Clostridium perfringens (C. perfringens) is an important opportunistic zoonotic pathogen, ubiquitous in nature, causing food poisoning, enteric disease, and histotoxic infections in humans and animals. Genomic investigation of C. perfringens from animal-derived food product chains remains limited. In current study, 33 isolates were analyzed and phylogenetic relationships were elucidated with 119 published genomes, five clusters were classified with predominance of Cluster V. All isolates were classified into 16 STs including 7 novel STs (ST1072-ST1079). Twenty-seven virulence genes with conserved virulence backbone but heterogeneous toxinotype-defining loci (cpe, etx, netB), pCW3, pCP13, pIP404 plasmid families in 54. 5% isolates, extensive diversity of ISs, ClostrᵥBCpeSCP51 (39. 4%) and phiSM101 (33. 3%) with phage-borne toxin genes (ccp, nanH, plc, and hlyA) were identified. tetA (P) (45. 5%) / tetB (P) (39. 4%) / erm (Q) (28. 6%) were dominated ARGs, 24. 2% of isolates showed multidrug resistance profile while WHD-1 (type G) harbored 8 ARGs. Notably, one optrA -positive isolate was recovered from beef slaughterhouse air. Further, 2 isolates carried cpe + IS1151 + becA linkage, nanH / nanI / nanJ sialidase genes, accompanying pIP404 but not pCW3 with IS1469 / IS1470, cpb2 and ARGs absent, is obvious different from characteristic of type F strain. cgMLST offers more accurately resolves fine-scale chromosomal relationship than seven-locus MLST. Together, this study provides an integrated genomic overview of C. perfringens from animal-derived food chains, showing that prophage gain/loss, IS expansion, and plasmid carriage vary semi-independently and jointly shape ARGs and virulence profiles. It highlights the need for lineage-resolved genomic surveillance that considers both conserved chromosomal scaffold and dynamic MGE landscape to control strategies for this zoonotic pathogen. • Seven novel MLST sequence types were identified among animal-derived C. perfringens isolates. • Both c-cpe and p-cpe isolate shared same cpe + IS1151 + becA linkage accompanying pIP404-like plasmid. • Type F isolates from ovine-origin possessing potential risk of C. perfringens food-borne disease. • cgMLST offers a more refined resolution of fine-scale chromosomal relationships among the isolates compare to MLST.
Chang et al. (Sun,) studied this question.