Genomic and Phenotypic Characterization of Mupirocin ResistantStaphylococcus aureusClinical Isolates

Background

Colonization withStaphylococcus aureusis a risk factor for subsequent infection. Decolonization with the topical antibiotic mupirocin is effective and reduces the risk of subsequentS. aureusinfection for both methicillin-sensitive (MSSA) and methicillin-resistant (MRSA) strains but may select for mupirocin-resistant isolates.

Methods

We characterized oxacillin and mupirocin susceptibility amongst 384S. aureusstrains isolated from clinical samples isolated 2017-2023 in Tampa, Florida, spanning strains collected before and after the onset of the COVID-19 pandemic. Whole genome sequencing of bacterial isolates was conducted in parallel and correlated with drug susceptibility profiles.

Results

Mupirocin resistance (MupR) was nearly exclusively present in MRSA strains (103/106 97.1% of MupR; 103/299 34.4% of MRSA). Although our hospital protocol for decolonization shifted to povidone iodine in the Post-COVID period, the overall prevalence of MupR did not change in Pre-COVID and Post-COVID samples (28.9% vs 26%). Genotype correlated with antibiotic susceptibility with low level MupR (MupLR), linked to mutations inileSand high level MupR (MupHR), linked to the presence ofmupA. Genome analysis revealed that most MupR strains fell into three sequence types (ST) falling into two major clonal complexes (CC): CC8 ST8 (including Community-Associated MRSA strains USA300 and USA500), CC5 ST5 (associated with Healthcare-Associated MRSA such as USA100), and CC5 ST3390. ST3390 isolates had the highest prevalence of MupR (30/36 83%; MupHR 20/36 55.6%; MupLR 10/36 27.8%).

Conclusions

Mupirocin resistance was prevalent in our hospital MRSA strains. We also found evidence for emergence and persistence of ST3390 MRSA-MupR strains in Florida.

Key points

• In a survey of clinical isolates in Florida, 34.4% of MRSA strains were mupirocin resistant.

• Mupirocin resistance correlated with mutations inileSor carriage ofmupA.

• We found evidence for emergence of MRSA mupirocin-resistant strains that were sequence type ST3390.