Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy.

Daniel R Knight,Daniel Paredes-Sabja,Kate E Dingle,Enzo Guerrero-Araya,César Rodríguez,Thomas V Riley,Brian Kullin,Korakrit Imwattana,Xavier Didelot,David W Eyre

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.

Highlights

We identified several uniquely present, absent, or organised gene clusters associated with ethanolamine catabolism (C-III), heavy metal uptake (CIII), polyamine biosynthesis (C-III), fructosamine utilization (C-I, contained within ΦSemix9P1 in ST343 (C-III)), zinc transport (C-II, Clade 5 (C5))
Through phylogenomic analysis of the largest and most diverse collection of C. difficile genomes to date, we identified major incoherence in C. difficile taxonomy, provide the first whole-genome sequencing (WGS)-based phylogeny for the Peptostreptococcaceae and provide new insight into intra-species diversity and evolution of pathogenicity in this major One Health pathogen
Our analysis found high nucleotide identity (ANI > 97%) between C. difficile clades Clade 1 (C1)-4, indicating that strains from these four clades belong to the same species

Summary

Introduction

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 and taxonomy of the Peptostreptococcaceae in general. Based on multi-locus sequence type (MLST), there are eight recognised monophyletic groups or ‘clades’ of C. difficile[11] Strains within these clades show many unique clinical, microbiological, and ecological features[11]. Whole-genome ANI, and pangenomic and Bayesian analyses are used to explore an international collection of over 12,000 C. difficile genomes, to provide new insights into ancestry, genetic diversity, and evolution of pathogenicity in this enigmatic pathogen

Results

Discussion

Materials and Methods