Genetic features of Mycobacterium tuberculosis modern Beijing sublineage
Mycobacterium tuberculosis (MTB) Beijing strains have caused a great concern because of their rapid emergence and increasing prevalence in worldwide regions. Great efforts have been made to investigate the pathogenic characteristics of Beijing strains such as hypervirulence, drug resistance and favo...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2016-01-01
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| Series: | Emerging Microbes and Infections |
| Subjects: | |
| Online Access: | https://www.tandfonline.com/doi/10.1038/emi.2016.14 |
| _version_ | 1797679079289257984 |
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| author | Qingyun Liu Tao Luo Xinran Dong Gang Sun Zhu Liu Mingyun Gan Jie Wu Xin Shen Qian Gao |
| author_facet | Qingyun Liu Tao Luo Xinran Dong Gang Sun Zhu Liu Mingyun Gan Jie Wu Xin Shen Qian Gao |
| author_sort | Qingyun Liu |
| collection | DOAJ |
| description | Mycobacterium tuberculosis (MTB) Beijing strains have caused a great concern because of their rapid emergence and increasing prevalence in worldwide regions. Great efforts have been made to investigate the pathogenic characteristics of Beijing strains such as hypervirulence, drug resistance and favoring transmission. Phylogenetically, MTB Beijing family was divided into modern and ancient sublineages. Modern Beijing strains displayed enhanced virulence and higher prevalence when compared with ancient Beijing strains, but the genetic basis for this difference remains unclear. In this study, by analyzing previously published sequencing data of 1082 MTB Beijing isolates, we determined the genetic changes that were commonly present in modern Beijing strains but absent in ancient Beijing strains. These changes include 44 single-nucleotide polymorphisms (SNPs) and two short genomic deletions. Through bioinformatics analysis, we demonstrated that these genetic changes had high probability of functional effects. For example, 4 genes were frameshifted due to premature stop mutation or genomic deletions, 19 nonsynonymous SNPs located in conservative codons, and there is a significant enrichment in regulatory network for all nonsynonymous mutations. Besides, three SNPs located in promoter regions were verified to alter downstream gene expressions. Our study precisely defined the genetic features of modern Beijing strains and provided interesting clues for future researches to elucidate the mechanisms that underlie this sublineage’s successful expansion. These findings from the analysis of the modern Beijing sublineage could provide us a model to understand the dynamics of pathogenicity of MTB. |
| first_indexed | 2024-03-11T23:09:13Z |
| format | Article |
| id | doaj.art-340b8199632d4488889cd7b646e697f6 |
| institution | Directory Open Access Journal |
| issn | 2222-1751 |
| language | English |
| last_indexed | 2024-03-11T23:09:13Z |
| publishDate | 2016-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Emerging Microbes and Infections |
| spelling | doaj.art-340b8199632d4488889cd7b646e697f62023-09-21T12:27:55ZengTaylor & Francis GroupEmerging Microbes and Infections2222-17512016-01-01511810.1038/emi.2016.14Genetic features of Mycobacterium tuberculosis modern Beijing sublineageQingyun Liu0Tao Luo1Xinran Dong2Gang Sun3Zhu Liu4Mingyun Gan5Jie Wu6Xin Shen7Qian Gao8Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, ChinaLaboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, Sichuan 610041, ChinaInstitute of Biostatistics, School of Life Sciences, Fudan University, Shanghai 200433, ChinaKey Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, ChinaInstitute of Biostatistics, School of Life Sciences, Fudan University, Shanghai 200433, ChinaKey Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, ChinaDepartment of TB Control, Shanghai Municipal Centers for Disease Control and Prevention, Shanghai 200336, ChinaDepartment of TB Control, Shanghai Municipal Centers for Disease Control and Prevention, Shanghai 200336, ChinaKey Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, ChinaMycobacterium tuberculosis (MTB) Beijing strains have caused a great concern because of their rapid emergence and increasing prevalence in worldwide regions. Great efforts have been made to investigate the pathogenic characteristics of Beijing strains such as hypervirulence, drug resistance and favoring transmission. Phylogenetically, MTB Beijing family was divided into modern and ancient sublineages. Modern Beijing strains displayed enhanced virulence and higher prevalence when compared with ancient Beijing strains, but the genetic basis for this difference remains unclear. In this study, by analyzing previously published sequencing data of 1082 MTB Beijing isolates, we determined the genetic changes that were commonly present in modern Beijing strains but absent in ancient Beijing strains. These changes include 44 single-nucleotide polymorphisms (SNPs) and two short genomic deletions. Through bioinformatics analysis, we demonstrated that these genetic changes had high probability of functional effects. For example, 4 genes were frameshifted due to premature stop mutation or genomic deletions, 19 nonsynonymous SNPs located in conservative codons, and there is a significant enrichment in regulatory network for all nonsynonymous mutations. Besides, three SNPs located in promoter regions were verified to alter downstream gene expressions. Our study precisely defined the genetic features of modern Beijing strains and provided interesting clues for future researches to elucidate the mechanisms that underlie this sublineage’s successful expansion. These findings from the analysis of the modern Beijing sublineage could provide us a model to understand the dynamics of pathogenicity of MTB.https://www.tandfonline.com/doi/10.1038/emi.2016.14ancient sublineageBeijing familymicroevolutionmodern sublineageMycobacterium tuberculosis |
| spellingShingle | Qingyun Liu Tao Luo Xinran Dong Gang Sun Zhu Liu Mingyun Gan Jie Wu Xin Shen Qian Gao Genetic features of Mycobacterium tuberculosis modern Beijing sublineage Emerging Microbes and Infections ancient sublineage Beijing family microevolution modern sublineage Mycobacterium tuberculosis |
| title | Genetic features of Mycobacterium tuberculosis modern Beijing sublineage |
| title_full | Genetic features of Mycobacterium tuberculosis modern Beijing sublineage |
| title_fullStr | Genetic features of Mycobacterium tuberculosis modern Beijing sublineage |
| title_full_unstemmed | Genetic features of Mycobacterium tuberculosis modern Beijing sublineage |
| title_short | Genetic features of Mycobacterium tuberculosis modern Beijing sublineage |
| title_sort | genetic features of mycobacterium tuberculosis modern beijing sublineage |
| topic | ancient sublineage Beijing family microevolution modern sublineage Mycobacterium tuberculosis |
| url | https://www.tandfonline.com/doi/10.1038/emi.2016.14 |
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