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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Microbiol. | doi: 10.3389/fmicb.2019.01993

The feasibility of metagenomic next-generation sequencing to identify pathogens causing tuberculous meningitis in cerebrospinal fluid

 shengnan Wang1,  Yingli Chen1, Dongmei Wang1, Yongming Wu1, Deqiang Zhao1,  Jianzhao Zhang2, Huifang Xie3, Yanping Gong4, Ruixue Sun4, Xifang Nie4,  Haishan Jiang1, Jian Zhang5, Wei Li1,  Guanghui Liu1, Xuan Li1,  Kaibin Huang1,  Yingwei Huang1, Yongjun Li6,  Hongzhi Guan7*,  Suyue Pan1* and  Yafang Hu1*
  • 1Department of Neurology, Nanfang Hospital, Southern Medical University, China
  • 2Department of Neurology, Beijing Children’s Hospital, Capital Medical University, China
  • 3Department of Neurology, Zhujiang Hospital, Southern Medical University, China
  • 4Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China, China
  • 5Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, China
  • 6Beijing Genomics Institute (BGI), China
  • 7Chinese Academy of Medical Sciences, Department of Neurology, Peking Union Medical College Hospital, China

Purpose: The application of metagenomic next-generation sequencing (mNGS) in the diagnosis of tuberculous meningitis (TBM) remains poorly characterized. Here, we retrospectively analyzed data from patients with TBM who had taken both mNGS and conventional tests including culture of Mycobacterium tuberculosis (MTB), polymerase chain reaction (PCR) and acid-fast bacillus (AFB) stain, and the sensitivity and specificity of these methods were compared.
Methods: We retrospectively recruited TBM patients admitted to the hospital between December 2015 and October 2018. The first collection of cerebrospinal fluid (CSF) samples underwent both mNGS and conventional tests. In addition, patients with bacterial/cryptococcal meningitis or viral meningoencephalitis were mNGS positive controls, and a patient with auto-immune encephalitis was a mNGS negative control.
Results: 23 TBM patients were classified as 12 definite and 11 clinical diagnoses, which were based on clinical manifestations, pathogen evidence, CSF parameters, cerebral imaging, and treatment response. The mNGS method identified sequences of Mycobacterium tuberculosis complex (MBTC) from 18 samples (18/23, 78.26%). In patients with definite TBM, the sensitivity of mNGS, AFB, PCR or culture to detect MTB in the first CSF samples were 66.67%, 33.33%, 25% or 8.33%, respectively. The specificity of each method was 100%. Among the four negative mNGS cases (4/23, 17.39%), three turned out positive by repeated AFB stain. The agreement of mNGS with the total of conventional methods was 44.44% (8/18). Combination of mNGS and conventional methods increased the detection rate to 95.65%. One patient was diagnosed as complex of TBM and cryptococcal meningitis, in which AFB stain and cryptococcal antigen enzyme immunoassay were positive and the DNA of Cryptococcus neoformans was detected by mNGS.
Conclusions: Our study indicates that mNGS is an alternative method to detect the presence of mycobacterial DNA in CSF samples from patients with TBM and deserves to apply as a front-line CSF test.

Keywords: Cerebrospical fluid (CSF), Mycobacterium tuberculosis, Meningitis, metagenomic next-generation sequencing, early diagnosis

Received: 02 Feb 2019; Accepted: 14 Aug 2019.

Copyright: © 2019 Wang, Chen, Wang, Wu, Zhao, Zhang, Xie, Gong, Sun, Nie, Jiang, Zhang, Li, Liu, Li, Huang, Huang, Li, Guan, Pan 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) and the copyright owner(s) 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:
Prof. Hongzhi Guan, Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China, guanhz@263.net
Prof. Suyue Pan, Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China, pansuyue82@126.com
Prof. Yafang Hu, Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China, yafanghu@smu.edu.cn