ORIGINAL RESEARCH article
Front. Cell. Infect. Microbiol.
Sec. Clinical Microbiology
Volume 15 - 2025 | doi: 10.3389/fcimb.2025.1590881
This article is part of the Research TopicExploring Clinical Application Scenarios of Metagenomic Next-Generation Sequencing for Pathogen DiagnosisView all articles
Application of targeted next-generation sequencing for pathogens diagnosis and drug resistance prediction in bronchoalveolar lavage fluid of pulmonary infections
Provisionally accepted
Qiugui Xu1
Qiumei Chen1Wen Qiu1
Lili Liu1Wan Zeng1Jinling Chen1Yangyang Li1Zhen Guo2
Ling Rong1Bigui Chen1Jinxiu Yao1
Li-Ye Yang1*- 1People's Hospital of Yangjiang, Yangjiang, China
- 2Chest Hospital of Zhengzhou University, Zhengzhou, China
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Background: Recently, targeted next-generation sequencing (tNGS) have been extensively utilized for the identification of pathogens in pulmonary infections, there have been some studies systematically evaluating differences in the efficacy of tNGS and conventional microbiological tests (CMTs) in bronchoalveolar lavage fluid (BALF) specimens. Methods: A retrospective analysis was conducted on 203 patients with pulmonary infections treated in one tertiary hospital from July 2023 to February 2024. BALF specimens underwent parallel testing via tNGS and CMTs. Pathogen detection consistency, the drug resistance genes concordance with phenotypic drug sensitivity, and clinical impact of tNGS-guided therapy adjustments were analyzed. Furthermore, two patients with complex infections were selected for tNGS microbiological surveillance to evaluate the efficacy of monitoring severe pneumonia. Results: This study included 205 confirmed infectious BALF specimens (two patients were tested twice). tNGS identified 56 putative pathogens, compared to 20 by CMTs, with a significantly higher positive rate (99.5% vs. 35.6%, P<0.0001). The detection of pathogenic microorganisms using tNGS showed a high concordance rate with the results of CMTs. tNGS-guided therapy adjustments occurred in 18.7% (38/203) of patients. Resistance gene predictions aligned with the drug sensitivity results in 40% (6/15) of carbapenem-resistant organisms (CROs) and 80% (4/5) of methicillin-resistant Staphylococcus aureus (MRSA) cases. Additionally, for monitored two patients with severe pneumonia, the tNGS results were consistent with the culture and imaging test results during treatment. Conclusions: The application of tNGS highlights its promise and significance in identifying potential pathogens, predicting drug resistance, and providing guidance for anti-infection therapies for severe pneumonia. It can be at least a complementary approach to CMTs reporting.
Keywords: Targeted next-generation sequencing (TNGS), Conventional microbiological tests (CMTs), pulmonary infection, Bronchoalveolar lavage fluid (BALF), pathogens
Received: 12 Mar 2025; Accepted: 22 May 2025.
Copyright: © 2025 Xu, Chen, Qiu, Liu, Zeng, Chen, Li, Guo, Rong, Chen, Yao and Yang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Li-Ye Yang, People's Hospital of Yangjiang, Yangjiang, China
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