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

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

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.

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.

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