Nasopharyngeal microbial communities of patients infected with SARS-COV-2 that developed COVID-19

  1. Maria Paz Ventero
  2. Rafael Ricardo Castro Cuadrat
  3. Inmaculada Vidal
  4. Bruno Gabriel N. Andrade
  5. Carmen Molina-Pardines
  6. Jose M. Haro-Moreno
  7. Felipe H. Coutinho
  8. Esperanza Merino
  9. Luciana CA Regitano
  10. Cynthia B Silveira
  11. Haithem Afli
  12. Mario López-Pérez
  13. Juan Carlos Rodríguez

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Abstract

Background

SARS-CoV-2 is an RNA virus causing COVID-19. The clinical characteristics and epidemiology of COVID-19 have been extensively investigated, however studies focused on the patient’s microbiota are still lacking. In this study, we investigated the nasopharyngeal microbiome composition of patients who developed different severity levels of COVID-19. We performed Rdna-SSU (16S) sequencing from nasopharyngeal swab samples obtained from SARS-CoV-2 positive (56) and negative (18) patients in the province of Alicante (Spain) in their first visit to the hospital. Positive SARS-CoV-2 patients were observed and later categorized in mild (symptomatic without hospitalization), moderate (hospitalization) and severe (admission to ICU). We compared the microbiome diversity and OTU composition among severity groups using Similarity Percentage (SIMPER) analysis and Maaslin2. We also built bacterial co-abundance networks for each group using Fastpar.

Results

Statistical analysis indicated differences in the nasopharyngeal microbiome of COVID19 patients. 62 OTUs were found exclusively in SARS-CoV-2 positive patients, mostly classified as members of the phylum Bacteroidetes (18) and Firmicutes (25). OTUs classified as Prevotella were found to be significantly more abundant in patients that developed more severe COVID-19. Furthemore, co-abundance analysis indicated a loss of network complexity among samples from patients that later developed more severe symptoms.

Conclusions

Our preliminary study shows that the nasopharyngeal microbiome of COVID-19 patients showed differences in the composition of specific OTUs and complexity of co-abundance networks. These microbes with differential abundances among groups could serve as biomarkers for COVID-19 severity. Nevertheless, further studies with larger sample sizes should be conducted to validate these results.

IMPORTANCE

This work has studied the microbiota of the nasopharyngeal tract in COVID19 patients using advanced techniques of molecular microbiology. Diverse microorganisms, most of which are harmless or even beneficial to the host, colonize the nasopharyngeal tract. These microorganisms are the microbiota, and they are present in every people. However, changes in this microbiota could be related to different diseases as cancer, gastrointestinal pathologies or even COVID19. This study has been performed to investigate the microbiota from patients with COVID19, in order to determinate its implication in the pathology severity. The results obtained showed that it is possible that several specific microorganisms are present only in patients with severe COVID19. These data, could be used as a prognostic biomarker to early detect whose patients will develop a severe COVID19 and improve their clinical management.

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  1. ScreenIT

    SciScore for 10.1101/2020.12.01.407486: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: The research project was conducted under the written approval of the Ethic Committee of Clinical Research with Drug (In Spanish, CEIm) of the “Hospital General Universitario de Alicante (Spain)”, and in collaboration with the Biobank of Clinical and Biomedical Research Institute of Alicante (ISABIAL), which are included in the Valencian Network of Biobanks.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The quality of raw sequences was assessed by FastQC software.
    FastQC
    suggested: (FastQC, RRID:SCR_014583)
    Sequences were trimmed using trimmomatic [12] and the resulting paired reads were merged using casper [13], generating individual fragments of about 460 bp.
    trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    Merged amplicon sequences were grouped in operational taxonomic units (OTUs) using cd-hit [14] with an identity of 97%.
    cd-hit
    suggested: (CD-HIT, RRID:SCR_007105)
    Sequences were queried against small subunits (16S) rRNA genes by the SILVA database [15] for taxonomic classification.
    SILVA
    suggested: (SILVA, RRID:SCR_006423)
    The network matrices were loaded in the Cytoscape 3.8 software, and connections filtered by p-value (≤ 0.05) and correlation (≤ −0.6 or ≥ 0.6).
    Cytoscape
    suggested: (Cytoscape, RRID:SCR_003032)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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.

    About SciScore

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  2. Version published to 10.1101/2020.12.01.407486 on bioRxiv