Intra-species diversity of Clostridium perfringens: A diverse genetic repertoire reveals its pathogenic potential

Abstract

<i>Clostridium perfringens</i> is the causative agent of many enterotoxic diseases in humans and animals, and it is present in diverse environments (soil, food, sewage, and water). Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) have provided a general approach about genetic diversity of <i>C. perfringens</i>; however, those studies are limited to specific locations and often include a reduced number of genomes. In this study, 372 <i>C. perfringens</i> genomes from multiple locations and sources were used to assess the genetic diversity and phylogenetic relatedness of this pathogen. <i>In silico</i> MLST was used for typing the isolates, and the resulting sequence types (ST) were assigned to clonal complexes (CC) based on allelic profiles that differ from its founder by up to double-locus variants. A pangenome analysis was conducted, and a core genome-based phylogenetic tree was created to define phylogenetic groups. Additionally, key virulence factors, toxinotypes, and antibiotic resistance genes were identified using ABRicate against Virulence Factor Database (VFDB), TOXiper, and Resfinder, respectively. The majority of the <i>C. perfringens</i> genomes found in publicly available databases were derived from food (<i>n</i> = 85) and bird (<i>n</i> = 85) isolates. A total of 195 STs, some of them shared between sources such as food and human, horses and dogs, and environment and birds, were grouped in 25 CC and distributed along five phylogenetic groups. Fifty-three percent of the genomes were allocated to toxinotype A, followed by F (32%) and G (7%). The most frequently found virulence factors based on > 70% coverage and 99.95% identity were <i>plc</i> (100%), <i>nanH</i> (99%), <i>ccp</i> (99%), and <i>colA</i> (98%), which encode an alpha-toxin, a sialidase, an alpha-clostripain, and a collagenase, respectively, while <i>tetA</i> (39.5%) and <i>tetB</i> (36.2%), which mediate tetracycline resistance determinants, were the most common antibiotic resistance genes detected. The analyses conducted here showed a better view of the presence of this pathogen across several host species. They also confirm that the genetic diversity of <i>C. perfringens</i> is based on a large number of virulence factors that vary among phylogroups, and antibiotic resistance markers, especially to tetracyclines, aminoglycosides, and macrolides. Those characteristics highlight the importance of <i>C. perfringens</i> as a one of the most common causes of foodborne illness.