Endotoxemia and circulating bacteriome in severe COVID-19 patients

  1. Phatadon Sirivongrangson
  2. Win Kulvichit
  3. Sunchai Payungporn
  4. Trairak Pisitkun
  5. Ariya Chindamporn
  6. Sadudee Peerapornratana
  7. Prapaporn Pisitkun
  8. Suwalak Chitcharoen
  9. Vorthon Sawaswong
  10. Navaporn Worasilchai
  11. Sarinya Kampunya
  12. Opass Putcharoen
  13. Thammasak Thawitsri
  14. Nophol Leelayuwatanakul
  15. Napplika Kongpolprom
  16. Vorakamol Phoophiboon
  17. Thitiwat Sriprasart
  18. Rujipat Samransamruajkit
  19. Somkanya Tungsanga
  20. Kanitha Tiankanon
  21. Nuttha Lumlertgul
  22. Asada Leelahavanichkul
  23. Tueboon Sriphojanart
  24. Terapong Tantawichien
  25. Usa Thisyakorn
  26. Chintana Chirathaworn
  27. Kearkiat Praditpornsilpa
  28. Kriang Tungsanga
  29. Somchai Eiam-Ong
  30. Visith Sitprija
  31. John A. Kellum
  32. Nattachai Srisawat

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Abstract

Background

When severe, COVID-19 shares many clinical features with bacterial sepsis. Yet, secondary bacterial infection is uncommon. However, as epithelium is injured and barrier function is lost, bacterial products entering the circulation might contribute to the pathophysiology of COVID-19.

Methods

We studied 19 adults, severely ill patients with COVID-19 infection, who were admitted to King Chulalongkorn Memorial Hospital, Bangkok, Thailand, between 13th March and 17th April 2020. Blood samples on days 1, 3, and 7 of enrollment were analyzed for endotoxin activity assay (EAA), (1 → 3)-β- d -glucan (BG), and 16S rRNA gene sequencing to determine the circulating bacteriome.

Results

Of the 19 patients, 13 were in intensive care and 10 patients received mechanical ventilation. We found 8 patients with high EAA (≥ 0.6) and about half of the patients had high serum BG levels which tended to be higher in later in the illness. Although only 1 patient had a positive blood culture, 18 of 19 patients were positive for 16S rRNA gene amplification. Proteobacteria was the most abundant phylum. The diversity of bacterial genera was decreased overtime.

Conclusions

Bacterial DNA and toxins were discovered in virtually all severely ill COVID-19 pneumonia patients. This raises a previously unrecognized concern for significant contribution of bacterial products in the pathogenesis of this disease.

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  1. Version published to 10.1186/s40635-020-00362-8
  2. ScreenIT

    SciScore for 10.1101/2020.05.29.20109785: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: The study was reviewed and approved by Faculty of Medicine, Chulalongkorn University ethics committee (IRB no. 336/63).
    Consent: The informed consent was waived due to the observational nature of the study.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    : Raw sequencing data were demultiplexed by MiSeq reporter software (version 2.6.2.3).
    MiSeq
    suggested: (A5-miseq, RRID:SCR_012148)
    Then, merged reads were deduplicated and clustered with 99% similarity by using VSEARCH [19].
    VSEARCH
    suggested: None
    Differential abundance analysis was conducted by Linear discriminant analysis Effect Size (LEfSe) [22].
    LEfSe
    suggested: (LEfSe, RRID:SCR_014609)
    Wilcoxon matched pairs test were analyzed using GraphPad Prism version 6.01.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Our study had several limitations. First, our 16s RNA gene amplification technique could not demonstrate the absolute number of bacterial DNA. Therefore, we could not correlate the burden of circulating bacterial DNA to the severity of the patients. However, our study aimed to be a starting point for future investigation. Second, our study did not include respiratory tract or gastrointestinal specimens, so we cannot completely establish the source of bacterial products in our patients. Future study should explore the effect of organ crosstalk between the lung and the intestine during COVID-19 infection.

    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.

    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 10.1101/2020.05.29.20109785v1 on medRxiv