Discordance between preoperative urine culture and intraoperative stone/pelvis culture as a predictor of post-PCNL sepsis: a single-center retrospective analysis for targeted antibiotic stewardship.

PURPOSE: To evaluate the diagnostic accuracy of preoperative midstream urine culture (PMUC) against intraoperative stone and pelvic urine cultures, and to determine if culture discordance independently predicts sepsis following percutaneous nephrolithotomy (PCNL).

METHODS

This retrospective cohort study analyzed 250 adult patients undergoing PCNL between January 2023 and October 2025. All participants had both PMUC and intraoperative stone/pelvic urine cultures. The primary outcome was post-PCNL sepsis defined by Sepsis-3 criteria. Diagnostic performance metrics were calculated, and the association between discordance and sepsis was assessed using multivariable logistic regression, LASSO penalization, and propensity-score matching to adjust for confounders.

RESULTS

Culture discordance was observed in 30% (75/250) of patients. The sensitivity of PMUC for detecting upper urinary tract colonization was only 48%. Sepsis occurred in 6.8% of the total cohort but was significantly more frequent in the discordant group (17.3 vs 2.3%, p < 0.0001). In multivariable analysis, discordance remained the strongest independent predictor of sepsis (adjusted OR 6.23, 95% CI 2.20-17.62, p < 0.001), displacing stone burden and operative time. Notably, patients with sterile preoperative urine but positive intraoperative cultures accounted for 92.3% of sepsis events within the discordant group.

CONCLUSION

PMUC is an unreliable surrogate for the upper tract microbiome, failing to detect colonization in over half of cases. Culture discordance is a robust predictor of post-PCNL sepsis, driven by untreated bacterial biofilms within stones. Routine intraoperative culturing is essential for targeted antibiotic stewardship to mitigate septic complications.