The application value of targeted next-generation sequencing using bronchoalveolar lavage fluid samples in community-acquired pneumonia in children.

Abstract

Background: The precise identification of pathogens responsible for community-acquired pneumonia (CAP) in children is essential for effective treatment. However, the performance of targeted next-generation sequencing (tNGS) in the detection of pathogens associated with CAP in children remains unclear.

Methods: In this study, 216 children diagnosed with CAP were enrolled, and bronchoalveolar lavage fluid (BALF) samples underwent detection through tNGS, culture, and multiplex quantitative polymerase chain reaction (qPCR).

Results: In 208 children, tNGS identified a total of 389 strains of microorganisms, including 111 Mycoplasma pneumoniae, 123 bacteria, 127 viruses, and 28 fungi. Among the cases, 89 presented as single-pathogen detection, while 119 exhibited multiple pathogens co-detection. The positive detection rates of bacteria and fungi through tNGS were significantly higher than those achieved through the traditional culture method, with rates of 56.9 % vs 8.3 % for bacteria and 13.0 % vs 4.2 % for fungi, respectively. The overall agreement between tNGS and multiplex qPCR ranged from 89.4 % to 99.1 %, with Kappa values ranging from 0.541 to 0.912 (P = 0.000).

Conclusions: The tNGS technique demonstrates rapid and effective capabilities in identifying a wide array of pathogens with a detection sensitivity that surpasses traditional culture methodologies while exhibiting a high degree of consistency with multiplex qPCR in detecting respiratory viruses. The tNGS detection method can serve as an important complement to traditional diagnostic approaches; however, caution must be exercised when interpreting tNGS findings due to its heightened sensitivity which may lead to identification of pathogens that are not necessarily responsible for causing disease.