Pangenome analysis of Clostridium perfringens and its virulence association with Carbohydrate Active Enzymes

Background Clostridium perfringens is an important foodborne pathogen responsible for severe economic loss in the food industry and around one million human gastrointestinal infections annually in the US. Carbohydrate Active Enzymes (CAZymes) are important to host-associated strains of C. perfringens , as they aid disease severity by degrading host tissues for nutrition. This study analyzed 126 publicly available C. perfringens genomes, clustering them into three major clades to investigate host-disease associations of CAZymes, alongside virulence and antimicrobial resistance factors. Results The pangenome analysis yielded hierarchical clustering of C. perfringens into three clades (clades 1-3), each of which was substantially (q < 0.05) enriched for functional genes. Clade 1 ( n = 38) was associated with avian necrotic enteritis (NE) and was functionally enriched with the CAZyme glycosyl hydrolase (GH) 18, essential for attachment and colonization to the host intestine. Additionally, antimicrobial resistance genes fosD ( n = 1), lnuD ( n = 5), and Mel ( n = 2) were exclusively found in clade 1, and the clostridial toxin TpeL was significantly ( p = 1.33E-07) associated with clade 1. Clade 2 ( n = 26) consisted primarily of canine and equine pathogens, whereas clade 3 ( n = 62) was composed largely of strains from diverse hosts, including all but one nonpathogenic isolate. Across all clades, genomes encoded an average of 101.50 ± 2.45, 104.31 ± 1.59, and 96.45 ± 9.22 CAZymes, respectively. Further genomic analysis of the NE-associated C. perfringens TAMU (CPT) strain revealed the absence of the canonical netB toxin gene and the presence of unique iron acquisition transporters, suggesting the involvement of alternative virulence mechanisms in disease development. Conclusion This study reveals clade- and host-specific CAZyme profiles and highlights the role of GH18 in colonization, while major clostridial toxins primarily drive severe infections. These insights enhance the understanding of C. perfringens pathogenicity and aid in developing targeted interventions.