Genetic characteristics and SCCmec variations in pet-associated MRSA CC398 and ST9 strains

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST) 9 and clonal complex (CC) 398 are primarily livestock-associated, with CC398 also being predominant in dogs and cats in Thailand. We employed whole-genome sequencing (WGS) to investigate the genomic characteristics, antimicrobial resistance (AMR), and virulence profiles of pet-associated MRSA isolates, highlighting features shared with livestock-associated MRSA (LA-MRSA). Between 2017 and 2023, 29 MRSA were identified among 184 S. aureus isolates from 13,984 canine and feline clinical samples. A representative subset of 17 MRSA isolates underwent antimicrobial susceptibility testing and WGS. Hybrid genome assembly revealed LA-MRSA characteristics, including ST9 carrying staphylococcal cassette chromosome mec (SCCmec) IX (1 isolate) and CC398 carrying either SCCmec V variants (5C2&5) (15 isolates) or a novel composite SCCmec containing class C2 mec gene complex, ccrA1B1, and ccrC (1 isolate). All strains exhibited multidrug resistance, harboring multiple AMR genes mainly on the chromosome. LA-MRSA-associated genes such as tet(L), fexA, lsa(E), and lnu(B) were detected. In CC398, IS256 was associated with SCCmec V variations. The composite SCCmec in MRSA ST398 strain CUVET18–370 shared homology with bovine-derived SCCmec IX variants, lacking erm(B). A mecA circular intermediate was identified in one canine CC398 strain, suggesting duplication and excision of the mec complex for potential horizontal transfer. These SCCmec V and IX variations highlight the adaptability of MRSA ST9 and CC398 and their possible dissemination among animal hosts under antimicrobial pressure. Our findings emphasize the need for integrated AMR surveillance across humans, livestock, and companion animals to support evidence-based MRSA prevention and control.