| Summary: | <i>Staphylococcus aureus</i> is an important pathogen associated with hospital, community, and livestock-acquired infections, with the ability to develop resistance to antibiotics. Nasal carriage by hospital inpatients is a risk for opportunistic infections. Antibiotic susceptibility patterns, virulence genes and genetic population structure of <i>S. aureus</i> nasal isolates, from inpatients at Busia County Referral Hospital (BCRH) were analyzed. A total of 263 inpatients were randomly sampled, from May to July 2015. The majority of inpatients (85.9%) were treated empirically with antimicrobials, including ceftriaxone (65.8%) and metronidazole (49.8%). Thirty <i>S. aureus</i> isolates were cultured from 29 inpatients with a prevalence of 11% (10.3% methicillin-susceptible <i>S. aureus</i> (MSSA), 0.8% methicillin resistant <i>S. aureus</i> (MRSA)). Phenotypic and genotypic resistance was highest to penicillin-G (96.8%), trimethoprim (73.3%), and tetracycline (13.3%) with 20% of isolates classified as multidrug resistant. Virulence genes, Panton-Valentine leukocidin (<i>pvl</i>), toxic shock syndrome toxin-1 (<i>tsst-1</i>), and <i>sasX</i> gene were detected in 16.7%, 23.3% and 3.3% of isolates. Phylogenetic analysis showed 4 predominant clonal complexes CC152, CC8, CC80, and CC508. This study has identified that inpatients of BCRH were carriers of <i>S. aureus</i> harbouring virulence genes and resistance to a range of antibiotics. This may indicate a public health risk to other patients and the community.
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