Targeted next-generation sequencing for pediatric lower respiratory tract infections: a retrospective study

Lower respiratory tract infections (LRTIs), including bronchitis and pneumonia, are common pediatric conditions. Accurate and timely pathogen identification is essential in this population, with targeted next-generation sequencing (tNGS) significantly improving detection rates. This study aimed to systematically assess the clinical utility of tNGS in identifying pathogens in pediatric LRTIs.

A retrospective analysis of 107 pediatric patients with lower respiratory tract infections (LRTIs) was conducted between January 2024 and December 2024. The concordance of tNGS, quantitative polymerase chain reaction (qPCR), and microbial culture results with clinical diagnoses was assessed. Data were analyzed using the Statistical Package for the Social Sciences (SPSS), with statistical significance set at P < 0.05.

Of the 107 pediatric patients, 34 (31.8%) had single-pathogen infections while 73 (68.2%) had multiple infections, with bacterial-viral co-infections comprising 42.5% of the latter group. The tNGS results demonstrated a concordance rate of over 66% with clinical diagnoses, which was significantly higher (P < 0.001) than that of qPCR and culture. The analysis revealed 80% concordance between tNGS and qPCR results. Notably, tNGS demonstrated 90% concordance with culture methods in approximately 70% of comparative detections. Furthermore, for Human rhinovirus and Mycoplasma pneumoniae, the RPM values for tNGS were significantly higher (P<0.05) in (tNGS+qPCR+) samples than in (tNGS+qPCR-) samples. Compared with Human rhinovirus (AUC=0.759), Mycoplasma pneumoniae exhibited stronger discriminatory power (AUC=0.917).

The tNGS results demonstrated high concordance with the clinical diagnosis, supporting its high applicability in diagnosing pathogens in pediatric patients with severe, mixed, or refractory infections.