SITVITWEB - A publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology
SITVITWEB - A publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology
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DOI：
10.1016/j.meegid.2012.02.004
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发表时间：
2012-06-01
影响因子：
3.2
通讯作者：
Rastogi, Nalin
中科院分区：
文献类型：
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作者：
Demay, Christophe;Liens, Benjamin;Rastogi, Nalin
在研究结核分枝杆菌复合群（MTC）基因型多态性的各种基因分型方法中，spoligotyping和分枝杆菌散布重复单位-可变数目的DNA串联重复序列（MIRU-VNTRs）最近获得了国际认可，作为稳健、快速和可重复的分型方法，以便携式格式生成数据。Spoligotyping构成了2006年发布的公开数据库SpolDB4的支柱;然而，这种方法在单独使用时具有较低的区分能力，理想情况下应与第二种分型方法（如MIRU-VNTR）结合使用，用于高分辨率流行病学研究。我们在此描述了一个名为SITVITWEB的公开可用的国际数据库，该数据库包含了这样的多标记数据，允许基于对应于153个患者来源国家（105个分离国家）的62，582个临床分离株对全世界MTC遗传多样性进行全球视野。我们共报告了7105种spoligotype模式（对应于58，180株临床分离株）-分为2740种共享型或spoligotype国际型（SIT），其中包含53，816株临床分离株和4364种孤儿模式。有趣的是，全世界只有7%的MTC分离株是孤儿，而超过一半的SITed分离株（n = 27，059）仅限于24种最流行的SIT。该数据库还包含来自87个患者来源国家（35个分离国家）的总计2379个MIRU模式（来自8161个临床分离株）;这些被分组为847个共享型或MIRU国际型（MIT），包含6626个分离株和1533个孤儿模式。最后，可获得来自59个患者来源国家（22个分离国家）的4626株分离株的5位点精确串联重复序列（ETR）数据;共观察到458种不同的VNTR模式-分为245种共享型或VNTR国际型（VIT）（包含4413株分离株）和213种孤儿模式。SITVITWEB的数据挖掘进一步允许更新定义MTC基因型谱系的规则，以及对MTC人口结构和国家，次区域和大陆层面的全球分布有新的见解。在进化水平上，汇编的数据可能是有用的，以区分偶尔收敛进化的基因型与特定进化的亚系基本上受适应宿主。该数据库可在www.example.com上公开获取。(C)2012爱思唯尔有限公司版权所有。
Among various genotyping methods to study Mycobacterium tuberculosis complex (MTC) genotypic polymorphism, spoligotyping and mycobacterial interspersed repetitive units-variable number of DNA tandem repeats (MIRU-VNTRs) have recently gained international approval as robust, fast, and reproducible typing methods generating data in a portable format. Spoligotyping constituted the backbone of a publicly available database SpolDB4 released in 2006; nonetheless this method possesses a low discriminatory power when used alone and should be ideally used in conjunction with a second typing method such as MIRU-VNTRs for high-resolution epidemiological studies. We hereby describe a publicly available international database named SITVITWEB which incorporates such multimarker data allowing to have a global vision of MTC genetic diversity worldwide based on 62,582 clinical isolates corresponding to 153 countries of patient origin (105 countries of isolation). We report a total of 7105 spoligotype patterns (corresponding to 58,180 clinical isolates) - grouped into 2740 shared-types or spoligotype international types (SIT) containing 53,816 clinical isolates and 4364 orphan patterns. Interestingly, only 7% of the MTC isolates worldwide were orphans whereas more than half of SITed isolates (n = 27,059) were restricted to only 24 most prevalent SITs. The database also contains a total of 2379 MIRU patterns (from 8161 clinical isolates) from 87 countries of patient origin (35 countries of isolation); these were grouped in 847 shared-types or MIRU international types (MIT) containing 6626 isolates and 1533 orphan patterns. Lastly, data on 5-locus exact tandem repeats (ETRs) were available on 4626 isolates from 59 countries of patient origin (22 countries of isolation); a total of 458 different VNTR patterns were observed - split into 245 shared-types or VNTR International Types (VIT) containing 4413 isolates) and 213 orphan patterns. Datamining of SITVITWEB further allowed to update rules defining MTC genotypic lineages as well to have a new insight into MTC population structure and worldwide distribution at country, sub-regional and continental levels. At evolutionary level, the data compiled may be useful to distinguish the occasional convergent evolution of genotypes versus specific evolution of sublineages essentially influenced by adaptation to the host. This database is publicly available at: http://www.pasteur-guadeloupe.fr:8081/SITVIT_ONLINE. (C) 2012 Elsevier B.V. All rights reserved.