Comparison and evaluation of metagenomic next-generation sequencing (mNGS) and real-time PCR for the detection of Mycobacterium tuberculosis

作者：Yan‐Hong Wang, Peng Guo, Yaoming Chen, Hongji Zhu, Xuegao Yu, Jiankai Deng · 发表于：Frontiers in Cellular and Infection Microbiology · 年份：2025 · DOI：10.3389/fcimb.2025.1694179 · 被引用次数：1 · 研究领域：Tuberculosis Research and Epidemiology、Mycobacterium research and diagnosis、Diagnosis and treatment of tuberculosis

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 standard, 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<Ct ≤ 20, 76.47% at 20<Ct ≤ 25. Among concordant positive samples (n=43), mNGS SMRNs showed a strong negative correlation with RT-PCR Ct values ( r = -0.668, P < 0.001). Analysis of nine discorda...