Background: Mupirocin, an RNA synthetase inhibitor produced by Pseudomonas fluorescens, is widely used for empiric methicillin-resistant Staphylococcus aureus (MRSA) decolonization in hospitalized patients. MRSA nares polymerase chain reaction (PCR) testing is frequently performed on admission to guide antimicrobial therapy; however, the effect of prior mupirocin exposure on PCR detectability is not well described. Methods: This retrospective cohort study was conducted across Ballad Health facilities from August 2022 to July 2025. Adults aged ≥18 years with documented MRSA colonization within one year who completed a five-day mupirocin decolonization course during a prior admission and underwent MRSA nares PCR testing on readmission were included. The primary endpoint was median time in days from mupirocin completion to repeat PCR testing, compared between PCR-positive and PCR-negative groups. Secondary endpoints included MRSA culture positivity on readmission and concordance between PCR and culture results, assessed using McNemar’s test and Cohen’s kappa. Results: Among 124 readmissions, 84 (68%) patients had positive and 40 (32%) had negative MRSA nares PCR results. Median time to PCR testing did not significantly differ between PCR-positive (77 days; IQR 38.3–120.8) and PCR-negative groups (52 days; IQR 26–118.5; p = 0.18). When stratified by time since mupirocin completion, PCR positivity was 59.5% (25/42) within ≤60 days, 78.6% (22/28) at 61–90 days, 66.7% (12/18) at 91–120 days, and 69.4% (25/36) at >120 days. Differences across these intervals were not statistically significant (χ² p = 0.15). MRSA was isolated in 11 cultures during the index admission and in 23 cultures on readmission, most commonly from wound, respiratory, and blood specimens. During the index admission, 18% (22/124) of patients with a positive PCR had a corresponding positive MRSA culture. On readmission, overall observed agreement between PCR and culture results was 52.4%, with a Cohen’s kappa coefficient of 0.20. McNemar’s test indicated statistically significant discordance between PCR and culture findings (p < 0.05), predominantly attributable to PCR-positive, culture-negative pairs. Conclusions: In this study, timing of prior mupirocin exposure was not associated with reduced MRSA nares PCR detectability on readmission. Although culture positivity increased on readmission, concordance between PCR and culture remained limited. Evaluation within a larger cohort is warranted.
