Metagenomic next-generation sequencing in pediatric infectious disease diagnosis: A comprehensive systematic...

Diagnosing pediatric infectious diseases is challenging due to nonspecific presentations, small sample volumes, and the limited sensitivity of conventional microbiological tests (CMTs). Metagenomic next-generation sequencing (mNGS) enables broad, hypothesis-free pathogen detection, but its diagnostic performance in children remains insufficiently characterized. This study evaluates the diagnostic accuracy of mNGS in pediatric infectious diseases and compares its performance with CMTs.

This systematic review and meta-analysis was registered in PROSPERO (CRD42024542444). Searches were performed using multiple databases through August 2024. Eligible studies evaluated mNGS and CMTs in pediatric patients (≤21 years) with suspected infectious diseases and compared their respective results with clinical diagnosis. Pooled sensitivity, specificity, and diagnostic odds ratios (DORs) were calculated using a bivariate random-effects model.

Thirty-three studies (n = 4,165) met inclusion criteria, and nine were eligible for meta-analysis. Pooled sensitivity and specificity of mNGS versus clinical diagnosis were 0.84 (95% CI: 0.82-0.86) and 0.71 (95% CI: 0.66-0.75), respectively, compared with 0.40 (95% CI: 0.37-0.43) and 0.82 (95% CI: 0.78-0.86) for CMTs. The pooled DOR favored mNGS (18.6 vs. 5.4). Respiratory infections were most frequently investigated, followed by bloodstream and mixed infections. Over two-thirds of studies reported changes in antimicrobial management following mNGS results.

mNGS demonstrates superior sensitivity and diagnostic accuracy compared with CMTs, enabling comprehensive pathogen detection, including rare and co-infecting organisms, and informing targeted antimicrobial therapy. Despite limitations related to cost, complex interpretation, and methodological standardization, mNGS represents a promising complement to conventional diagnostics in pediatric infectious disease management.