The application of next-generation sequencing in preoperative evaluation for urologic stone surgery.

Introduction NGS is a new molecular technique for identifying microorganisms. Treating bacteriuria in patients undergoing stone removal procedures is important for preventing postoperative UTI. The objective of this study is to assess the usefulness of preoperative urine NGS testing by comparing NGS with standard urine culture in predicting postoperative UTI after URSL and PCNL. Materials and methods This prospective study was conducted from February 16th, 2022, to January 11th, 2024. Sixty subjects who underwent URSL or PCNL were included. Pre-operative voided urine samples were collected for urine culture and tested by MicroGenDX for urine PCR and urine NGS. Stone specimens obtained intraoperatively were also sent for stone culture and MicrogenDx. Patients were monitored for four weeks post-operation for recording clinical outcomes related to infections and complications. Results 26 (43.3%) male and 34 (56.7%) female participants were included. 26 (43.3%) patients underwent PCNL (15 standard PCNL and 11 mini PCNL), and 34 (56.7%) underwent URSL. Standard urine culture identified positive results in 26 cases (43.3%), PCR for 17 cases (28.3%) and NGS for 31 cases (51.7%). The overall postoperative UTI rate was 6 (10%). Standard urine culture demonstrated a sensitivity of 50%, specificity of 57.4%, and accuracy of 56.7%. PPV was notably poor at 11.5%. Urine NGS showed a higher sensitivity of 83.3%, specificity of 53.7%, accuracy of 55%, and PPV of 16.7%. Conclusion Urine NGS significantly improves the sensitivity of detecting microorganisms in preoperative urine compared to standard urine culture. Despite its high sensitivity and capability to identify non-culturable bacteria, utilizing NGS alongside standard urine culture is recommended. This parallel approach harnesses the strengths of both methods. Integrating NGS into standard practice could elevate the quality of care, especially for patients at high risk of urinary tract infections, such as those undergoing invasive stone removal procedures.