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Efficacy of hc-tNGS for pathogen identification for pediatric cUTIs: a real-world observational study
Lin Huang1, Juanjuan Ding1, Baolong Zhang2
1Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China.
Insights
Hybrid Capture-Based targeted next-generation sequencing (hc-tNGS) offers superior pathogen detection for pediatric complicated urinary tract infections (cUTIs) compared to traditional urine culture. This advanced method identifies polymicrobial infections and aids in optimizing antibiotic therapy.
Area of Science:
- Pediatric infectious diseases
- Clinical microbiology
- Genomic diagnostics
Background:
- Complicated urinary tract infections (cUTIs) in children pose significant health risks, potentially leading to invasive renal parenchymal infection (IRPI).
- Conventional urine culture methods for diagnosing cUTIs have limitations, including long turnaround times and reduced sensitivity, especially after antibiotic treatment.
- Hybrid Capture-Based targeted next-generation sequencing (hc-tNGS) is an emerging culture-independent diagnostic tool with potential benefits for pediatric cUTI management.
Purpose of the Study:
- To evaluate the performance of hc-tNGS compared to urine culture in diagnosing pediatric cUTIs.
- To assess the utility of hc-tNGS in identifying polymicrobial infections and guiding antibiotic therapy optimization.
Main Methods:
- A retrospective study involving 88 pediatric patients diagnosed with cUTIs.
- Sequential analysis using both conventional urine culture and hc-tNGS.
- Comparison of pathogen detection rates, spectrum, and implications for antibiotic treatment adjustments.
Main Results:
- Hc-tNGS exhibited significantly higher pathogen detection sensitivity (92.5%) than urine culture (33.0%, p < 0.001).
- Hc-tNGS identified polymicrobial infections in 58% of cases, which were missed by culture.
- Pathogen genetic profiling identified *Klebsiella* species as an independent risk factor for IRPI and revealed key virulence and resistance genes in *E. coli*.
- In patients with vesicoureteral reflux (VUR), hc-tNGS-guided profiling led to antibiotic adjustments in 71% of cases.
Conclusions:
- Sequential hc-tNGS serves as a valuable clinical diagnostic approach for pediatric cUTIs, complementing urine culture.
- Hc-tNGS accurately detects polymicrobial and difficult-to-culture pathogens, proving especially useful after antibiotic exposure or in cases of suspected renal involvement.
- Integration of hc-tNGS into routine diagnostics can enhance targeted therapy and improve patient management in complex UTI cases.
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.
