Pan-genomic insights into resistance, virulence, and stress adaptation in Clostridium perfringens from the Tibetan Plateau.

Clostridium perfringens is a ubiquitous foodborne and zoonotic pathogen responsible for necrotizing enteritis, food poisoning, and gas gangrene in humans and livestock, with mortality reaching 100% in specific subtypes. The Qinghai-Tibetan Plateau, with its high altitude, hypoxia, large temperature fluctuations, and strong UV radiation, imposes a strong selective regime that drives distinctive, plateau-specific microbial evolution. We isolated and sequenced eight C. perfringens isolates from yaks and Tibetan pigs and analyzed them with 129 public genomes. Multilocus sequence typing (MLST) revealed extensive genetic heterogeneity, with 35 novel alleles and 18 novel sequence types (STs), all plateau isolates carrying novel alleles or STs. Toxinotyping identified six toxinotypes, dominated by A (43.0%) and F (42.3%), with virulence gene repertoires matching toxinotype assignments. Sixteen antimicrobial resistance (AMR) genes across eight drug classes were detected, with vancomycin- and defensin-like genes present in >96.0% of isolates; four were linked to mobile genetic elements (MGEs) or type IV secretion systems (T4SS). Environmental tolerance assays showed that three plateau isolates maintained growth at pH 7.5 under anaerobic conditions, while the growth of all isolates was inhibited at pH 7.0. Pan-genomic association analysis identified a 146-node, 3,390-edge network, with IS family transposases (ISCbt3/ISCpe4), sigma factors (sigL and sigA), and DNA polymerase I (polA) as central hubs potentially mediating stress adaptation. Genomic epidemiology of C. perfringens from the Tibetan Plateau reveals marked genetic diversity, broad resistance, toxinotype-defined virulence, and genetic signatures of high-altitude adaptation, underpinning evidence-based control in plateau ecosystems.IMPORTANCEClostridium perfringens is a widespread pathogen, but its adaptation to extreme environments like high-altitude plateaus remains a mystery. Our integrated genomic analysis of 137 strains, including 8 newly sequenced from the plateau, uncovers a startling reality: this region harbors a highly diverse population with near-universal resistance to critical antibiotics. We identified new sequence types (STs) and genetic "hubs" that may drive this adaptation. These findings have profound implications for One Health as they highlight an environmental niche where resistance can evolve and potentially spread, underscoring the urgent need for surveillance in unique ecosystems.