Clostridium perfringensis a major enteric pathogen known to cause gastroenteritis in humans. Although major outbreak cases are frequently reported, to date no Whole Genome Sequencing (WGS) based studies have been performed to understand the genomic epidemiology and virulence gene content of C. perfringens-associated outbreak strains.


We have applied both genomic and phylogenetic analyses on a sub-set of 109 newly-sequenced C. perfringens strains isolated from gastroenteritis-associated disease cases (including food-poisoning and care-home diarrhoea) from England and Wales between 2011 – 2017 to probe virulence profiles including toxin and AMR genes, plasmid features and genomic epidemiology of these case isolates.


Our data identified that highly-similar C. perfringens strains were associated with 9 care home-associated individual outbreaks over a 5 year interval, indicating potential common sources linked to these distinct outbreaks. Enterotoxin gene cpe was encoded in all but 4 isolates (96.4 % type-F strains), and it was further determined that virulence plasmids encoding cpe were extensively distributed in the isolates (97 % care-home isolates carry pCPF5603 plasmid; 60 % food-poisoning isolates carry pCPF4969 plasmid). Further virulence factors, such as β2-toxin, were enriched in these isolates (46.7 %). Phage proteins were also commonly identified, with additional analysis indicating phages may contribute to spread of virulence determinants.


This study highlights the genotypic and epidemiological relatedness of a large collection of C. perfringens strains isolated from gastroenteritis-associated cases from across the UK and Wales. Key points revealed include the potential circulation of disease-associated strains, and impact of cpe-encoding-plasmid disseminations, linked to outbreak cases.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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