Genetic background and plasmid-associated contig profiles of the beta-2 toxin coding genes cpb2 and atypical cpb2 in...

Beta-2 toxin is considered an accessory toxin of C. perfringens encoded by both the cpb2 and atypical cpb2 (aty.cpb2) genes. However, the prevalence patterns and genomic backgrounds of cpb2/aty.cpb2 remain incompletely understood.

In this study, we performed a large-scale comparative genomic analysis of 865 cpb2- or aty.cpb2-positive C. perfringens strains. Genetic variation was detected across the full-length nucleotide sequences of both cpb2 and aty.cpb2, resulting in distinct predicted protein variants. Compared with aty.cpb2-positive strains, cpb2-positive strains exhibited clearer phylogenetic clustering, although the presence of cpb2 alone did not fully account for this pattern, indicating that cpb2 is associated with broader lineage-related genomic features. At the contig level, all cpb2-positive sequences were associated with pCP13-like plasmid backbones, whereas most aty.cpb2-positive sequences were linked to pCW3-like plasmid markers; the remaining aty.cpb2-positive sequences were distributed in distinct contig groups showing similarity to phage-associated or plasmid-associated reference sequences. Sequence annotation further showed that both cpb2 and aty.cpb2 were commonly adjacent to hp and a PadR-family transcriptional regulator, forming related local genetic segments.

Overall, this study provides a comparative genomic characterization of cpb2/aty.cpb2-associated genetic contexts and identifies two distinct phage-like contig groups carrying aty.cpb2, thereby offering new insights into the genomic diversity and potential mobility of beta-2 toxin genes in C. perfringens.