1. Genetics and Genomics
  2. Microbiology and Infectious Disease
Download icon

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
  • Cited 0
  • Views 36
  • Annotations
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)

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.

Metrics

  • 36
    Page views
  • 6
    Downloads
  • 0
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Developmental Biology
    2. Genetics and Genomics
    Brent A Wilkerson et al.
    Research Article Updated

    This study provides transcriptomic characterization of the cells of the crista ampullaris, sensory structures at the base of the semicircular canals that are critical for vestibular function. We performed single-cell RNA-seq on ampullae microdissected from E16, E18, P3, and P7 mice. Cluster analysis identified the hair cells, support cells and glia of the crista as well as dark cells and other nonsensory epithelial cells of the ampulla, mesenchymal cells, vascular cells, macrophages, and melanocytes. Cluster-specific expression of genes predicted their spatially restricted domains of gene expression in the crista and ampulla. Analysis of cellular proportions across developmental time showed dynamics in cellular composition. The new cell types revealed by single-cell RNA-seq could be important for understanding crista function and the markers identified in this study will enable the examination of their dynamics during development and disease.

    1. Genetics and Genomics
    2. Medicine
    Matthew William Grol et al.
    Research Article Updated

    Osteogenesis imperfecta (OI) is characterized by short stature, skeletal deformities, low bone mass, and motor deficits. A subset of OI patients also present with joint hypermobility; however, the role of tendon dysfunction in OI pathogenesis is largely unknown. Using the Crtap-/- mouse model of severe, recessive OI, we found that mutant Achilles and patellar tendons were thinner and weaker with increased collagen cross-links and reduced collagen fibril size at 1- and 4-months compared to wildtype. Patellar tendons from Crtap-/- mice also had altered numbers of CD146+CD200+ and CD146-CD200+ progenitor-like cells at skeletal maturity. RNA-seq analysis of Achilles and patellar tendons from 1-month Crtap-/- mice revealed dysregulation in matrix and tendon marker gene expression concomitant with predicted alterations in TGF-β, inflammatory, and metabolic signaling. At 4-months, Crtap-/- mice showed increased αSMA, MMP2, and phospho-NFκB staining in the patellar tendon consistent with excess matrix remodeling and tissue inflammation. Finally, a series of behavioral tests showed severe motor impairments and reduced grip strength in 4-month Crtap-/- mice – a phenotype that correlates with the tendon pathology.