Abstract
Staphylococcal food poisoning is widespread, causing significant public health problems. This study aimed to characterize the genomic profiles and antimicrobial susceptibility of Staphylococcus aureus isolates obtained from food products in Northern Kazakhstan using whole-genome sequencing. The study included 42 food-derived isolates from raw food products (milk, chicken fillet, beef, horse meat, semi-finished meat products) and ready-to-eat (RTE) products (sour cream, butter, canned tuna, culinary dishes). All isolates were recovered from individual samples collected between June 2024 and June 2025 in Northern Kazakhstan (Astana and Kostanay regions). They were characterized using antibiotic susceptibility testing, whole-genome sequencing, multilocus sequence typing (MLST), and analysis of resistance, enterotoxin, and virulence genes. Phenotypic resistance to cefoxitin (MRSA phenotype) was detected in 21.4% (9/42) of food-derived isolates; all corresponding strains carried the mecA gene associated with methicillin resistance. Multidrug resistance (MDR) was identified in 9.5% (4/42) of food-derived isolates. The predominant ST type among MRSA strains was ST22 (8 of 9 strains). Only a single strain, Sa847_KZ, has a truly indeterminate/unresolved profile. Among classical enterotoxin genes, sea was detected in 4.8% (2/42) and sec was detected in 9.5% (4/42) of food-derived isolates. Non-classical enterotoxin genes were more prevalent: seg was found in 57.1% (24/42) and sei in 19.0% (8/42) of food-derived samples. The tsst gene, encoding a toxin capable of causing severe acute illness, was detected in 28.6% (12/42) of food-derived isolates - a prevalence substantially higher than reported for the tsst gene in food-derived S. aureus from most other regions worldwide. The results emphasize the need for enhanced food quality control and monitoring of antimicrobial resistance in Northern Kazakhstan to prevent cases of food poisoning.