Genotypic characterization of antibiotic resistance genes in multidrug-resistant Staphylococcus aureus isolated from companion and livestock animals in Indonesia

Background and Aim: Antimicrobial resistance (AMR) in Staphylococcus aureus represents a critical threat to veterinary and public health, with multidrug-resistant (MDR) strains facilitating zoonotic transmission across animal species. This study aimed to investigate the prevalence and diversity of key antibiotic resistance genes in MDR S. aureus isolates from companion and livestock animals in Indonesia, and to assess their potential for interspecies dissemination within a One Health framework. Materials and Methods: A total of 121 bacterial isolates were collected from bovine milk (n = 30), cats (n = 61), dogs (n = 18), rabbits (n = 7), and goats (n = 5) between June 2024 and August 2025 in Yogyakarta and Central Java, Indonesia. Phenotypic identification involved biochemical tests (catalase, coagulase, mannitol fermentation), antimicrobial susceptibility testing via disk diffusion against seven antibiotics (tetracycline, gentamicin, erythromycin, penicillin G, cefoxitin, ciprofloxacin, clindamycin), and genotypic confirmation using polymerase chain reaction (PCR) for 23S rRNA, nuc, and coa genes. Resistance genes (mecA, blaZ, aacA-D, ermA, tetK, tetM, msrB, linA, norA) were detected via targeted PCR. MDR was defined as resistance to ≥ 3 antimicrobial classes. Statistical analysis included Fisher's exact test (p < 0.05) for comparing resistance patterns across hosts. Results: Of the isolates, 55 (45.5%) were confirmed as S. aureus, with the highest prevalence in bovine milk (80%) and rabbits (85.7%). All exhibited MDR phenotypes, predominantly to penicillin (20%–72%), tetracycline (17%–28%), and clindamycin. Erythromycin resistance varied significantly across sources (p < 0.05). Genotypically, tetK was universal (100%), followed by linA (85.5%), norA (81.8%), mecA (76.4%), and blaZ (69.1%). Significant differences (p < 0.05) occurred in tetM, blaZ, aacA-D, norA, and msrB distribution. Co-occurrence of mecA, blaZ, and tetK suggested horizontal gene transfer. Phenotypic-genotypic discrepancies were noted, potentially due to alternative genes (e.g., mecC, ermC) or regulatory mechanisms. MDR patterns were prominent in bovine and cat isolates, with complex gene combinations (≥ 4 genes) in over 50% of cases. Conclusion: This study reveals shared resistance gene profiles in MDR S. aureus from Indonesian animals, highlighting zoonotic risks and the need for integrated AMR surveillance. Limitations include the targeted PCR's scope; future work should employ whole-genome sequencing to enable comprehensive resistome analysis and transmission studies. Keywords: antimicrobial resistance, companion animals, Indonesia, livestock animals, multidrug resistance, One Health, Staphylococcus aureus, zoonotic transmission.