The Feasibility of Metagenomic Next-Generation Sequencing to Identify Pathogens Causing Tuberculous Meningitis in Cerebrospinal Fluid
PurposeThe 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 tuber...
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Frontiers Media S.A.
2019-09-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2019.01993/full |
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| author | Shengnan Wang Yingli Chen Dongmei Wang Yongming Wu Deqiang Zhao Jianzhao Zhang Huifang Xie Yanping Gong Ruixue Sun Xifang Nie Haishan Jiang Jian Zhang Wei Li Guanghui Liu Xuan Li Kaibin Huang Yingwei Huang Yongjun Li Hongzhi Guan Suyue Pan Yafang Hu |
| author_facet | Shengnan Wang Yingli Chen Dongmei Wang Yongming Wu Deqiang Zhao Jianzhao Zhang Huifang Xie Yanping Gong Ruixue Sun Xifang Nie Haishan Jiang Jian Zhang Wei Li Guanghui Liu Xuan Li Kaibin Huang Yingwei Huang Yongjun Li Hongzhi Guan Suyue Pan Yafang Hu |
| author_sort | Shengnan Wang |
| collection | DOAJ |
| description | PurposeThe 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.MethodsWe 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 an mNGS negative control.ResultsTwenty three TBM patients were classified as 12 definite and 11 clinical diagnoses, which were based on clinical manifestations, pathogen evidence, CSF parameters, brain 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, and culture to detect MTB in the first CSF samples were 66.67, 33.33, 25, and 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.ConclusionOur 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 be applied as a front-line CSF test. |
| first_indexed | 2024-12-21T17:10:17Z |
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| language | English |
| last_indexed | 2024-12-21T17:10:17Z |
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| spelling | doaj.art-c6c62a668ce8439bb2f419a665e042c22022-12-21T18:56:25ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-09-011010.3389/fmicb.2019.01993452433The Feasibility of Metagenomic Next-Generation Sequencing to Identify Pathogens Causing Tuberculous Meningitis in Cerebrospinal FluidShengnan Wang0Yingli Chen1Dongmei Wang2Yongming Wu3Deqiang Zhao4Jianzhao Zhang5Huifang Xie6Yanping Gong7Ruixue Sun8Xifang Nie9Haishan Jiang10Jian Zhang11Wei Li12Guanghui Liu13Xuan Li14Kaibin Huang15Yingwei Huang16Yongjun Li17Hongzhi Guan18Suyue Pan19Yafang Hu20Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Neurology, Beijing Children’s Hospital, Capital Medical University, Beijing, ChinaDepartment of Neurology, Zhujiang Hospital, Southern Medical University, Guangzhou, ChinaTianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, ChinaTianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, ChinaTianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, ChinaDepartment of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaBGI Genomics, BGI-Shenzhen, Shenzhen, ChinaDepartment of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, ChinaDepartment of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaDepartment of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaPurposeThe 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.MethodsWe 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 an mNGS negative control.ResultsTwenty three TBM patients were classified as 12 definite and 11 clinical diagnoses, which were based on clinical manifestations, pathogen evidence, CSF parameters, brain 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, and culture to detect MTB in the first CSF samples were 66.67, 33.33, 25, and 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.ConclusionOur 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 be applied as a front-line CSF test.https://www.frontiersin.org/article/10.3389/fmicb.2019.01993/fullcerebrospinal fluidMycobacterium tuberculosismeningitismetagenomic next-generation sequencingearly diagnosis |
| spellingShingle | Shengnan Wang Yingli Chen Dongmei Wang Yongming Wu Deqiang Zhao Jianzhao Zhang Huifang Xie Yanping Gong Ruixue Sun Xifang Nie Haishan Jiang Jian Zhang Wei Li Guanghui Liu Xuan Li Kaibin Huang Yingwei Huang Yongjun Li Hongzhi Guan Suyue Pan Yafang Hu The Feasibility of Metagenomic Next-Generation Sequencing to Identify Pathogens Causing Tuberculous Meningitis in Cerebrospinal Fluid Frontiers in Microbiology cerebrospinal fluid Mycobacterium tuberculosis meningitis metagenomic next-generation sequencing early diagnosis |
| title | The Feasibility of Metagenomic Next-Generation Sequencing to Identify Pathogens Causing Tuberculous Meningitis in Cerebrospinal Fluid |
| title_full | The Feasibility of Metagenomic Next-Generation Sequencing to Identify Pathogens Causing Tuberculous Meningitis in Cerebrospinal Fluid |
| title_fullStr | The Feasibility of Metagenomic Next-Generation Sequencing to Identify Pathogens Causing Tuberculous Meningitis in Cerebrospinal Fluid |
| title_full_unstemmed | The Feasibility of Metagenomic Next-Generation Sequencing to Identify Pathogens Causing Tuberculous Meningitis in Cerebrospinal Fluid |
| title_short | The Feasibility of Metagenomic Next-Generation Sequencing to Identify Pathogens Causing Tuberculous Meningitis in Cerebrospinal Fluid |
| title_sort | feasibility of metagenomic next generation sequencing to identify pathogens causing tuberculous meningitis in cerebrospinal fluid |
| topic | cerebrospinal fluid Mycobacterium tuberculosis meningitis metagenomic next-generation sequencing early diagnosis |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2019.01993/full |
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