Precision diagnosis of preoperative infection in urolithiasis: integrating targeted next-generation sequencing for enhanced accuracy-a multicenter cohort study.

BACKGROUND

Preoperative infection in urolithiasis patients poses significant risks for surgical complications. Traditional urine culture methods have limitations in detection speed and accuracy, necessitating more precise and rapid diagnostic approaches for preoperative infection assessment.

METHODS

This multicenter cohort study evaluated urolithiasis patients with suspected preoperative infections (discovery cohort: n = 114; validation cohort: n = 64), comparing the diagnostic performance of traditional urine culture, metagenomic next-generation sequencing (mNGS), and targeted next-generation sequencing (tNGS).

RESULTS

In urolithiasis patients with suspected preoperative infections, both NGS methods demonstrated 100% sensitivity and negative predictive values (NPV) for pathogen detection, with tNGS showing superior specificity and positive predictive values (PPV) compared to mNGS. tNGS significantly reduced detection time (13 h vs. 48–72 h for traditional culture). mNGS detected 43 distinct pathogens while tNGS identified 42, both revealing previously undetected microorganisms including viruses and fungi. Among culture-positive cases, Escherichia coli (E. coli) was the predominant pathogen with higher prevalence in female patients. In polymicrobial infection patterns, tNGS identified bacterial-viral combinations as the dominant pattern (50.79%), followed by bacterial-mycoplasma/chlamydia (17.46%), and bacterial-viral-fungal (12.70%) combinations. These findings were validated in the second cohort, where bacterial-viral co-infections remained predominant (73.68%). Both NGS methods maintained 100% concordance with culture-positive results in clear and turbid urine samples, with tNGS demonstrating fewer false positives.

CONCLUSIONS

For urolithiasis patients with suspected preoperative infections, tNGS emerges as a superior diagnostic tool due to its higher specificity, faster turnaround time, and ability to detect complex pathogen patterns. While mNGS offers advantages in broad-spectrum screening, tNGS provides a more practical approach for precise preoperative infection assessment, potentially improving surgical timing decisions and patient outcomes. CLINICAL TRIAL: Not applicable.