ORIGINAL RESEARCH article
Front. Cell. Infect. Microbiol.
Sec. Clinical Microbiology
Volume 15 - 2025 | doi: 10.3389/fcimb.2025.1534519
This article is part of the Research TopicAdvances in the Diagnosis and Management of Infectious DiseasesView all 16 articles
Comparative of Metagenomic and Targeted Next-Generation Sequencing in Lower Respiratory Tract Fungal Infections
Provisionally accepted
Zhiyang Chen1,2,3Xin Liu1,2,3Li Tan1,2,3Xing Lyu1,2,3Qichen Long1,2,3Weimin Wu1,2,3Zhe Guo1,2,3Zhenni Liu1,2,3
Ziyang Li1,2,3*
Min Hu1,2,3*- 1Department of Clinical Laboratory, the Second Xiangya Hospital of Central South University, Changsha, China
- 2Clinical Medical Research Center for Molecular Diagnosis of infectious diseases in Hunan Province, Changsha, China
- 3Molecular Diagnostic Technology Hunan Engineering Research Center, Changsha, China
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Objectives: This study aims to compare the diagnostic efficiency and consistency of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in patients with lower respiratory tract fungal infections.September 2022 and April 2023 were enrolled at the second Xiangya Hospital, Changsha, China. Of which 61 were clinically diagnosed with invasive pulmonary fungal infection (IPFI) and 54 were non-IPFI cases. All patients received bronchoalveolar lavage, with mNGS, tNGS, and cultures being conducted paralleled.Diagnostic effectiveness and consistency in detecting microorganisms were compared.Results: Both mNGS and tNGS showed high sensitivity rates of 95.08% each, with specificity of 90.74% and 85.19%, respectively. They also demonstrated positive predictive values (PPV) of 92.1% and 87.9%, and negative predictive values (NPV) of 94.2% and 93.9%, respectively, in diagnosing IPFI. The sensitivity and NPV of mNGS and tNGS were superior to that of any individual or combined conventional microbiological tests (CMTs) (P<0.05). The consistency of culture with mNGS and tNGS was 48.70% and 50.43%, respectively. For fungal detection, Pneumocystis jirovecii (26/61, 42.6%; 28/61, 45.9%), Candida albicans (19/61, 31.1%; 21/61, 34.4%) and Aspergillus fumigatus (16/61, 26.2%; 15/61, 24.6%) being most prevalent for mNGS and tNGS in enrolled cases, and the detection rate was greatly higher than culture. Furthermore, mNGS and tNGS were capable of diagnosing mixed infections in 65 and 55 out of 115 cases, whereas only 9 cases of bacteria-fungal infection were detected by culture.The diagnostic efficacy of mNGS and tNGS were comparable in identify IPFI. NGS-based methodologies present a promising tool for detecting IPFI, which can be a good supplement to CMT.
Keywords: MNGs, TNGS, diagnosis, Invasive pulmonary fungal infection, Fungal
Received: 26 Nov 2024; Accepted: 23 Apr 2025.
Copyright: © 2025 Chen, Liu, Tan, Lyu, Long, Wu, Guo, Liu, Li and Hu. 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:
Ziyang Li, Clinical Medical Research Center for Molecular Diagnosis of infectious diseases in Hunan Province, Changsha, China
Min Hu, Department of Clinical Laboratory, the Second Xiangya Hospital of Central South University, Changsha, China
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