Targeted next-generation sequencing for pathogen detection and epidemiological analysis of pediatric acute respiratory infections in Xiantao, China

BACKGROUND: Acute respiratory infections (ARIs) are a leading cause of pediatric morbidity and mortality globally, yet comprehensive pathogen epidemiology in children remains understudied. This study aimed to characterize the pathogen profiles, co-infection patterns, and epidemiological trends of pediatric ARIs in Xiantao, China, using targeted next-generation sequencing (tNGS). METHODS: A retrospective analysis was conducted on 4,330 children hospitalized with ARIs from May 2022 to September 2023. Oropharyngeal swab specimens were tested by tNGS for 96 pathogens via ultra-multiplex PCR and high-throughput sequencing. RESULTS: Pathogens were detected in 99.3 % (4,298/4,330) of cases, with multi-pathogen co-infections in 88.7 % (3811/4298) of samples, including dual (26.1 %), triple (28.2 %), and ≥quadruple pathogens (34.4 %), demonstrating high co-infection complexity. Bacterial pathogens (57.7 %) exceeded viral (35.7 %) and Mycoplasma/ Chlamydial (6.6 %). Age-stratified analysis revealed significant variability in 37 pathogens (p < 0.05), with incidence inversely correlated to age. Seasonal peaks occurred in spring (March-May) and early summer (June), driven first by bacterial then viral agents. Pneumonia (57.8 %, 2,407/4,162) and acute upper respiratory infections (24.1 %, 1,005/4,162) were the most frequent clinical diagnoses. CONCLUSIONS: tNGS provides rapid, comprehensive pathogen identification in pediatric ARIs while uncovering intricate co-infection patterns. The findings highlight the importance of age-specific and seasonal considerations in managing respiratory infections, and suggest that tNGS has the potential to provide information useful for clinical decision-making, reduce antibiotic misuse, and improve pediatric outcomes-although these advantages await confirmation in future studies.