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The application value of targeted next-generation sequencing using bronchoalveolar lavage fluid samples in
Shiyi He1, Weishi Xue1, Xiaoning Wu1
1Department of Clinical Laboratory, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China.
Insights
Targeted next-generation sequencing (tNGS) effectively identifies diverse pathogens in pediatric community-acquired pneumonia (CAP), surpassing traditional methods. While highly sensitive, tNGS results require careful interpretation to distinguish causative agents from colonizers.
Area of Science:
- Pediatric infectious diseases
- Molecular diagnostics
- Microbiology
Background:
- Accurate pathogen identification is crucial for treating pediatric community-acquired pneumonia (CAP).
- The diagnostic performance of targeted next-generation sequencing (tNGS) for pediatric CAP pathogens is not well-established.
Purpose of the Study:
- To evaluate the efficacy of tNGS in detecting a broad spectrum of pathogens in children with CAP.
- To compare tNGS performance against conventional culture and multiplex quantitative polymerase chain reaction (qPCR) methods.
Main Methods:
- Bronchoalveolar lavage fluid (BALF) samples from 216 children with CAP were analyzed using tNGS, culture, and multiplex qPCR.
- Pathogen detection rates and agreement between methods were assessed.
Main Results:
- tNGS identified 389 microbial strains in 208 children, including bacteria, viruses, fungi, and Mycoplasma pneumoniae.
- tNGS demonstrated significantly higher detection rates for bacteria (56.9% vs 8.3%) and fungi (13.0% vs 4.2%) compared to culture.
- High agreement (89.4%–99.1%) was observed between tNGS and multiplex qPCR for respiratory virus detection.
Conclusions:
- tNGS offers rapid and comprehensive pathogen identification in pediatric CAP, exceeding traditional culture sensitivity.
- tNGS shows high concordance with multiplex qPCR for viral detection.
- The heightened sensitivity of tNGS necessitates cautious interpretation to differentiate causative pathogens from non-pathogenic organisms.
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.
