Characteristics and comparative genomic analysis of Clostridium perfringens isolates from a foodborne outbreak

Clostridium perfringens is a widely distributed Gram-positive pathogen associated with a range of foodborne illnesses. In this study, a foodborne outbreak linked to a group meal was investigated, from which 25C. perfringens isolates were recovered from 116 samples collected from food (n = 3), kitchen environmental surfaces (n = 10), food handlers (n = 5), and clinical patients (n = 7). Comprehensive molecular typing using multilocus sequence typing (MLST), core-genome MLST (cgMLST), and single-nucleotide polymorphism (SNP) analysis were performed, and the results showed progressively increasing discriminatory power. MLST divided the C. perfringens isolates into 18 STs, including 14 novel STs. Whole-genome sequencing (WGS) revealed a high level of genetic diversity among the isolates, with 7 enterotoxin-producing type F strains (ST1039) showing notable genetic homogeneity, while 18 type A strains exhibited substantial heterogeneity. High-resolution cgSNP analysis identified a close genomic relationship (15-50 SNP differences) between food isolates-from simmered aged duck soup (hot dish) and salted boiled broad beans (cold dish)-and clinical isolates. Notably, the 15-SNP difference between the duck soup isolate and a clinical isolate suggests a potential epidemiological link to the outbreak cases. This study highlights the superior resolution and accuracy of WGS molecular typing in foodborne outbreak investigations, enabling precise source tracing. It underscores the importance of integrating genomics into routine food safety surveillance and outbreak response to improve public health outcomes.