Evaluation of Diagnostic Efficacy of Targeted Next-Generation Sequencing on Nasopharyngeal Swabs in Pediatric Community-Acquired Pneumonia.

Abstract

Objective: The objective of this study is to evaluate diagnostic efficacy of targeted next-generation sequencing (tNGS) on nasopharyngeal (NP) swabs in pediatric community-acquired pneumonia (CAP).

Methods: We conducted a retrospective analysis, compiling nasal and bronchoalveolar lavage fluid (BALF) specimens from a cohort of 147 children diagnosed with CAP at Tongling Maternal and Child Health Hospital from May 2023 to October 2024. The diagnostic accuracy of nasal tNGS was evaluated and compared against BALF tNGS and conventional microbiological tests (CMT), which included microbial culture and targeted polymerase chain reaction assays.

Results: Nasal tNGS detected a broader range of 25 pathogens, while CMT identified 17, and BALF tNGS identified 21, with significant differences in detection rates favoring tNGS methods (P<0.001). Single pathogen detection rates were 35.6% for nasal tNGS and 54.4% for BALF tNGS, with Mycoplasma pneumoniae being the most prevalent. Concordance in pathogen detection between nasal swabs and BALF using tNGS was highest for Human respiratory syncytial virus (Cohen's kappa, 0.92; 95% CI, 0.81-1), indicating almost perfect agreement.

Conclusion: NP swab-based tNGS technique offers valuable insights for the early etiological diagnosis and treatment of pneumonia, particularly in identifying viral pneumonia.