About Oral and Gut Microbiota in Intensive Care Unit : SARS-CoV-2 (COVID-19) Infection Impact.

Study Overview
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Brief Summary
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The objective of the present study is to describe the negative impact on oral and gut microbiota of a severe acute respiratory syndrome SARS-CoV-2 infection in patients hospitalized in intensive care units (ICU). The study would like to compare their microbiota to the microbiota of ICU patients, non-infected by the SARS-CoV-2.

Detailed Description
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Gut microbiota in ICU patients is sorely distorted, there is an important loss of diversity which can be traduced by a decrease of commensal bacteria and an increase of pathogens. The virulence, infectivity, and transmissibility of the emerging SARS-Coronavirus 2 is a reason for us to find strategies and therapeutics to curb the epidemic. Gut mucosa is very probably a target for the virus and it seems likely that feces are a way of transmissibility. It suppose too that gut microbiota is more weathered in patients with a SARS-CoV-2 infection, moreover if they have to be hospitalized in ICU. For this reason, the present study would like to collect oral and rectal swab from patients hospitalized in ICU for a serious SARS-CoV-2 infection and from patients hospitalized in ICU for another reason that a SARS-CoV-2 infection at day 1, each 7 days and at the end of their ICU stay. Other objectives are to know if this distorted microbiota is a risk factor for poor outcomes in our ICU patients, if antibiotics and artificial nutrition are too a risk factor of weathered microbiota and finally if we can connect oral and rectal dysbiosis to use the oral dysbiosis to predict the rectal dysbiosis in view of the ease to collect oral sample.

Official Title
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About Oral and Gut Microbiota in Intensive Care Unit : SARS-CoV-2 (COVID-19) Infection Impact. (CO-MIC Study)

Conditions
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SARS-CoV-2 Acute Respiratory Disease

Intervention / Treatment
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* Other: Fecal and oral samples


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: Controls: - Hospitalized patient with non-SARS-CoV-2 hypoxemic pneumonia Patients COVID 19: - Patient hospitalized for SARS-CoV-2 hypoxemic pneumonia All: Patient hospitalized for less than 48 hours in a general intensive care unit Patient who has given free, informed and express (oral) consent to participate in the research (or a close relative or trusted person of the patient if the patient cannot express himself/herself) Patient covered by a social security system or equivalent Expected hospitalization of more than 48 hours Exclusion Criteria: gut inflammatory disease recent gut surger ostomy recent antibiotics artificial nutrition in the long term

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 |
| --- | --- |
| control<br>patients not suffering from COVID-19 hospitalized in intensive care unit | Other: Fecal and oral samples<br>* oral and rectal swab from patients hospitalized at day 1, each 7 days and at the end of their ICU stay<br>|
| patients COVID-19<br>patients suffering from COVID-19 hospitalized in intensive care unit | Other: Fecal and oral samples<br>* oral and rectal swab from patients hospitalized at day 1, each 7 days and at the end of their ICU stay<br>|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Constitution of the oral and faecal microbiota obtained by sequencing of bacterial DNA | measuring the difference in bacterial DNA sequencing from oral and fecal samples among ICU patients infected by the SARS-CoV-2 and ICU patients without SARS-CoV-2 at day 1 | day 1 | 
| Measuring the difference in bacterial DNA sequencing from oral and fecal samples of patients infected by the SARS-COV-2 and patient without SARS-COV-2 at day 7 | Measuring difference in bacterial DNA sequencing from oral and fecal samples among ICU patients infected by the SARS-CoV-2 and ICU patients without SARS-CoV-2 | day 7 | 
| Measuring the difference in bacterial DNA sequencing from oral and fecal samples of patient infected by the SARS-COV-2 and patient without SARS-COV-2 at day 14 | difference in bacterial DNA sequencing from oral and fecal samples among ICU patients infected by the SARS-CoV-2 and ICU patients without SARS-CoV-2 | day 14 | 

 Terms related to the study
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Keywords Provided by Centre Hospitalier Valida
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SARS-CoV-2, COVID 19, Critical care, microbiota, microbiome