We aimed to determine the prevalence of genes associated with high-level mupirocin and biocide resistance in methicillin-resistant Staphylococcus aureus (MRSA) isolates among hospitalized patients and to characterize their genomic and epidemiologic features. Study conducted on an integrated health system. Clinical cultures with MRSA from hospitalized patients collected between March 1, 2023, and January 20, 2024 underwent prospective whole-genome sequencing (WGS), including assessment for the presence of markers of resistance against mupirocin (mupA) and biocides (qac). Demographic and clinical characteristics were reviewed. We analyzed 463 MRSA isolates. The overall prevalence of mupA(+), qacA(+), and qacC(+) genes was 22.0%, 2.4%, and 19.0%, respectively. Most mupA(+) isolates belonged to ST8, but ST8732 (a novel variant of ST8) had the highest prevalence of mupA(+) isolates at 95%. Patients mupA(+) were older, and none of the isolates from pediatric patients harbored this gene. Through prospective WGS of MRSA isolates we detected a prevalence of genes conferring mupirocin resistance considerably higher than previously reported, particularly among MRSA ST8 variants. Our findings highlight the need for monitoring resistance to agents used for the prevention of Staphylococcus aureus infections, as these trends have implications for infection prevention programs and public health at large.
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