scholarly journals SARS-CoV-2 detection in the lower respiratory tract of invasively ventilated ARDS patients

Critical Care ◽  
2020 ◽  
Vol 24 (1) ◽  
Author(s):  
Niccolò Buetti ◽  
Paul-Henri Wicky ◽  
Quentin Le Hingrat ◽  
Stéphane Ruckly ◽  
Timothy Mazzuchelli ◽  
...  
Keyword(s):  
Viral Load ◽  
Respiratory Tract ◽  
Critically Ill ◽  
Critically Ill Patients ◽  
Lower Respiratory Tract ◽  
Logistic Models ◽  
Time Interval ◽  
Mixed Effect ◽  
Viral Shedding ◽  
Binational Study

Abstract Background Data on SARS-CoV-2 load in lower respiratory tract (LRT) are scarce. Our objectives were to describe the viral shedding and the viral load in LRT and to determine their association with mortality in critically ill COVID-19 patients. Methods We conducted a binational study merging prospectively collected data from two COVID-19 reference centers in France and Switzerland. First, we described the viral shedding duration (i.e., time to negativity) in LRT samples. Second, we analyzed viral load in LRT samples. Third, we assessed the association between viral presence in LRT and mortality using mixed-effect logistic models for clustered data adjusting for the time between symptoms’ onset and date of sampling. Results From March to May 2020, 267 LRT samples were performed in 90 patients from both centers. The median time to negativity was 29 (IQR 23; 34) days. Prolonged viral shedding was not associated with age, gender, cardiac comorbidities, diabetes, immunosuppression, corticosteroids use, or antiviral therapy. The LRT viral load tended to be higher in non-survivors. This difference was statistically significant after adjusting for the time interval between onset of symptoms and date of sampling (OR 3.78, 95% CI 1.13–12.64, p = 0.03). Conclusions The viral shedding in LRT lasted almost 30 days in median in critically ill patients, and the viral load in the LRT was associated with the 6-week mortality.

scholarly journals Paired nasopharyngeal and deep lung testing for SARS-CoV2 reveals a viral gradient in critically ill patients: a multi-centre study

2020 ◽  
Author(s):  
Islam Hamed ◽  
Nesreen Shaban ◽  
Marwan Nassar ◽  
Sam Love ◽  
Martin D Curran ◽  
...  
Keyword(s):  
Viral Load ◽  
Respiratory Tract ◽  
Critically Ill ◽  
Critically Ill Patients ◽  
Lower Respiratory Tract ◽  
Limit Of Detection ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Multi Centre Study ◽  
Upper Respiratory

Introduction Samples for diagnostic tests for SARS-CoV-2 can be obtained from the upper (nasopharyngeal/oropharyngeal swabs) or lower respiratory tract (sputum or tracheal aspirate or broncho-alveolar lavage - BAL). Data from different testing sites indicates different rates of positivity. Reverse-transcriptase polymerase chain reaction (RT-PCR) allows for semi-quantitative estimates of viral load as time to crossing threshold (Ct) is inversely related to viral load. Objectives The objective of our study was to evaluate SARS-CoV2 RNA loads between paired nasopharyngeal (NP) and deep lung (endotracheal aspirate or BAL) samples from critically ill patients. Methods SARS-CoV-2 RT-PCR results were retrospectively reviewed for 51 critically ill patients from 5 intensive care units in 3 hospitals ; Addenbrookes Hospital Cambridge (3 units), Royal Papworth Cambridge (1 unit), and Royal Sunderland Hospital (1 unit). At the times when paired NP and deep lung samples were obtained, one patient had been on oxygen only, 6 patients on non-invasive ventilation, 18 patients on ECMO, and 26 patients mechanically ventilated. Results Results collected showed significant gradient between NP and deep lung viral loads. Median Ct value was 29 for NP samples and 24 for deep lung samples. Of 51 paired samples, 16 were negative (below limit of detection) on NP swabs but positive (above limit of detection) on deep lung sample, whilst 2 were negative on deep sample but positive on NP (both patients were on ECMO). Conclusions It has been suggested that whilst SARS-CoV1 tends to replicate in the lower respiratory tract, SARS-CoV2 replicates more vigorously in the upper respiratory tract. These data challenge that assumption. These data suggest that viral migration to, and proliferation in, the lower respiratory tract may be a key factor in the progression to critical illness and the development of severe acute respiratory syndrome (SARS). Factors which promote this migration should be examined for association with severe COVID-19. From a practical point of view, patients with suspected severe COVID-19 should have virological samples obtained from the lower respiratory tract where-ever possible, as upper respiratory samples have a significant negative rate.

scholarly journals The lower respiratory tract microbiome of critically ill patients with COVID-19

