Background/Objectives: Staphylococcus aureus is a multifaceted pathogen responsible for diseases in humans and in several animal species, including dairy cows. This study aimed to characterize and compare the genetic diversity, lineage distribution, and antimicrobial resistance profiles of S. aureus isolates from bovine milk with human-derived reference genomes to investigate host adaptation and inter-species transmission. Methods: Genomic analyses were performed on S. aureus isolates from quarter milk samples of dairy cows together with human-derived sequences from public databases. Whole-genome sequencing and multi-locus sequence typing (MLST) were used to determine sequence type (ST) distribution, and the presence of key antibiotic resistance genes and mobile genetic elements (MGEs) was assessed. Comparative genomics was applied to evaluate gene content, phylogenetic relationships, and lineage–host associations. Results: The dataset encompassed bovine-adapted lineages (CC97, CC133, CC151) and human-associated lineages (CC1, CC5, CC8, CC30, CC45), as well as livestock-associated ST398 in bovine samples and human-adapted ST5 and ST6 in animals. ST8 was the only ST shared between animal and human isolates and showed differing resistance profiles, with animal ST8 carrying resistance determinants absent from human ST8. Bovine-adapted strains were characterized by recurrent loss of human-associated virulence genes and acquisition of bovine-associated mobile genetic elements, and blaZ and mecA were rarely detected in bovine-adapted CC97 but were frequently present in human CC5 and CC8. Overall, animal isolates carried fewer resistance genes than human isolates. Conclusions: S. aureus from dairy cows and humans displayed substantial genetic diversity, with evidence of host-associated lineages and dynamic changes in gene and mobile element content. These findings support the need for integrated One Health surveillance to track shared and host-adapted lineages and their antibiotic resistance determinants.
Meroni et al. (2026) studied this question.