Comparative genomic and functional analysis of Staphylococcus caprae clinical isolates: insights into genetic diversity and opportunistic pathogenic potential

Abstract

Staphylococcus caprae, a coagulase-negative staphylococcus (CoNS), is an opportunistic microorganism increasingly identified in clinical specimens. However, its genomic and functional characterization in human infection have not yet been fully elucidated. In this study, we characterized the genomic and phenotypic diversity of two clinical S. caprae isolates, M89 and S13, to elucidate their opportunistic traits. Whole-genome sequencing was performed to evaluate genomic differences in antimicrobial resistance, virulence determinants, and protein-coding sequences, while their pathogenic potential was assessed using a murine subcutaneous catheter model. Our results revealed that both isolates harbored core resistance genes, such as mecA and blaZ; however, the healthcare-associated strain S13 displayed a broader antimicrobial resistance profile. Although virulence profiling identified conserved factors shared by both strains, including icaABCR, atl, and clfB, a key genomic differentiator was the presence of the accessory Sec (aSec) secretion system in M89, which was absent in S13. Functionally, M89 exhibited significantly greater adherence to endothelial cells and higher colonization efficiency in vivo. Furthermore, M89 infection induced epidermal thickening and elevated proinflammatory cytokine expression in mouse skin tissue. These findings demonstrate significant intra-species heterogeneity in S. caprae regarding host interaction capabilities and underscore the importance of integrating genomic and phenotypic analyses to delineate the pathogenic mechanisms of this emerging opportunistic pathogen.