Exploring human-to-food contamination potential: Genome-based analysis of diversity, toxin repertoire, and antimicrobial resistance of methicillin-resistant Staphylococcus aureus in United Arab Emirates retail meat

Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) has moved beyond healthcare settings and is increasingly documented in food, yet genomic data from the Arabian Peninsula are scarce. This study aimed to characterize the genomic diversity, antimicrobial-resistance (AMR), and virulence repertoire of MRSA in retail red meat sold in Dubai, United Arab Emirates (UAE), and to evaluate evidence for potential human-to-food transmission. In a cross-sectional survey (September 2024 - February 2025), 140 red-meat samples (beef, mutton, camel) were collected from supermarket chains. Fifty-one MRSA isolates were confirmed by multiplex PCR and phenotypic testing. Short-read whole-genome sequencing was followed by bioinformatic characterization of the isolates for clonal complex (CC) multilocus sequence typing (ST), <i>spa</i> typing, SCC<i>mec</i> assignment, AMR and virulence genes identification, plasmid-replicon detection, and core-genome phylogeny. Genotype, meat commodity, and products' origin associations were statistically assessed. Eight sequence types were detected; CC5-ST6 (27.5 %) and CC8-ST789 (23.5 %) predominated. SCC<i>mec</i> IV and V accounted for 82.3 % of genomes, and no livestock-associated CC398 was found. CC5/ST6-t304 and CC8-t091 comprised 47 % of isolates but showed no association with meat type (<i>p</i> = 0.451). Core-genome analysis split the collection into six clusters with shallow branch lengths, signaling recent clonal expansion across local and imported meat products. All genomes carried the methicillin resistance <i>mecA</i> gene plus a median of five additional resistance genes; 41 % carried multidrug-resistant determinants. Classical enterotoxin genes occurred in 80.4 % of isolates, and Panton-Valentine leukocidin genes in 27.5 %, mainly within CC8 and CC22. Distinct plasmid backbones-RepA_N-RepL-Rep_trans in CC5-ST6 and Inc18-Rep3 in CC8-ST789-were associated with lineage-specific AMR profiles. Retail red meat in the UAE is contaminated by clinically important, community-associated MRSA clones, likely introduced via human handling rather than animal reservoirs. Genomic surveillance at the human-food interface can guide regional One Health policies and help curb foodborne antimicrobial resistance dissemination.