Genome characterization of a Clostridium chauvoei strain 23CCJK from India and comparative analysis revealing novel insight into species lineages, associated SNPs and virulence factors.

Clostridium chauvoei is a spore-forming bacterium responsible for black quarter (BQ) in cattle, a disease leading to high mortality. Despite its economic significance in India, genomic characterization of C. chauvoei strains from the country remains scarce. This study reports the genome of a C. chauvoei strain, 23CCJK, associated with a black quarter outbreak in Leh, India. The genome, approximately 2.7 Mb, encodes 2557 protein-coding genes including important known virulence determinants such as CctA, NanA, hyaluronidase, and collagenase. Species pan-genome analysis involving 85 global strains revealed 2357 core and 381 accessory genes, indicative of limited gene acquisition. CRISPR analysis revealed conserved repeat patterns among Indian strains, supporting regional relatedness. Phylogenetic analysis indicated three major lineages (L1, L2, and L3), with Indian strains clustering among L3. The major lineage (L3; n = 80) represented mainland strains, whereas L1 (n = 2) and L2 (n = 3) represented strains mainly from Australia and New Zealand. Notably, several novel genes were identified in this analysis with hypermutations, possibly involved in vital metabolism, host-pathogen interaction and virulence. This included discoidin domain-containing proteins, glycerophosphoryl diester phosphodiesterase, ABC transporters, and histidine kinases, suggesting possible roles in faster adaptation during infection. These findings enrich our understanding of C. chauvoei evolution, population structure, and virulence, while highlighting key genetic markers that may be associated with pathogen adaptation during infections.