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 Staphylococcus aureus (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), spa typing, SCCmec 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. SCCmec 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 (p = 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 mecA 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.