1. Genetics and Genomics
  2. Microbiology and Infectious Disease
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Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy

  1. Daniel R Knight  Is a corresponding author
  2. Korakrit Imwattana
  3. Brian Kullin
  4. Enzo Guerrero-Araya
  5. Daniel Paredes-Sabja
  6. Xavier Didelot
  7. Kate E Dingle
  8. David W Eyre
  9. César Rodríguez
  10. Thomas V Riley  Is a corresponding author
  1. Murdoch University, Australia
  2. University of Western Australia, Australia
  3. University of Cape Town, South Africa
  4. Universidad Andrés Bello, Chile
  5. Universidad Andrés Bello, United Kingdom
  6. University of Warwick, United Kingdom
  7. University of Oxford, United Kingdom
  8. Universidad de Costa Rica, Costa Rica
Research Article
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Cite this article as: eLife 2021;10:e64325 doi: 10.7554/eLife.64325

Abstract

Clostridioides difficile infection (CDI) remains an urgent global One Health threat. The genetic heterogeneity seen across C. difficile underscores its wide ecological versatility and has driven the significant changes in CDI epidemiology seen in the last 20 years. We analysed an international collection of over 12,000 C. difficile genomes spanning the eight currently defined phylogenetic clades. Through whole-genome average nucleotide identity, and pangenomic and Bayesian analyses, we identified major taxonomic incoherence with clear species boundaries for each of the recently described cryptic clades CI-III. The emergence of these three novel genomospecies predates clades C1-5 by millions of years, rewriting the global population structure of C. difficile specifically and taxonomy of the Peptostreptococcaceae in general. These genomospecies all show unique and highly divergent toxin gene architecture, advancing our understanding of the evolution of C. difficile and close relatives. Beyond the taxonomic ramifications, this work may impact the diagnosis of CDI.

Data availability

All data generated or analysed during this study are included in the manuscript and Supplementary Data which is hosted at Figshare http://doi.org/10.6084/m9.figshare.12471461.Data files on figshare include:[1] Full MLST data for all 12000+ C. difficile genomes (Fig 1).[2] Whole-genome ANI analyses (Table 1, Fig 3, Fig 5).[3] Tree files for phylogenetic analyses (Fig 2, Fig 4).[4] Pangenome data (Fig 6).[5] Pan-GWAS data (Table 2).[6] Comparative genomic analysis of virulence gene architecture (Fig 7).Note: Regarding the question below - Did your work use any previously published datasets (e.g., DNA sequence data, clinical trial data, field data)?We retrieved the entire collection of C. difficile genomes (taxid ID 1496) held at the NCBI Sequence Read Archive [https://www.ncbi.nlm.nih.gov/sra/]. The raw dataset (as of 1st January 2020) comprised 12,621 genomes. These genomes comprise hundreds, maybe thousands of publications. The individual accession numbers for all genomes analysed in this study are provided in the Supplementary Data at http://doi.org/10.6084/m9.figshare.12471461.

Article and author information

Author details

  1. Daniel R Knight

    Murdoch University, Murdoch, Australia
    For correspondence
    daniel.knight@murdoch.edu.au
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9480-4733
  2. Korakrit Imwattana

    School of Biomedical Sciences, University of Western Australia, Nedlands, Australia
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2538-9775
  3. Brian Kullin

    Department of Pathology, University of Cape Town, Cape Town, South Africa
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5460-1977
  4. Enzo Guerrero-Araya

    Microbiota-Host Interactions and Clostridia Research Group, Universidad Andrés Bello, Santiago, Chile
    Competing interests
    No competing interests declared.
  5. Daniel Paredes-Sabja

    Microbiota-Host Interactions and Clostridia Research Group, Universidad Andrés Bello, Santiago, United Kingdom
    Competing interests
    No competing interests declared.
  6. Xavier Didelot

    University of Warwick, Coventry, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1885-500X
  7. Kate E Dingle

    Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
  8. David W Eyre

    Big Data Institute, University of Oxford, Oxford, United Kingdom
    Competing interests
    David W Eyre, DWE declares lecture fees from Gilead, outside the submitted work..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5095-6367
  9. César Rodríguez

    Facultad de Microbiología & Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5599-0652
  10. Thomas V Riley

    School of Biomedical Sciences, University of Western Australia, Nedlands, Australia
    For correspondence
    thomas.riley@uwa.edu.au
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1351-3740

Funding

Raine Medical Research Foundation

  • Daniel R Knight

National Health and Medical Research Council

  • Daniel R Knight

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Vaughn S Cooper, University of Pittsburgh, United States

Publication history

  1. Received: October 25, 2020
  2. Accepted: June 8, 2021
  3. Accepted Manuscript published: June 11, 2021 (version 1)
  4. Version of Record published: June 29, 2021 (version 2)

Copyright

© 2021, Knight et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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