Results from EDIFICE : A French pilot study on COVID-19 and the gut microbiome in a hospital environment

  1. A.C.L. Cervino
  2. R. Fabre
  3. J. Plassais
  4. G. Gbikpi-Benissan
  5. E. Petat
  6. E. Le Quellenec
  7. L. Neuberger-Castillo
  8. J-M. Laurent
  9. L Iordache
  10. M. Bouchahda
  11. G. Marti
  12. G. Chapelet

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Abstract

Early reports suggest that both fecal shedding and dysbiosis of the gut microbiome are associated to disease severity in COVID-19 patients. We investigated the gut microbiome as well as the prevalence of SARS-CoV-2 in stool samples from two French populations: exposed healthcare workers and elderly hospitalized COVID-19 patients. The predictive power of bacterial loss of diversity and detection of SARS-CoV-2 in stool was assessed at 4 weeks against clinical outcomes in the patient group.

METHODS

79 healthcare workers in contact with COVID-19 patients and 64 elderly patients hospitalised in a COVID-19 unit in France were included in the EDIFICE trial from April 2020 until May 2021. Stool samples were collected at inclusion. Loss of bacterial diversity was diagnosed based on 16S rRNA gene sequencing. Stool positivity to SARS-CoV-2 was determined by RT-PCR. Clinical outcomes were recorded at a 4 weeks follow up visit. In particular, these include whether the patient had been put under oxygen during the 4 weeks follow up, whether he had been discharged with or without aggravation from initial symptoms or whether the patient had died. The primary end point was to validate the hypothesis that hospitalized COVID-19 patients had more often lost their bacterial diversity than highly exposed active healthcare workers.

RESULTS

Elderly hospitalised patients with COVID-19 had more frequently lost their bacterial diversity when compared to exposed healthcare workers (p-value = 0.005), their severe dysbiosis was characterized by enrichment of the family Erysipelotrichaceae and depletion of beneficial bacteria at the genus level such as butyrate producers (Butyrivibrio, Roseburia, Faecalibacterium) and Bifidobacterium. The virus was detected in 61% of hospitalized patients and in only one healthcare workers (2%) who had previously been diagnosed with COVID-19 (p-value<0.001). No significant difference in the gut microbiome composition at the genus level of patients that tested positive in stool versus patients that tested negative was observed. Neither bacterial loss of diversity nor positivity to SARS-CoV-2 were associated to clinical outcome at 4 weeks.

CONCLUSIONS

We report findings of the first French trial investigating the clinical interest of stool based diagnosis of SARS-CoV-2 and loss of bacterial diversity in a population of elderly hospitalised COVID-19 patients and highly exposed healthcare workers. Our findings of reduced bacterial diversity and a strong gut dysbiosis in elderly hospitalized COVID-19 patients are highly consistent with previous reports mostly from Chinese populations. A major limitation is that observed differences in the gut microbiome between the two studied groups cannot be attributed to COVID-19 per se given the large number of confounding factors. SARS-CoV-2 was detected in the stool of the majority of hospitalized patients even several weeks after initial diagnosis by nasopharyngeal swabs. This high prevalence warrants further investigation by the scientific community into mechanism.

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  1. ScreenIT

    SciScore for 10.1101/2022.02.06.22269945: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsIRB: Subject recruitment and sample collection: EDIFICE was approved by the French ethics committee, Comité de Protection des Personnes Est-III, under number 2020-A00979-30 on April 21st, 2020.
    Field Sample Permit: Stool samples were thus collected using the DNA/RNA Shield™ Fecal Collection Tubes (Zymo Research, Irvine, California).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line AuthenticationAuthentication: The cutoff was further validated in a real life cohort of 100 participants who self reported their health status as one of five categories (“Excellent “, “Very good “, “Good “, “Not so good “, “Poor “).

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Raw sequence data generated for this study are available in the Sequence Read Archive under BioProject accession PRJNA787810.
    BioProject
    suggested: (NCBI BioProject, RRID:SCR_004801)
    The pipeline first removes expected 5’ and 3’ primers, CCTACGGGNGGCWGCAG and GACTACHVGGGTATCTAATCC, respectively, from the paired-end reads in the Fastq files, using the Cutadapt tool.
    Cutadapt
    suggested: (cutadapt, RRID:SCR_011841)
    Statistical analysis was performed internally using (“R: The R Project for Statistical Computing” n.d.) (v 4.1.0) and (“RStudio | Open Source & Professional Software for Data Science Teams” n.d.) (v 1.4.1106) according to the Statistical Analysis Plan established prior to database lock.
    R Project for Statistical
    suggested: (R Project for Statistical Computing, RRID:SCR_001905)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    The EDIFICE trial suffers from various limitations, additionally to the lack of matching between groups, such as the lack of systematic testing of healthcare workers due to the non-interventional nature of the trial and it would have been interesting to systematically perform a follow up fecal RT-PCR test at 4 weeks in both groups. Additional exploration of inflammatory and antibody markers in blood and intestinal biopsies would also have been of great interest.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  2. Version published to 10.1101/2022.02.06.22269945v1 on medRxiv