ORIGINAL RESEARCH article
Front. Cell. Infect. Microbiol.
Sec. Clinical and Diagnostic Microbiology and Immunology
Volume 15 - 2025 | doi: 10.3389/fcimb.2025.1694179
Comparison and evaluation of metagenomic next-generation sequencing (mNGS) and real-time PCR for the detection of Mycobacterium tuberculosis diagnosis
Provisionally accepted
- The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Objective: This study aimed to evaluate and compare the performance of metagenomic next-generation sequencing (mNGS) and real-time polymerase chain reaction (RT-PCR) for the detection of Mycobacterium tuberculosis (MTB) in patients with suspected tuberculosis (TB).
Methods: Samples from patients undergoing routine clinical testing for MTB using both mNGS and RT-PCR were included. The diagnostic agreement between the two methods was assessed. Discordant results were further validated using the Xpert MTB/RIF assay on cryopreserved aliquots.
Results: A total of 556 samples from suspected TB patients were analyzed. The majority were lower respiratory tract specimens, including bronchoalveolar lavage fluid (BALF; 94.06%), sputum (3.24%), and extrapulmonary samples (2.70%). Compared with Xpert MTB/RIF and clinical diagnosis as composite reference standards, both mNGS and RT-PCR showed high sensitivity (92.31% and 90.38%, respectively) and perfect specificity (100%). There was a high level of agreement between mNGS and RT-PCR, with a positive agreement of 82.69%, negative agreement of 98.25%, overall agreement of 98.38%, and a kappa value of 0.896 (P<0.001). Concordance was higher in samples with lower RT-PCR cycle threshold (Ct) values: 100% at Ct≤15, 100% at 15
Keywords: metagenomic next-generation sequencing, Real-Time PCR, Tuberculosis DIagnosis, pulmonary tuberculosis, Extrapulmonary tuberculosis
Received: 28 Aug 2025; Accepted: 22 Oct 2025.
Copyright: © 2025 Wang, Guo, Chen, Zhu, Yu and Deng. 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: Jiankai Deng, dengjk0417@126.com
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