MLVA based classification of Mycobacterium tuberculosis complex lineages for a robust phylogeographic snapshot of its worldwide molecular diversity.
MLVA based classification of Mycobacterium tuberculosis complex lineages for a robust phylogeographic snapshot of its worldwide molecular diversity.
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DOI：
10.1371/journal.pone.0041991
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Rastogi N
中科院分区：
文献类型：
--
作者：
Hill V;Zozio T;Sadikalay S;Viegas S;Streit E;Kallenius G;Rastogi N
多位点可变数目串联重复序列分析（MLVA）可用于确定包括结核分枝杆菌复合群（MTC）在内的各种微生物的传播途径和感染源。最近发布的SITVITWEB数据库包含12个位点的分枝杆菌分散重复单位-可变串联DNA重复数（MIRU-VNTR）概况和数千种MTC菌株的spoligotype模式;它使用MIRU国际类型（MIT）和Spoligotype国际类型（SIT）来指定全球的聚类模式。考虑到现有的怀疑的能力spoligotyping单独揭示MTC菌株之间的确切的系统发育关系，我们开发了一个MLVA为MTC基因型谱系的分类。我们研究了6种不同的MTC分离株亚群，包括全球7793株。最小生成树（MST）被构建来识别主要的谱系，并以位于中心节点的最常见的代表作为原型来定义不同的系统发育组。共鉴定出7个主要谱系及其各自的原型：印度洋-大洋洲/MIT 57、东亚和非洲印第安/MIT 17、欧洲美洲/MIT 116、西非-I/MIT 934、西非-II/MIT 664、M.牛/MIT 49、卡氏支原体/MIT 60。进一步的MST细分确定了另外34个亚系MIT原型。使用基于baidu方法的分类算法推断了37个新定义的MIRU-VNTR谱系之间的系统发育关系。这些信息被用来构建一个更新的系统发育和地理快照的全球MTC多样性研究在区域，次区域和国家一级，根据联合国的规格。我们还寻找了已知在特定情况下修改spoligotyping结果的IS 6110插入事件，并表明导致目前观察到的菌株系统发育分类偏倚的相当一部分收敛可以追溯到IS 6110的存在。这些结果揭示了新的光的病原体的进化历史与历史的人口和人类迁移。
Multiple-locus variable-number tandem repeat analysis (MLVA) is useful to establish transmission routes and sources of infections for various microorganisms including Mycobacterium tuberculosis complex (MTC). The recently released SITVITWEB database contains 12-loci Mycobacterial Interspersed Repetitive Units – Variable Number of Tandem DNA Repeats (MIRU-VNTR) profiles and spoligotype patterns for thousands of MTC strains; it uses MIRU International Types (MIT) and Spoligotype International Types (SIT) to designate clustered patterns worldwide. Considering existing doubts on the ability of spoligotyping alone to reveal exact phylogenetic relationships between MTC strains, we developed a MLVA based classification for MTC genotypic lineages. We studied 6 different subsets of MTC isolates encompassing 7793 strains worldwide. Minimum spanning trees (MST) were constructed to identify major lineages, and the most common representative located as a central node was taken as the prototype defining different phylogenetic groups. A total of 7 major lineages with their respective prototypes were identified: Indo-Oceanic/MIT57, East Asian and African Indian/MIT17, Euro American/MIT116, West African-I/MIT934, West African-II/MIT664, M. bovis/MIT49, M.canettii/MIT60. Further MST subdivision identified an additional 34 sublineage MIT prototypes. The phylogenetic relationships among the 37 newly defined MIRU-VNTR lineages were inferred using a classification algorithm based on a bayesian approach. This information was used to construct an updated phylogenetic and phylogeographic snapshot of worldwide MTC diversity studied both at the regional, sub-regional, and country level according to the United Nations specifications. We also looked for IS6110 insertional events that are known to modify the results of the spoligotyping in specific circumstances, and showed that a fair portion of convergence leading to the currently observed bias in phylogenetic classification of strains may be traced back to the presence of IS6110. These results shed new light on the evolutionary history of the pathogen in relation to the history of peopling and human migration.
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影响因子：
9.4
作者：
Filliol, I;Sola, C;Rastogi, N
通讯作者：
Rastogi, N
影响因子：
9.4
作者：
Legrand, E;Filliol, I;Rastogi, N
通讯作者：
Rastogi, N
影响因子：
3.2
作者：
Asgharzadeh, Mohammad;Kafil, Hossein Samadi;Hanifi, Gholam Reza
通讯作者：
Hanifi, Gholam Reza
影响因子：
3.2
作者：
Filliol, I;Motiwala, AS;Alland, D
通讯作者：
Alland, D
影响因子：
9.4
作者：
Kamerbeek, J;Schouls, L;vanEmbden, J
通讯作者：
vanEmbden, J