Targeted next-generation sequencing for pediatric community-acquired pneumonia pathogen detection: a single-center study.

BACKGROUND: Community-acquired pneumonia (CAP) is a major contributor to the high burden of acute lower respiratory tract infections in children, characterized by significant incidence and mortality. While targeted next-generation sequencing (tNGS) provides a rapid, accurate, and comprehensive approach to pathogen identification, potentially enabling timely and precise clinical decisions, its application in pediatric populations is not well established. Therefore, this study was designed to investigate the clinical utility of tNGS for detecting pathogens in children with CAP. METHODS: This retrospective study enrolled 838 children diagnosed with CAP, who were admitted to Chengdu Women and Children's Central Hospital and underwent tNGS testing between February 2023 and May 2025. Additionally, the results of conventional microbiological tests were collected for comparative analysis to characterize the respiratory pathogen profile in this pediatric cohort. RESULTS: The effective detection rate of tNGS (94.0% 788/838) was significantly higher than that of conventional microbiological tests (CMTs) (71.0% 483/680), and the combination of both methods increased the rate to 97.3% (815/838) (P < 0.0001). In contrast to its superior bacterial and atypical pathogen detection, tNGS showed a lower viral detection rate than CMTs. A high positive agreement between the two methods was observed for Mycoplasma pneumoniae (MP) and Haemophilus influenzae, whereas a high negative agreement was found for viral infections. MP was the most frequently detected pathogen overall, followed by Haemophilus influenzae and Streptococcus pneumoniae among bacteria, and rhinovirus and respiratory syncytial virus (RSV) among viruses. Age-specific analysis revealed distinct patterns: viral pathogens were more frequently detected in infants, who also showed the highest detection rate of Staphylococcus aureus; preschool children were prone to bacterial infections; and school-aged children were predominantly affected by atypical pathogens. CONCLUSION: Compared to CMTs, tNGS demonstrated superior capability in detecting a broader range of pathogens with higher sensitivity, making it particularly valuable for identifying coinfections. When interpreted alongside clinical manifestations, tNGS provides clinicians with a precise diagnostic tool for the early identification of lower respiratory tract pathogens. This information, when integrated with clinical presentation, can guide more timely and appropriate therapeutic decisions, which may help mitigate disease severity and reduce mortality in children with CAP.