Comprehensive Determination of Mycobacterium tuberculosis and Nontuberculous Mycobacteria From Targeted Capture Sequencing
Infection of Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM) challenges effective pulmonary infectious disease control. Current phenotypic and molecular assays could not comprehensively and accurately diagnose MTB, NTM, and drug resistance. Next-generation sequencing allows an...
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| Format: | Article |
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Frontiers Media S.A.
2020-09-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fcimb.2020.00449/full |
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| author | Ya He Ziying Gong Ziying Gong Xiaokai Zhao Xiaokai Zhao Daoyun Zhang Daoyun Zhang Zhongshun Zhang |
| author_facet | Ya He Ziying Gong Ziying Gong Xiaokai Zhao Xiaokai Zhao Daoyun Zhang Daoyun Zhang Zhongshun Zhang |
| author_sort | Ya He |
| collection | DOAJ |
| description | Infection of Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM) challenges effective pulmonary infectious disease control. Current phenotypic and molecular assays could not comprehensively and accurately diagnose MTB, NTM, and drug resistance. Next-generation sequencing allows an “all-in-one” approach providing results on expected drug susceptibility testing (DST) and the genotype of NTM strains. In this study, targeted capture sequencing was used to analyze the genetic backgrounds of 4 MTB strains and 32 NTM pathogenic strains in 30 clinical samples, including 14 sputum specimens and 16 bronchoalveolar lavage fluid samples. Through comparing with other TB diagnostic tests, we proved that targeted capture sequencing could be used as a highly sensitive (91.3%) and accurate (83.3%) method to diagnose TB, as well as MGIT 960. Also, we identified 7 NTM strains in 11 patients; among them, seven patients were MTB/NTM co-affected, which indicated that it was a meaningful tool for the diagnosis and treatment of NTM infection diseases in clinic. However, based on a drug-resistant mutation library (1,325 drug resistance loci), only 9 drug resistance strains and 22 drug resistance loci were discovered, having considerable discordance with the drug-resistant results of MGIT 960. Our finding indicated that targeted capture sequencing approach was applicable for the comprehensive and accurate diagnosis of MTB and NTM. However, from data presented here, the DST results identified by next-generation sequencing (NGS) showed a relatively low consistency with MGIT 960, especially in sputum samples. Further work should be done to explore the reasons for low drug-resistance detection rate of NGS. |
| first_indexed | 2024-12-14T11:27:58Z |
| format | Article |
| id | doaj.art-7a7e781075dd4c86ba9481dad3414cc8 |
| institution | Directory Open Access Journal |
| issn | 2235-2988 |
| language | English |
| last_indexed | 2024-12-14T11:27:58Z |
| publishDate | 2020-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj.art-7a7e781075dd4c86ba9481dad3414cc82022-12-21T23:03:25ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882020-09-011010.3389/fcimb.2020.00449532928Comprehensive Determination of Mycobacterium tuberculosis and Nontuberculous Mycobacteria From Targeted Capture SequencingYa He0Ziying Gong1Ziying Gong2Xiaokai Zhao3Xiaokai Zhao4Daoyun Zhang5Daoyun Zhang6Zhongshun Zhang7Clinic and Research Center of Tuberculosis, Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, ChinaShanghai Yunying Medical Technology Co., Ltd., Shanghai, ChinaJiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, ChinaShanghai Yunying Medical Technology Co., Ltd., Shanghai, ChinaJiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, ChinaShanghai Yunying Medical Technology Co., Ltd., Shanghai, ChinaJiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, ChinaClinic and Research Center of Tuberculosis, Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, ChinaInfection of Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM) challenges effective pulmonary infectious disease control. Current phenotypic and molecular assays could not comprehensively and accurately diagnose MTB, NTM, and drug resistance. Next-generation sequencing allows an “all-in-one” approach providing results on expected drug susceptibility testing (DST) and the genotype of NTM strains. In this study, targeted capture sequencing was used to analyze the genetic backgrounds of 4 MTB strains and 32 NTM pathogenic strains in 30 clinical samples, including 14 sputum specimens and 16 bronchoalveolar lavage fluid samples. Through comparing with other TB diagnostic tests, we proved that targeted capture sequencing could be used as a highly sensitive (91.3%) and accurate (83.3%) method to diagnose TB, as well as MGIT 960. Also, we identified 7 NTM strains in 11 patients; among them, seven patients were MTB/NTM co-affected, which indicated that it was a meaningful tool for the diagnosis and treatment of NTM infection diseases in clinic. However, based on a drug-resistant mutation library (1,325 drug resistance loci), only 9 drug resistance strains and 22 drug resistance loci were discovered, having considerable discordance with the drug-resistant results of MGIT 960. Our finding indicated that targeted capture sequencing approach was applicable for the comprehensive and accurate diagnosis of MTB and NTM. However, from data presented here, the DST results identified by next-generation sequencing (NGS) showed a relatively low consistency with MGIT 960, especially in sputum samples. Further work should be done to explore the reasons for low drug-resistance detection rate of NGS.https://www.frontiersin.org/article/10.3389/fcimb.2020.00449/fullMycobacterium tuberculosisnontuberculous mycobacteriadiagnostic methodsdrug resistancetargeted capture sequencing |
| spellingShingle | Ya He Ziying Gong Ziying Gong Xiaokai Zhao Xiaokai Zhao Daoyun Zhang Daoyun Zhang Zhongshun Zhang Comprehensive Determination of Mycobacterium tuberculosis and Nontuberculous Mycobacteria From Targeted Capture Sequencing Frontiers in Cellular and Infection Microbiology Mycobacterium tuberculosis nontuberculous mycobacteria diagnostic methods drug resistance targeted capture sequencing |
| title | Comprehensive Determination of Mycobacterium tuberculosis and Nontuberculous Mycobacteria From Targeted Capture Sequencing |
| title_full | Comprehensive Determination of Mycobacterium tuberculosis and Nontuberculous Mycobacteria From Targeted Capture Sequencing |
| title_fullStr | Comprehensive Determination of Mycobacterium tuberculosis and Nontuberculous Mycobacteria From Targeted Capture Sequencing |
| title_full_unstemmed | Comprehensive Determination of Mycobacterium tuberculosis and Nontuberculous Mycobacteria From Targeted Capture Sequencing |
| title_short | Comprehensive Determination of Mycobacterium tuberculosis and Nontuberculous Mycobacteria From Targeted Capture Sequencing |
| title_sort | comprehensive determination of mycobacterium tuberculosis and nontuberculous mycobacteria from targeted capture sequencing |
| topic | Mycobacterium tuberculosis nontuberculous mycobacteria diagnostic methods drug resistance targeted capture sequencing |
| url | https://www.frontiersin.org/article/10.3389/fcimb.2020.00449/full |
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