Clinical trial NCT04669938: Role of the Microbiota in the Evolution of the SARS-CoV-2 Disease,COVID-19, in Hospitalized Patients
Official title: Role of the Microbiota in the Evolution of the SARS-CoV-2 Disease in Hospitalized Patients
Study type: OBSERVATIONAL
Overall status: UNKNOWN
Conditions: Covid19
Lead sponsor: Assistance Publique - Hôpitaux de Paris
Sponsor class: OTHER
First posted: 2020-12-17
Enrollment: 200
Sex: ALL
Minimum age (years): 18
Standard ages: ADULT
OLDER_ADULT
Accepts healthy volunteers: no
Observational model: CASE_ONLY
Time perspective: PROSPECTIVE
Sampling method: NON_PROBABILITY_SAMPLE
Study population: Adult patient with documented SARS-CoV-2 infection requiring hospitalization.

Brief summary: Patients hospitalized for COVID-19 may need intensive care (e.g. mechanical ventilation) during hospitalization. Some risk factors are already known but better targeting of such patients is still needed, at least because existing risk factors are not strong enough to provide an accurate prediction. Care organization would benefit for such a predictive tool.

Oropharyngeal and gut microbiota could potentially fill a significant gap in predictive performances. The investigators therefore propose to sample 200 patients (oropharyngeal and rectal swab) admitted in infectious disease department at Bichat Hospital and at high risk of needing intensive care during hospitalization. The investigators plan to perform metagenomic sequencing and bioinformatic analysis of these samples to characterize the diversity of bacterial species present in the oropharynx and the gut and to identify new factors associated with the need for intensive care. Aside metagenomic analyses, The investigators will perform semi-quantitative cultures of the oropharyngeal and gut microbiota to identify and quantify pathogens in order to predict the risk of bacterial infections in COVD-19 patients.

For patients transferred in intensive care unit, The investigators will to perform another series of samples to better characterize the evolution of microbiota during mechanical ventilation and identify factors associated with the risk of developing a ventilator-associated pneumonia.

Microbiota data will be considered together with the host genotype, the viral sequence and a deep immunological profiling to identify the main determinants of the evolution toward severity of COVID-19.

Detailed description: Patients hospitalized for COVID-19 may need intensive care (e.g. mechanical ventilation) during hospitalization. Some risk factors are already known (e.g. sex, comorbidities, initial clinical presentation inflammatory cytokines), but better targeting of such patients is still needed, at least because existing risk factors are not strong enough to provide an accurate prediction. Care organization would benefit for such a predictive tool.

Oropharyngeal and gut microbiota could fill a significant gap in predictive performances. The investigators therefore propose to take advantage of the French-COVID cohort and sample 200 patients (oropharyngeal and rectal swab) admitted in infectious disease department at Bichat Hospital and at high risk of needing intensive care during hospitalization. The investigators plan to perform metagenomic sequencing and bioinformatic analysis of these samples to characterize the diversity of bacterial species present in the oropharynx and the gut and to identify new factors associated with the need for intensive care. Aside metagenomic analyses, The investigators will perform semi-quantitative cultures of the oropharyngeal and gut microbiota to identify and quantify pathogens in order to predict the risk of bacterial infections in COVD-19 patients.

The genetic determinants of the host (the patient) could also be predictive of the severity of the disease and so does the immunological response to the COVID-19. Likewise, it has been suggested that certain mutations (notably the D614G mutation) of the viral sequence could be associated with the infectivity of the virus.

In addition to the direct role of the microbiota in the course of infection, the immune characteristics specific to the host, by themselves or in interaction with the microbiota, could play an important role in the progression of the disease.

This project focuses on the clinical characterization of COVID-19 and its evolution, as well as disease management.

The research focuses on 4 main areas:

* Characterization of the oropharyngeal and intestinal microbiota of patients with COVID-19
* Characteristics of the host (genotype)
* Immune characteristics of the host
* Characteristics of the SARS-CoV-2 viral genome

For patients transferred in intensive care unit, The investigators will to perform another series of samples to better characterize the evolution of microbiota during mechanical ventilation and identify factors associated with the risk of developing a ventilator-associated pneumonia.

Eligibility criteria: Inclusion Criteria:

* Adult patient with documented SARS-CoV-2 infection requiring hospitalization.

Exclusion Criteria:

* Lack of consent
* Patients hospitalized in an intensive care unit
* Patient under guardianship or curatorship

Primary outcomes:
measure: Identify risk factors associated with severe forms of COVID-19 requiring transfer to ICU
timeFrame: day 14
Secondary outcomes:
measure: Link between the composition of the gut microbiota and admission to intensive care
timeFrame: 3 months
measure: Predictive performance of semi-quantitative culture and rapid metagenomic evaluation
timeFrame: 3 months
Other outcomes:
Locations:
city: Paris
country: France
facility: LESCURE
Study officials:
References: