Nasopharyngeal Microbiota as an early severity biomarker in COVID-19 hospitalised patients

  1. Maria Paz Ventero
  2. Oscar Moreno-Perez
  3. Carmen Molina-Pardines
  4. Andreu Paytuví-Gallart
  5. Vicente Boix
  6. Isabel Escribano
  7. Irene Galan
  8. Pilar González-delaAleja
  9. Mario López-Pérez
  10. Rosario Sánchez-Martínez
  11. Esperanza Merino
  12. Juan Carlos Rodríguez

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Abstract

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  1. Version published to 10.1016/j.jinf.2021.12.030
  2. ScreenIT

    SciScore for 10.1101/2021.09.28.461924: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Ethics statement and data availability: This project was performed in the Clinical and Biomedical Research Institute of Alicante (ISABIAL), under the written approval of the Ethics Committee of Clinical Research with Drugs (in Spanish, CEIm) of the General University Hospital of Alicante (Ref CEIm approval: PI2020-052).
    Sex as a biological variablenot detected.
    RandomizationOf the 1526 patients hospitalised in the study period, nasopharyngeal samples from 324 patients were randomly processed and preserved.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The V3 and V4 region from 16S rRNA gene were amplified by PCR, and then the fragments obtained were sequenced in the MiSeq system with V3 reagents (600 cycle, 2×300bp).
    MiSeq
    suggested: (A5-miseq, RRID:SCR_012148)
    The taxonomy was assigned using the SILVA Database (Release 132) [22].
    SILVA
    suggested: (SILVA, RRID:SCR_006423)
    Multiple logistic regression models adjusted for age, gender, and comorbidity were built to evaluate the association between microbiota diversity indexes or the differentially represented genus (obtained by DESeq2) with the primary outcomes, and the odds ratios (OR) with the 95%CI were estimated.
    DESeq2
    suggested: (DESeq, RRID:SCR_000154)
    IBM SPSS Statistics v25 (Armonk, NY) was used for the analyses.
    SPSS
    suggested: (SPSS, RRID:SCR_002865)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Our study has several limitations, this was an observational, retrospective, single-centre study, and collection of data was not standardized in advance. The sample size and the absence of differences in the characteristics of the global cohort of patients admitted to our hospital during the duration of the study reinforce the present data. Multiple factors can condition changes in microbiota, including the use of antibiotics. Nonetheless, the design of the statistical analysis adjusted for the use of antibiotic therapy in the 3 months prior to the inclusion of the study, allowing us to limit this bias. The exclusion of these patients from the study would have greatly limited the external validity of our results. Finally, the 16S ribosomal RNA amplicon sequencing approach to study the microbiota could introduce bias in the obtained data because this method does not allow the study of the whole microbiome, but only the genera amplified by PCR. Nevertheless, it is the most common technique to study microbiota in clinical samples. Moreover, the microbiota bioinformatics analysis has not been standardized yet, which hampered comparison interpretations of our results. In summary, the higher diversity found in patients without IMV or a fatal outcome, together with the presence of certain genera in the nasopharyngeal microbiota, seemed to be an early biomarker of a favourable clinical evolution in a cohort of Mediterranean hospitalised patients with SARS-CoV-2 infection. Our finding...

    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

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.09.28.461924v1 on bioRxiv