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ORIGINAL RESEARCH article
Front. Cell. Infect. Microbiol.
Sec. Clinical Microbiology
Volume 15 - 2025 | doi: 10.3389/fcimb.2025.1513603
This article is part of the Research Topic Infectious disease control in the microbial functional genomics era View all 4 articles
Application of metagenomic next-generation sequencing in pathogen detection of lung infections
Provisionally accepted
Song Chen 1,2
Tanglin Ouyang 1,2
Kai-yang Wang 1
Xuan Hou 1,2
Rong Zhang 1,2 Meiyong Li 1
Hai Zhang 1 Qinghua He 1
Xiuzhen Li 1
Zezhang Liu 3,4
Bo Huang 1*
Xiaozhong Wang 1*- 1 Second Affiliated Hospital of Nanchang University, Nanchang, China
- 2 School of Public Health, Nanchang University, Nanchang, Jiangxi Province, China
- 3 Beijing Genomics Institute (BGI), Shenzhen, China
- 4 Clin Lab, BGI Genomics, Wuhan, China
Background: Metagenomic next-generation sequencing (mNGS) has been widely reported to provide crucial information for the diagnosis and treatment of infectious diseases. In this study, we aimed to evaluate mNGS in pathogens diagnosis of lung infections.: A total of 188 patients who were suspected of pulmonary infection and received medical treatment at the Second Affiliated Hospital of Nanchang University from August 2022 to December 2023 were enrolled in this study. Conventional microbiological tests (CMTs) and mNGS were employed for pathogens diagnosis.Results: Statistical results indicated that mNGS were significantly better than CMTs in sensitivity, negative predictive value, and negative likelihood ratio. Remarkably, the positive detection rate of mNGS was significantly higher than that of CMTs (86.17% vs 67.55%, P < 0.01). Through mNGS, we identified 96 pathogens, comprising 59 bacteria, 18 fungi, 15 viruses, and 4 special pathogens. In contrast, CMTs detected 28 species, including 25 bacteria and 3 fungi. The effectiveness rate of antibiotic treatment decisions based on mNGS results was 40.60%. Out of 54 cases with positive treatment impacts, mNGS results contributed to the treatment and improved prognosis of 16 infections caused by atypical pathogens.Our results proved the essential role of mNGS in lung infection diagnosis, enabling early detection and the prompt development of targeted anti-infection therapies. We recommended that the clinical application of mNGS can enhance treatment effectiveness and improve patient prognosis.
Keywords: metagenomic next-generation sequencing, lung infection, Bronchoalveolar Lavage Fluid, conventional microbiological test, pathogens diagnosis, antibiotic treatment adjustment
Received: 18 Oct 2024; Accepted: 04 Apr 2025.
Copyright: © 2025 Chen, Ouyang, Wang, Hou, Zhang, Li, Zhang, He, Li, Liu, Huang and Wang. 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:
Bo Huang, Second Affiliated Hospital of Nanchang University, Nanchang, China
Xiaozhong Wang, Second Affiliated Hospital of Nanchang University, Nanchang, China
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