Abstract
Clostridium perfringens is an opportunistic Gram-positive bacterium that causes necrotic enteritis and other severe infections in animals, as well as food poisoning in humans. In this study, we introduce a framework consisting of rpoB sequence typing (RSTing) and network analysis to investigate the evolutionary trajectories of C. perfringens. By analyzing 319 rpoB sequences—300 from public databases and 19 newly sequenced isolates from chicken and cattle sources—we identified 84 rpoB sequence types (RSTs). Among them, the early emerging RST 1-1 was the most prevalent (21.3%), while the putative ancestral type, RST 0, was the fifth most common (4.7%). The high RST diversity and the predominance of RST 1-1, mainly from chickens, suggest that chickens may serve as an important reservoir. By integrating virulence gene profiling, MLST, and comparative genomics, we separated identical RSTs into distinct genotypes and uncovered genomic evidence of possible interspecies transmission between chickens and cattle, two major food-producing species. These findings indicate that RSTing provides a useful complementary approach to investigating the evolutionary and epidemiological dynamics of C. perfringens.