Bacterial and Fungal Microbiota of Patients With Severe Viral Pneumonia With COVID-19

Study Overview
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Brief Summary
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Observational pilot single-center study aiming to determine the microbiota of critically ill patients infected with SARS-CoV-2. COVID-19 patients will be compared to historical critically ill controls with no SARS-CoV-2 infection.

Detailed Description
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Observational pilot single-center study aiming to determine the microbiota of critically ill patients infected with SARS-CoV-2. COVID-19 patients will be compared to historical critically ill controls with no SARS-CoV-2 infection. Respiratory and fecal microbiota (microbial and fungal) will be determined in COVID-19 patients on bronchoalveolar lavage and rectal swab. Inflammatory biomarkers will also be measured in COVID-19 patients. Characteristics of study patients will be collected at ICU admission and during ICU stay.

Official Title
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Bacterial and Fungal Microbiota of Patients With Severe Viral Pneumonia With SARS-CoV2

Conditions
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Sars-CoV2

Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: For the Covid-19 Group: with a confirmed severe lung infection with CoV2-SARS-Cov2 admitted to the ICU. For the Control Group: Historic cohort of non SARS -CoV2-infected adults admitted to the ICU (between March and October 2019), that was investigated for fecal microbiota in a previous study (control patients in a fecal microbiota study in patients included in the SEAT study). Exclusion Criteria: For the Covid-19 group: Lack of coverage Patients who received antibiotic therapy within 6 weeks prior to Covid-19 symptomatology, Pregnant women, Severe immunosuppression: Neutropenia < 0.5 G/L, Chemotherapy < 6 months, Bone marrow transplant recipients, HIV with CD4+ lymphocytes < 0.4 G/L Impossible to perform bronchoalveolar lavage, Non-socially insured, Refusal to participate in the social study

Ages Eligible for Study
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Minimum Age: 18 Years

Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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Arms and Interventions

| Participant Group/Arm | Intervention/Treatment |
| --- | --- |
| Covid-19 group<br>Critically ill patients with SARS-CoV-2 infection | |
| control group<br>Historical critically ill patients with no SARS-CoV-2 infection | |

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Composition of the fecal bacterial and fungal microbiota | relative abundances and diversity indices | At 28 days | 

Secondary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Analysis of the faecal microbiota from rectal swab | Alterations in fecal microbiota composition (including virose, bacteria and fungi) in COVID-19 patients compared with controls | at baseline and every 7 days during 28 days | 
| Analysis of the respiratory microbiota from the bronchoalveolar lavage liquid | Alterations in respiratory microbiota composition (including virose, bacteria and fungi) in COVID-19 patients compared with controls | at baseline and every 7 days during 28 days | 
| Serum inflammatory markers changes | Changes in blood, c-reactive protein, leucocyte, lymphocyte from baseline | at 28 days, | 
| Inflammatory markers changes | changes in Cytokine/ chemokine from baseline | at 28 days, | 
| Mortality | death | at 28 days, | 
| mechanical ventilation free days | Number of days alive without mechanical ventilation | at 28 days, |