Abstract

Introduction The emergence of methicillin-resistant Staphylococcus species (MRS) poses a growing threat to both human and veterinary health.Methods We performed a comparative genomic characterisation of 49 methicillin-resistant Staphylococcus isolates collected from humans, dogs, and cats in a veterinary hospital from Central Chile.Results Whole-genome sequencing revealed S. aureus, S. pseudintermedius, and S. epidermidis as the most prevalent species, with distinct patterns of antimicrobial resistance and virulence. Average Nucleotide Identity (ANI) and phylogenetic analyses highlighted species-specific clustering but also revealed divergent lineages among Staphylococcus aureus and Staphylococcus epidermidis isolates. Resistance to beta-lactams was widespread, with the blaZ and mecA genes predominating, while macrolide and aminoglycoside resistance genes were variably distributed. S. aureus exhibited the highest virulence gene content, whereas S. pseudintermedius isolates carried superantigen-encoding enterotoxin genes, suggesting potential zoonotic risk. MLST and SCCmec typing confirmed the circulation of community-associated MRS lineages, notably SCCmec type IV.Conclusions This study provides a first comprehensive characterisation of methicillin-resistant Staphylococcus spp. isolates from human and animal hosts at a veterinary hospital in Santiago, Chile. These findings underscore the need for continuous surveillance under the One Health approach to monitor the potential transmission of high-risk clones and resistance determinants between humans and companion animals.