Abstract
Staphylococcus aureus is a leading cause of foodborne illness in animal-derived food products, yet comprehensive data on its antimicrobial resistance and toxigenic potential from Central Asia remain scarce. We examined 711 food samples (meat, milk, and dairy products) from the Kostanay region of Kazakhstan (2024–2025). Isolates were identified by MALDI-TOF mass spectrometry; antimicrobial susceptibility was assessed by disk diffusion (EUCAST v.16.0); enterotoxin production (types A–E) by ELISA; and resistance and toxin genes by PCR. Concordance between methods was evaluated using Cohen’s kappa coefficient. S. aureus was recovered from 11.8% of samples (84/711), with raw cow’s milk carrying the highest contamination risk (OR = 2.75; 95% CI: 1.74–4.38). High resistance to ampicillin (52.4%) and benzylpenicillin (50.0%) was found; 20.2% of strains were multidrug-resistant. Among the 17 cefoxitin-resistant isolates, only 4 harbored mecA, suggesting that 13 isolates (15.5%) should be interpreted as cefoxitin-resistant, mecA-negative isolates with a putative BORSA-like phenotype rather than as confirmed MRSA. Staphylococcal enterotoxins A–E were detected in 26.2% of isolates, and egc-cluster genes seg and sei were present in 9.5% each. The strongest genotype–phenotype concordance was observed for aph(3′)/kanamycin (κ = 0.65) and blaZ/benzylpenicillin (κ = 0.64). These results underscore the need for combined molecular and phenotypic surveillance for regional food safety monitoring.