Temporal evolution of urinary microbiology between acute obstructive pyelonephritis and delayed ureteroscopy

Urolithiasis is a common disease associated with severe infectious complications such as acute obstructive pyelonephritis (AOP). This emergency requires antibiotic therapy and urinary drainage, with bladder and renal pelvic urine cultures (BUCap and PUCap, respectively) that are often discordant. However, microbiological evolution between AOP and delayed ureteroscopy remains poorly studied. This study evaluated the concordance between BUCap, PUCap, and preoperative bladder urine cultures before delayed ureteroscopy (poBUC).

This retrospective single-center study included patients with stone-related AOP undergoing urgent drainage and delayed ureteroscopy between 2015 and 2025. Clinical and microbiological data were collected. The primary endpoint was concordance between BUCap vs. poBUC and between PUCap vs. poBUC. Secondary analyses assessed concordance between BUCap vs. PUCap.

A total of 200 patients were included (63% female; median age 65.5 years). BUCap, PUCap, and poBUC were positive in 51.5%, 49.5%, and 39.5%, respectively. The median interval between drainage and ureteroscopy was 86.5 days. Concordance was 55.6% between BUCap vs. poBUC, 40.9% between PUCap vs. poBUC, and 61% between BUCap vs. PUCap. Pathogen discordance between AOP and poBUC was observed in 50.5 and 32.0% for BUCap and PUCap, respectively. Reliance on acute-phase cultures alone would have resulted in potentially inappropriate antimicrobial management in 37.8-42.5% of the cases, with overall microbiological discordance exceeding 70% when culture status changes were considered.

Concordance between BUCap, PUCap, and poBUC was limited. These findings support the routine use of poBUC before delayed ureteroscopy, as microbiological findings may substantially differ from those observed during the acute infectious episode.