Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 18 1 2026 02 14 82 90 Ali Abbas Hashemi Department of Microbiology, Faculty of Veterinary Sciences, Ilam University, Ilam, Iran Mostafa Nemati Department of Microbiology, Faculty of Veterinary Sciences, Ilam University, Ilam, Iran Fazel Pourahmad Department of Microbiology, Faculty of Veterinary Sciences, Ilam University, Ilam, Iran 2025 04 10 2026 01 29 Background and Objectives: Antimicrobial resistance (AMR), particularly from methicillin-resistant Staphylococcus aureus (MRSA), poses a significant public health threat, exacerbated by antibiotic misuse in livestock and food production. This study aimed to evaluate the prevalence of MRSA in traditional dairy products from Ilam, Iran, and explore the role of prophages in enhancing bacterial virulence and resistance, assessing their implications for food safety. Materials and Methods: Between January and April 2021, 116 dairy samples (raw milk, traditional cheese, and toof) were collected from Ilam, Iran. Staphylococcus aureus was identified using bacteriological and molecular methods, including PCR targeting femA, mecA, and prophage markers (SGB, SGFa, SGFb). Antibiotic susceptibility was tested via the Kirby-Bauer method, and data were analyzed using SPSS. Results: S. aureus was detected in 25.9% of samples (30/116), with raw milk showing the highest contamination (57.9%). MRSA, identified by the mecA gene, was present in 6.7% of isolates, and 73.3% exhibited multidrug resistance. Prophages were found in 13.3% of isolates, with SGB linked to β-lactam resistance (p = 0.04). High resistance to doxycycline (87%) and tetracycline (67%) was observed. Conclusion: The study highlights a significant presence of MRSA and multidrug-resistant S. aureus in Ilam’s dairy products, with prophages contributing to the virulence of these bacteria. Enhanced hygiene and monitoring are crucial for mitigating food safety risks. https://ijm.tums.ac.ir/index.php/ijm/article/view/5418 https://ijm.tums.ac.ir/index.php/ijm/article/download/5418/1865