test negative by qPCR for a panel of respiratory pathogens, feces already submitted to the laboratory should be tested for ECoV.

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