Efficacy of hc-tNGS for pathogen identification for pediatric cUTIs: a real-world observational study

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Background Complicated urinary tract infections (cUTIs) represent a critical subset of pediatric UTIs, characterized by diverse complex factors stemming from the patient, disease status, and pathogen-related attributes. Without timely and precise management, cUTIs may progress to invasive renal parenchymal infection (IRPI), posing long−term health risks. A central challenge in cUTI management lies in the limitations of urine culture, including prolonged turnaround time and suboptimal sensitivity, particularly post-antibiotic exposure. Hybrid Capture-Based targeted next-generation sequencing (hc-tNGS), a culture-independent emerging etiological assay, provides a potential solution to optimize clinical care. However, evidence regarding its utility in pediatric cUTI cohorts remains limited. Methods This single−center, retrospective study enrolled 88 pediatric cUTI patients. All participants underwent sequential urine culture followed by hc−tNGS. The performance of the two methods in terms of pathogen spectrum, detection rate, and potential implications for antibiotic therapy optimization were compared. Results Hc−tNGS demonstrated significantly higher pathogen detection sensitivity compared to conventional urine culture (92.5% vs. 33.0%, p < 0.001). Meanwhile, hc−tNGS uniquely identified polymicrobial bacterium-bacterium or bacterial-fungal infections in 58% cases, a profile missed by culture. Furthermore, Klebsiella species infection was identified as an independent risk factor for IRPI. Pathogen genetic profiling revealed that virulence and resistance genes were primarily clustered within E. coli -associated monomicrobial or polymicrobial pathogens, mainly including adhesion−related ompA , siderophore genes ( iucA/B/C ), and CTX−M resistance genotypes, respectively. In the vesicoureteral reflux (VUR) subgroup, this comprehensive profiling was associated with antibiotic adjustments in 71% cases. Conclusion Sequential hc−tNGS provides a clinical diagnostic approach for cUTI as a complement to urine culture, especially after prior antibiotic use or suspected renal involvement. It enables accurate detection of polymicrobial and difficult−to−culture pathogens. These findings suggest that hc−tNGS may be integrated into routine diagnostic workflows to help guide targeted therapy and improve patient management in complex UTI settings.