Pan-genome insights into genetic diversity, evolutionary dynamics, and pathogenic traits of Staphylococcus agnetis

BACKGROUND STAPHYLOCOCCUS AGNETIS: is an emerging pathogen primarily associated with bovine mastitis and avian lameness. Despite increasing reports of its occurrence across animal hosts, its genomic diversity and the distribution of antimicrobial resistance (AMR) and virulence-associated genes remain insufficiently characterized. RESULTS: The species S. agnetis possesses an open pan-genome, dominated by cloud gene families enriched in defense mechanisms and genomic plasticity, consistent with gene flux. Evolutionary reconstruction indicated that purifying selection and gene loss are the main signatures of evolutionary dynamics in the S. agnetis pan-genome, with extensive gene loss particularly affecting cell wall biogenesis functions. Notably, significant gene gain events were observed at early-diverging internal nodes of the phylogeny, suggesting that gene acquisition occurred during the early diversification of S. agnetis. AMR profiling identified a limited repertoire of AMR genes. However, the detection of a plasmid-borne AMR gene and the distribution of plasmids highlight the potential for plasmid-mediated dissemination of AMR in S. agnetis. Virulence profiling identified 28 chromosomally located putative virulence-related genes, predominantly homologous to S. aureus, including core adherence factors and sporadically distributed enterotoxin homologs suggestive of acquisition via horizontal gene transfer (HGT). CONCLUSIONS: Collectively, this study provides comprehensive insights into the genomic diversification of S. agnetis and highlights its emerging AMR traits and putative virulence potential in animal-associated settings.