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Role of the Microbiota in the Evolution of the SARS-CoV-2 Disease,COVID-19, in Hospitalized Patients (MicrobioCOVID)

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ClinicalTrials.gov Identifier: NCT04669938
Recruitment Status : Recruiting
First Posted : December 17, 2020
Last Update Posted : December 17, 2020
Sponsor:
Information provided by (Responsible Party):
Assistance Publique - Hôpitaux de Paris

Study Description
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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.


Condition or disease Intervention/treatment
Covid19 Other: oropharyngeal and intestinal microbiota Other: host genotype Other: host immune factors Other: viral sequence

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.

Study Design
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Study Type : Observational
Estimated Enrollment : 200 participants
Observational Model: Case-Only
Time Perspective: Prospective
Official Title: Role of the Microbiota in the Evolution of the SARS-CoV-2 Disease in Hospitalized Patients
Actual Study Start Date : December 4, 2020
Estimated Primary Completion Date : March 31, 2022
Estimated Study Completion Date : March 31, 2022

Resource links provided by the National Library of Medicine


Groups and Cohorts
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Group/Cohort Intervention/treatment
Patients hospitalized for COVID-19 Other: oropharyngeal and intestinal microbiota
analysis of oropharyngeal and intestinal microbiota

Other: host genotype
analysis of a part of host genotype

Other: host immune factors
analysis of host immune factors

Other: viral sequence
analysis of viral sequence


Outcome Measures
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Primary Outcome Measures :
  1. identify risk factors associated with severe forms of COVID-19 [ Time Frame: day 14 ]
    The main endpoint is the indication of worsening of the general condition


Secondary Outcome Measures :
  1. link between the composition of the gut microbiota and admission to intensive care [ Time Frame: 3 months ]
    composition of the gut microbiota on admission to intensive care to predict the outcome of severe COVID-19 in patients transferred to the ICU (subgroup analysis);

  2. predictive performance of semi-quantitative culture and rapid metagenomic evaluation [ Time Frame: 3 months ]
    predictive performance of semi-quantitative culture and rapid metagenomic evaluation of the oropharyngeal microbiota to predict the occurrence of VAP in patients admitted to an ICU and mechanically ventilated (subgroup analysis).


Eligibility Criteria
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Ages Eligible for Study:   18 Years and older   (Adult, Older Adult)
Sexes Eligible for Study:   All
Accepts Healthy Volunteers:   No
Sampling Method:   Non-Probability Sample
Study Population
Adult patient with documented SARS-CoV-2 infection requiring hospitalization.
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
Contacts and Locations
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Top of Page Study Description Study Design Groups and Cohorts Outcome Measures Eligibility Criteria Contacts and Locations More Information

Information from the National Library of Medicine

To learn more about this study, you or your doctor may contact the study research staff using the contact information provided by the sponsor.

Please refer to this study by its ClinicalTrials.gov identifier (NCT number): NCT04669938


Contacts
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Contact: Etienne Ruppé 1 40 25 80 00 ext 33 etienne.ruppe@aphp.fr
Contact: Xavier Lescure 1 40 25 80 00 ext 33 xavier.lescure@aphp.fr

Locations
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France
LESCURE Recruiting
Paris, France
Contact: xavier lescure       xavier.lescure@aphp.fr   
Sponsors and Collaborators
Assistance Publique - Hôpitaux de Paris
More Information
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Top of Page Study Description Study Design Groups and Cohorts Outcome Measures Eligibility Criteria Contacts and Locations More Information
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Responsible Party: Assistance Publique - Hôpitaux de Paris
ClinicalTrials.gov Identifier: NCT04669938    
Other Study ID Numbers: APHP201083
First Posted: December 17, 2020    Key Record Dates
Last Update Posted: December 17, 2020
Last Verified: November 2020
Individual Participant Data (IPD) Sharing Statement:
Plan to Share IPD: Undecided

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Studies a U.S. FDA-regulated Drug Product: No
Studies a U.S. FDA-regulated Device Product: No
Additional relevant MeSH terms:
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COVID-19
Respiratory Tract Infections
Infections
Pneumonia, Viral
Pneumonia
Virus Diseases
Coronavirus Infections
 Coronaviridae Infections
Nidovirales Infections
RNA Virus Infections
Lung Diseases
Respiratory Tract Diseases
Immunologic Factors
Physiological Effects of Drugs