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

Abstract

Clostridium perfringens 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 C. perfringens; however, those studies are limited to specific locations and often include a reduced number of genomes. In this study, 372 C. perfringens genomes from multiple locations and sources were used to assess the genetic diversity and phylogenetic relatedness of this pathogen. In silico 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 C. perfringens genomes found in publicly available databases were derived from food (n = 85) and bird (n = 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 plc (100%), nanH (99%), ccp (99%), and colA (98%), which encode an alpha-toxin, a sialidase, an alpha-clostripain, and a collagenase, respectively, while tetA (39.5%) and tetB (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 C. perfringens 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 C. perfringens as a one of the most common causes of foodborne illness.

Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates - MosAIC (Mosquito-Associated Isolate Collection)

“…Virulence factors were predicted using ABRicate (139,140) v1.0.1 (https://github.com/tseemann/ABRicate). The default virulence factor database included in ABRicate was replaced with DNA sequences from the full dataset to include all genes related to known and predicted virulence factors (141), (http://www.mgc.ac.cn/VFs/download.html).…”

Approaching pathogenicClostridiafrom a One Health perspective

“…Additional strain phenotypic data, including antibiograms, biochemical, or serologic strain typing also enhances available datasets to provide functional assessments of antibiotic resistance and known antigenic or biochemical properties 23,47,51 . The phenotypic analyses, particularly when conducted under a recognized international standards such as CLIA (Clinical Laboratory Improvement Amendments) 52 or ISO 15189 53 , offer means to correlate phenotypic findings from strains collected across geographic locations with genomic findings 39 .…”

Extensive genome analysis identifies novel plasmid families in Clostridium perfringens

“…Targeted genome-wide phylogenetic analysis provides the capacity to understand these host-specific disease relationships, yet existing analysis has largely focused on specific pathogenic strains from one disease host or phenotype [21][22][23][24][25] or has only just recently begun to include rarely sequenced toxinotypes, such as B, C, D and E strains [26][27][28]. Large-scale genomic studies of C. perfringens have suggested that there are either four [27] or five [26] clades, two of which are disease-specific, whilst the remaining three are independent of the host or disease caused by isolates.…”

“…Targeted genome-wide phylogenetic analysis provides the capacity to understand these host-specific disease relationships, yet existing analysis has largely focused on specific pathogenic strains from one disease host or phenotype [21–25] or has only just recently begun to include rarely sequenced toxinotypes, such as B, C, D and E strains [26–28]. Large-scale genomic studies of C.…”