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Paolo Gaibani ◽  
Elisa Viciani ◽  
Michele Bartoletti ◽  
Russell E. Lewis ◽  
Tommaso Tonetti ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Critically Ill ◽  
Critically Ill Patients ◽  
Lower Respiratory Tract ◽  
Multidrug Resistant ◽  
Carbapenem Resistant ◽  
Lung Microbiome ◽  
Bacterial Microbiome ◽  
Unweighted Unifrac ◽  
Bacterial Superinfection

AbstractCOVID-19 infection may predispose to secondary bacterial infection which is associated with poor clinical outcome especially among critically ill patients. We aimed to characterize the lower respiratory tract bacterial microbiome of COVID-19 critically ill patients in comparison to COVID-19-negative patients. We performed a 16S rRNA profiling on bronchoalveolar lavage (BAL) samples collected between April and May 2020 from 24 COVID-19 critically ill subjects and 24 patients with non-COVID-19 pneumonia. Lung microbiome of critically ill patients with COVID-19 was characterized by a different bacterial diversity (PERMANOVA on weighted and unweighted UniFrac Pr(> F) = 0.001) compared to COVID-19-negative patients with pneumonia. Pseudomonas alcaligenes, Clostridium hiranonis, Acinetobacter schindleri, Sphingobacterium spp., Acinetobacter spp. and Enterobacteriaceae, characterized lung microbiome of COVID-19 critically ill patients (LDA score > 2), while COVID-19-negative patients showed a higher abundance of lung commensal bacteria (Haemophilus influenzae, Veillonella dispar, Granulicatella spp., Porphyromonas spp., and Streptococcus spp.). The incidence rate (IR) of infections during COVID-19 pandemic showed a significant increase of carbapenem-resistant Acinetobacter baumannii (CR-Ab) infection. In conclusion, SARS-CoV-2 infection and antibiotic pressure may predispose critically ill patients to bacterial superinfection due to opportunistic multidrug resistant pathogens.

Clinical correlates of herpes simplex virus type 1 loads in the lower respiratory tract of critically ill patients

2013 ◽  
Vol 58 (1) ◽  
pp. 79-83 ◽  
Author(s):  
Evelien Assink-de Jong ◽  
A.B. Johan Groeneveld ◽  
Annika M. Pettersson ◽  
Alex Koek ◽  
Christina M.J.E. Vandenbroucke-Grauls ◽  
...  
Keyword(s):  
Herpes Simplex Virus ◽  
Herpes Simplex ◽  
Respiratory Tract ◽  
Critically Ill ◽  
Herpes Simplex Virus Type ◽  
Critically Ill Patients ◽  
Lower Respiratory Tract ◽  
Clinical Correlates ◽  
Simplex Virus

Aspergillus in the lower respiratory tract of immunocompetent critically ill patients

2014 ◽  
Vol 69 (3) ◽  
pp. 284-292 ◽  
Author(s):  
Maxime Lugosi ◽  
Corinne Alberti ◽  
Jean-Ralph Zahar ◽  
Maité Garrouste ◽  
Virginie Lemiale ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Critically Ill ◽  
Critically Ill Patients ◽  
Lower Respiratory Tract

scholarly journals Segregation of Virulent Influenza A(H1N1) Variants in the Lower Respiratory Tract of Critically Ill Patients during the 2010–2011 Seasonal Epidemic

PLoS ONE ◽  
2011 ◽  
Vol 6 (12) ◽  
pp. e28332 ◽  
Author(s):  
Antonio Piralla ◽  
Elena Pariani ◽  
Francesca Rovida ◽  
Giulia Campanini ◽  
Alba Muzzi ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Critically Ill ◽  
Critically Ill Patients ◽  
Lower Respiratory Tract ◽  
Influenza A ◽  
Influenza A H1n1 ◽  
Seasonal Epidemic

scholarly journals COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and may be modified by dexamethasone

2021 ◽  
Author(s):  
Aartik Sarma ◽  
Stephanie A. Christenson ◽  
Eran Mick ◽  
Catherine DeVoe ◽  
Thomas Deiss ◽  
...  
Keyword(s):  
Gene Expression ◽  
Respiratory Tract ◽  
Critically Ill ◽  
Critically Ill Patients ◽  
Host Response ◽  
Lower Respiratory Tract ◽  
Transcriptional Profiling ◽  
Cytokine Storm

AbstractWe performed comparative lower respiratory tract transcriptional profiling of 52 critically ill patients with ARDS from COVID-19 or other etiologies, or without ARDS. We found no evidence of cytokine storm but instead observed complex host response dysregulation driven by genes with non-canonical roles in inflammation and immunity that were predicted to be modulated by dexamethasone. Compared to other viral ARDS, COVID-19 was characterized by impaired interferon-stimulated gene expression.

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