Genomic and Phenotypic Characterization of Mupirocin-resistant Staphylococcus aureus Clinical Isolates

Abstract

Background: Colonization with Staphylococcus aureus is a risk factor for subsequent infection. Decolonization with the topical antibiotic mupirocin is effective and reduces the risk of subsequent S. aureus infection for both methicillin-sensitive and methicillin-resistant (MRSA) strains but may select for mupirocin-resistant isolates.

Methods: We characterized oxacillin and mupirocin susceptibility amongst 384 S. aureus strains isolated from clinical samples isolated in 2017-2023 in Tampa, Florida, spanning strains collected before and after the onset of the coronavirus disease 2019 (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, linked to mutations in ileS and high-level MupR, linked to the presence of mupA. Genome analysis revealed that most MupR strains fell into 3 sequence types (ST) falling into 2 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%; high-level MupR 20/36 55.6%; low-level MupR 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.

Keywords: MRSA; antimicrobial resistance; decolonization; mupirocin; staphylococcus aureus.

Figure 1.

Mupirocin resistance and sequence typing of Tampa S. aureus isolates. (A) 384 S. aureus clinical strains from 2017 to 2023 were characterized. Oxacillin sensitivity (MSSA, n = 85), mupirocin sensitivity (MupS, n = 278), and the distribution of MRSA and MSSA strains among mupirocin resistant (MupR n = 106) strains is shown. (B) Results of classification of strains into sequence types (ST) are shown with numbers of pre-COVID isolates (2017–2020) and post-COVID isolates (2021–2023) within each ST. Numbers of USA300 and USA500 within ST8 are shown. ST5 includes USA100 strains. “UT” signifies strains that were untypeable using the methods deployed here. ST was determined by analysis of whole genome sequence of each strain.

Figure 2.

Mupirocin resistance as a function of sequence type. Shown are the sequence types for high-level mupirocin resistance (MupHR) and low/intermediate-level mupirocin resistance (MupLR) of the 106 MupR strains as determined by analysis of whole genome sequence. Mupirocin susceptibility was determined by Etests. Two MupHR and 4 MupLR strains were untypeable.

Figure 3.

Distribution of mupA across sequence types and correlation with mupirocin resistance. Summary of the distribution of mupA⁺ isolates and ST across: (A) the entire 384 strain collection, (B) the Pre-COVID strains and the Post-COVID strains. Shown are the percentages and number of strains for each ST. C. The distribution of clinical strains with and without mupA and its phenotypic impact are shown. Most mupA⁺ strains were MupHR as determined by eTest. Strains are arrayed by isolation site, isolation period, the presence-absence of mupA, and its phenotypic impact on mupirocin resistance/sensitivity. Strains with mutations in ileS that are phenotypically MupLR are not included in this depiction.

Figure 4.

Correlation of MupLR and ileS (V588F) as a Function of Sequence Type and Isolation Site. Summary of the distribution of ileS (V588F) positive isolates (A) pre-COVID and (B) post-COVID. C, Shown is a recombination masked core SNP alignment maximum-likelihood tree of post-COVID USA300 isolates (ST8). The clade of 7 mupirocin-resistant USA300 isolates that possess the R112Q IleS mutation are designated in red. The reference USA300 strain FPR_3757 used for SNP alignment is shown in blue.