A comparative study of mNGS and tNGS for pathogen detection in paired upper and lower respiratory tract specimens from pediatric pneumonia patients

ABSTRACT High-throughput sequencing technologies have become essential tools in clinical diagnostics, but the comparative performance of targeted next-generation sequencing (tNGS) versus metagenomic next-generation sequencing (mNGS) in pediatric respiratory infections remains unclear. In this study, paired throat swab and bronchoalveolar lavage fluid (BALF) specimens were collected from children with lower respiratory tract infections. Both tNGS and mNGS were used to detect pathogens in paired samples. For the same specimen type, tNGS and mNGS showed strong agreement, with Kappa coefficients of 0.791 ( P < 0.001) for BALF and 0.757 ( P < 0.001) for throat swabs. Although the pathogen profiles of the upper and lower respiratory tracts differed, when using the same detection method, the agreement between the two anatomical sites remained substantial, with Kappa values of 0.659 ( P < 0.001) for mNGS and 0.590 ( P < 0.001) for tNGS—both approaching or reaching the threshold for strong consistency. These findings confirm that tNGS is a reliable alternative to mNGS for pediatric respiratory pathogen detection, and that even between different respiratory sites, the diagnostic agreement is high enough to support clinical decision-making. IMPORTANCE This study demonstrates that, for the same specimen type, tNGS and mNGS achieve substantial agreement in detecting respiratory pathogens in children (Kappa 0.791 for BALF and 0.757 for throat swabs). Thus, tNGS offers a cost-effective alternative to mNGS for routine pediatric respiratory diagnostics. Importantly, despite distinct pathogen profiles between the upper respiratory tract (URT) and lower respiratory tract (LRT), substantial diagnostic concordance was observed between paired throat swab and BALF specimens tested with identical sequencing approaches (Kappa = 0.659 for mNGS, 0.590 for tNGS). This observation bears meaningful clinical relevance, suggesting that URT throat swabs could provide diagnostically helpful etiological clues. Still, BALF sampling retains critical value for identifying pathogens predominantly residing in the lower respiratory tract, and throat swab results require prudent clinical interpretation.