Genomic Characterization of Multidrug-Resistance mecC-MRSA in Portuguese Rabbit Production

Staphylococcus aureus is a major zoonotic pathogen increasingly associated with livestock reservoirs. Rabbit production remains underexplored in antimicrobial resistance surveillance despite its in Southern Europe. This study characterized whole-genome sequencing (WGS) based characterization of S. aureus isolates from rabbits intended for consumption in Portugal.

Forty-six S. aureus isolates were subjected to WGS. Genomic data were analyzed using PlasmidFindr, SCCmecFinder, AMRFinder, CARD, and VirulenceFinder databases. Antimicrobial susceptibility testing (AST) was performed on 44 isolates by disk diffusion.

Multilocus sequence typing identified ST28855 (n=31) and ST4774 (n=10) as dominant lineages, alongside ST15 (n=3), ST398 (n=1), and one novel ST. Twenty-seven isolates were classified as MRSA, carrying mecA (n=16) with SCCmec type III(3A), or mecC (n=11) with SCCmec type XI (8E). AST revealed widespread resistance to penicillin and ciprofloxacin across MRSA and MSSA, with erythromycin, clindamycin, and tetracycline resistance also observed. Resistance genes included blaZ, tet (38), erm(C), vga(A), fosB, dfrK, and str. Efflux pump genes norC, sdrM, norA, and sepA were identified in 45 isolates. Biocide resistance genes lmrS and qacC were widely distributed, and arsenic resistance genes (arsB, arsC) were detected in 10 isolates. The transcriptional regulators arlR, arlS, kdpD, mepR, and mgrA were ubiquitous. Virulence profiling revealed near-universal presence of hlgABC, lukE, aur, icaC, splAB, and hld, with lukD and can detected in 70% and 59% of isolates, respectively. Plasmid analysis identified rep7c_1_rep(MSSA476) as the predominant replicon.

These findings reveal that rabbits for consumption harbor multidrug-resistant S. aureus with diverse resistance mechanisms and substantial virulence potential. The detection of mecC-MRSA in dominant livestock-associated lineages, combined with widespread biocide and metal resistance determinants, underscores the importance of integrating rabbit farming into One Health AMR surveillance frameworks.

Acknowledgements:
This work was supported by the project UID/00772/2025 DOI https://doi.org/10.54499/UID/00772/2025 funded by the Portuguese Foundation for Science and Technology (FCT).