Not All “Contamination” Is the Same: Rethinking Management of Mixed-Flora and Contaminated Pre-Operative Urine Cultures

PURPOSE: Optimal management of polymicrobial pre-operative urine cultures (UCx) reported as mixed non-pathogenic urogenital skin flora (USF) or contaminated remains unclear. We evaluated whether UCx classification predicts post-operative urinary tract infection (UTI). MATERIALS AND METHODS: We retrospectively reviewed endoscopic urologic procedures at a multi-hospital academic center between January 2022 and May 2026 with a pre-operative UCx within 30 days. UCx were categorized as positive, negative, USF, or contaminated (polymicrobial with ≥1 uropathogen). The primary outcome was ICD-10-coded UTI within 30 days. Secondary outcomes included post-operative fever, post-operative positive UCx, readmission, and ninety-day mortality. Primary statistical analysis was performed per patient utilizing the index procedure. Secondary analysis was performed per procedure, utilizing clustering with generalized estimating equations (GEE). RESULTS: The index cohort comprised 10,117 patients. Post-operative UTI occurred within 30 days in 19% of patients, and was more common after pre-operative positive (39%, p<0.001) and contaminated (23%, p=0.002) than negative UCx (12%), whereas USF was not. Positive (aOR 2.78, 95% CI 2.42-3.20) and contaminated UCx (aOR 1.42, 1.16-1.73) remained independently associated with UTI, whereas USF did not (aOR 0.83, 0.70-0.99). Among the 13,804 procedures performed, risk estimates were consistent in secondary clustered GEE analysis. Contaminated UCx were independently associated with readmission and ninety day all-cause mortality (aOR 1.98, 1.20-3.25). CONCLUSIONS: Contaminated urine cultures, defined by at least one nondominant uropathogen, were associated with post-operative UTI, whereas USF was not. Polymicrobial cultures with a uropathogen may warrant repeat collection or speciation.