Methicillin-resistant (MRSA) and multidrug-resistant (MDR) Staphylococcus aureus, and the serotype (ST) 398 have been associated with human and livestock infections, being also detected in retail meat. The aim of this study was to determine the prevalence and molecular types of S. aureus strains from animals, retail raw meat, deli meat, and humans, determining the genetic similarity between the strains. A two-step selective enrichment followed by selective plating were used to isolate S. aureus from animals (n=167), retail raw meat (n=145), and deli meat (n=46). In addition, S. aureus from healthy people (n=550) was isolated by culture method. Positive isolates and MRSA isolates from clinical cases (n=108) were subjected to multiplex PCR (16S rRNA, mecA, and PVL genes), molecular typing and antimicrobial susceptibility testing. In addition, a real-time PCR assay was developed in order to decrease the time of detection of target genes of S. aureus in animal and meat samples, comparing the results with the standard culture/PCR method. The prevalence of S. aureus was 34.7% in animals, 47.6% in meat, and 13.0% in deli meat. The mecA gene was detected in S. aureus isolated from five pork meat samples and exhibited penicillin resistance. The ST398 was found in sheep, pigs, and pork meat. The S. aureus nasal carriage in healthy people was 7.6%. A total of 105 MRSA strains (97.2%) from clinical cases harbored the mecA gene and 11 (10.2%) the PVL gene. The rate of MDR was 70% in humans. A genetic similarity between strains from animals and meat, and from humans and meat was observed. Total agreement between the culture/PCR method and real-time PCR for detection of S. aureus was 68.9 to 97.8% (k=0.68-0.88), and the mecA gene, 86.7 to 98.7% (k=0-0.49). Therefore, the real-time PCR assay may be recommended as a rapid method for the detection of S. aureus, with confirmation of MRSA using the standard culture method. The presence of emerging S. aureus strains in the meat production chain and the genetic similarity between strains of different origin, suggests the contamination of meat, and a potential risk of transmission to humans.