Genome analysis of Staphylococcus caprae indicates potential health risks associated with antimicrobial resistance and virulence factors.

Staphylococcus caprae is an emerging coagulase-negative staphylococcal pathogen. This study performed pan-genome analysis to comprehensively characterize the genomic landscape of S. caprae. Phylogenomic reconstruction confirmed that it forms a distinct monophyletic clade from closely related species (Staphylococcus epidermidis and Staphylococcus capitis). Pan-genome analysis revealed an open genome (γ = 0.149 according to Heap's law) comprising 3967 gene families, 53.5% of which constitute the core genome enriched in essential metabolic functions. Cloud gene families showed enrichment in defense mechanisms and traits associated with genomic plasticity. A total of 17 antimicrobial resistance (AMR) genes were identified, most of which were scattered sporadically across S. caprae genomes in the form of cloud genes, which indicates horizontal gene transfer. The coexistence of multiple resistance determinants (e.g., mecA, blaZ, erm(A)) could potentially lead to the development of high-risk multidrug-resistant phenotypes, which would severely limit the available therapeutic options. Virulence genotypic profiling revealed conserved pathogenic mechanisms, including the complete icaADBC operon (involved in biofilm formation), a type VII secretion system and iron acquisition systems (isd). These findings provide a pan-genome-level view of S. caprae and highlight its potential role as a reservoir of AMR genes and conserved virulence-related traits.