Isolation, Genomic Evolution, and Pathogenicity of Clostridium perfringens Type A Causing Hemorrhagic Enteritis in Adult Yaks in Southwest China

Clostridium perfringens type A causes neonatal clostridial enteritis, hemorrhagic enteritis, and sudden death syndrome in cattle. This study examined a fatal outbreak at a fattening farm housing 58 adult yaks in Southwest China, with an incidence of 22.41% (13/58) and a 100% case fatality rate. Histopathology of deceased yaks showed widespread multi-organ hemorrhage and severe hemorrhagic enteritis. A specific PCR assay amplified the alpha-toxin gene of Clostridium perfringens, while no other pathogens were detected. Clostridium perfringens was isolated from small intestinal contents using TSC agar, designated strain CQ1, and identified as type A through toxinotyping. Whole-genome sequencing revealed that strain CQ1 carries the core alpha-toxin gene along with key accessory virulence determinants (pfoA, colA, and cloSI). Phylogenomic analysis based on core single-nucleotide polymorphisms revealed that strain CQ1 is clustered into a distinct, independent evolutionary lineage with an existing historical yak isolate and a canine-origin isolate. Intraperitoneal challenge in mice confirmed its extreme lethality, causing 100% mortality within 36 h with severe intestinal necrosis. These findings provide fundamental genetic resources for understanding the virulence mechanisms and genetic background of this pathogen and offer critical insights for preventing and controlling clostridial diseases in high-altitude yak farming.