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Staphylococcus aureus is one of the predominant bacteria isolated from skin and soft tissue infections and a common cause of bloodstream infections. The aim of this study was to compare the rate of resistance to various antimicrobial agents and virulence patterns in a total of 200 S. aureus strains isolated from patients with bacteremia and chronic wounds. Disk diffusion assay and in the case of vancomycin and teicoplanin-microdilution assay, were performed to study the antimicrobial susceptibility of the isolates. The prevalence of genes encoding six enterotoxins, two exfoliative toxins, the Panton–Valentine leukocidin and the toxic shock syndrome toxin was determined by PCR. Of the 100 blood strains tested, the highest percentage (85.0%, 31.0%, and 29.0%) were resistant to benzylpenicillin, erythromycin and clindamycin, respectively. Out of the 100 chronic wound strains, the highest percentage (86.0%, 32.0%, 31.0%, 31.0%, 30.0%, and 29.0%) were confirmed as resistant to benzylpenicillin, tobramycin, amikacin, norfloxacin, erythromycin, and clindamycin, respectively. A significantly higher prevalence of resistance to amikacin, gentamicin, and tobramycin was noted in strains obtained from chronic wounds. Moreover, a significant difference in the distribution of sea and sei genes was found. These genes were detected in 6.0%, 46.0% of blood strains and in 19.0%, and 61.0% of wound strains, respectively. Our results suggest that S. aureus strains obtained from chronic wounds seem to be more often resistant to antibiotics and harbor more virulence genes compared to strains isolated from blood.