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Background  Antimicrobial resistance is an increasingly serious problem in public health globally. Monitoring resistance levels within healthcare and community settings is critical to combat its ongoing increase. This study aimed to describe the rates and molecular mechanisms of mupirocin resistance in clinical  Staphylococcus aureus  isolates from Tygerberg Hospital, and to describe its association with strain types.    Methods  We retrospectively selected 212  S. aureus  isolates which were identified from blood samples and pus swabs during the years 2009–2011 and 2015–2017. The isolates were identified using conventional microbiological methods and genotyping was done using  spa  typing. Cefoxitin (30 μg) disc diffusion and the two disc strategy (5 μg and 200 μg) were used to determine susceptibility to methicillin and mupirocin, respectively. Isolates with high-level resistance were screened for the plasmid mediated genes  mupA  and  mupB  by PCR, and sequencing of the  ile S gene was done for all isolates exhibiting low-level resistance to describe the mutations associated with this phenotype. Chi-square test was used to assess the associations between mupirocin resistance and  S. aureus  genotypes.    Results  Of 212  S. aureus  isolates, 12% ( n  = 25) were resistant to mupirocin, and 44% ( n  = 93) were methicillin resistant. Strain typing identified 73  spa  types with  spa  t045 being the most predominant constituting 11% of the isolates. High-level mupirocin resistance was observed in 2% ( n  = 5), and low-level resistance in 9% ( n  = 20) of the isolates. The prevalence of high-level mupirocin resistance amongst MRSA and MSSA was 4 and 1% respectively, while the prevalence of low-level mupirocin resistance was significantly higher in MRSA (18%) compared to MSSA (3%), ( p  = 0.032).  mupA  was the only resistance determinant for high-level resistance, and the  IleS  mutation V588F was identified in 95% of the isolates which showed low-level resistance. A significant association was observed between  spa  type t032 and high-level mupirocin resistance, and types t037 and t012 and low-level resistance ( p  <  0.0001).    Conclusion  The study reported higher rates of low-level mupirocin resistance compared to high-level resistance, and in our setting, mupirocin resistance was driven by certain genotypes. Our study advocates for the continuous screening for mupirocin resistance in  S. aureus  in clinical settings to better guide treatment and prescribing practices.

The prevalence and molecular mechanisms of mupirocin resistance in Staphylococcus aureus isolates from a Hospital in Cape Town, South Africa