Prevalence and antimicrobial resistance of foodborne microorganisms in Egypt identified by MALDI-TOF MS

Antimicrobial resistance (AMR) and foodborne infections represent significant public health concerns, with food products serving as potential vehicles for the transmission of pathogenic and antimicrobial-resistant microorganisms. In this study, a total of 133 food samples, including vegetables, dairy products, meats, seafood, ready-to-eat foods, and beverages, were collected and analyzed. Microbiological investigation revealed microbial growth in 128 samples, yielding 128 bacterial and fungal microorganisms. Among the identified microorganisms, Escherichia coli (20.3%), Staphylococcus aureus (20.3%), Salmonella spp. (14.8%), and Bacillus cereus (11.7%) were the most prevalent taxa. Fungal isolates accounted for 14.9% of the identified microorganisms and included Penicillium spp., Candida spp., Aspergillus spp ., and unidentified yeasts. Microbial identification was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), which achieved species-level identification for 125 microorganisms (97.7%), while three microorganisms (2.3%) yielded low-confidence identifications. Antimicrobial susceptibility testing demonstrated variable resistance patterns among the recovered microorganisms, with higher resistance frequencies generally observed among Gram-negative bacteria. Multidrug-resistant (MDR) phenotypes were detected among several isolates, particularly Escherichia coli and Pseudomonas aeruginosa , with additional MDR patterns observed in Enterobacter cloacae complex and Staphylococcus aureus . This study provides updated region-specific data on the diversity and antimicrobial resistance profiles of foodborne microorganisms recovered from different food categories in Egypt. The findings underscore the importance of continuous surveillance of foodborne pathogens and antimicrobial resistance to support food safety monitoring, risk assessment, and public health interventions.