Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology.
Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology.
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结核分枝杆菌复杂的遗传多样性：挖掘第四个国际螺旋型数据库（SpoldB4），用于分类，种群遗传学和流行病学。
DOI：
10.1186/1471-2180-6-23
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发表时间：
2006-03-06
期刊：
影响因子：
4.2
通讯作者：
Sola C
中科院分区：
文献类型：
--
作者：
Brudey K;Driscoll JR;Rigouts L;Prodinger WM;Gori A;Al-Hajoj SA;Allix C;Aristimuño L;Arora J;Baumanis V;Binder L;Cafrune P;Cataldi A;Cheong S;Diel R;Ellermeier C;Evans JT;Fauville-Dufaux M;Ferdinand S;Garcia de Viedma D;Garzelli C;Gazzola L;Gomes HM;Guttierez MC;Hawkey PM;van Helden PD;Kadival GV;Kreiswirth BN;Kremer K;Kubin M;Kulkarni SP;Liens B;Lillebaek T;Ho ML;Martin C;Martin C;Mokrousov I;Narvskaïa O;Ngeow YF;Naumann L;Niemann S;Parwati I;Rahim Z;Rasolofo-Razanamparany V;Rasolonavalona T;Rossetti ML;Rüsch-Gerdes S;Sajduda A;Samper S;Shemyakin IG;Singh UB;Somoskovi A;Skuce RA;van Soolingen D;Streicher EM;Suffys PN;Tortoli E;Tracevska T;Vincent V;Victor TC;Warren RM;Yap SF;Zaman K;Portaels F;Rastogi N;Sola C
结核分枝杆菌复合群（MTC）的直接重复基因座是CRISPR（规则间隔短回文重复序列）序列家族的成员。Spoligotyping是一种广泛使用的基于PCR的反向杂交印迹技术，用于检测该位点的遗传多样性，并可用于临床实验室，分子流行病学，进化和群体遗传学。它是简单的，强大的，便宜的，并产生高度多样化的便携式数值结果，作为（1）独特的事件多态性（UEP）（2）插入序列介导的遗传重组的组合的结果。遗传趋同虽然罕见，但以前也被证明。以前的三个国际spoligotype数据库部分揭示了全球和地方的MTC杆菌种群的地理结构，但是，有必要发布一个新的，更有代表性和扩展，国际spoligotyping数据库。第四个国际spoligotyping数据库SpolDB 4描述了来自122个国家的39，295个菌株的1939个共享型（ST），使用基于专家和生物信息学的混合方法将其初步分为62个分支/谱系。SpolDB 4更新增加了26个新的潜在地理特异性MTC基因型家族。它提供了一个更清晰的画面，目前MTC基因组多样性，以及对遗传属性（spoligotypes）和种内分类和物种的进化历史之间的关系。事实上，一个独立的朴素贝叶斯混合模型分析已经验证了以前的监督SpolDB 3分类结果的主要部分，证实了监督和无监督模型作为理解MTC种群结构的方法的有用性。最新的结果的spoligotypes的流行病学状况，以及六个主要谱系的遗传患病率地图也显示。我们的研究结果表明，在MTC人群中存在优良的地理遗传渐变群，可以反映过去和现在的智人的人口统计学和分枝杆菌的共同进化历史，其结构可以进一步重建和建模，从而提供了一个大规模的全球结核病流行病学网络的概念框架。我们的研究结果拓宽了对MTC复杂的全球生物地理学的认识。SpolDB 4应该是一个非常有用的工具，可以更好地定义给定MTC临床分离株的身份，并更好地分析其当前传播和以前的进化历史之间的联系。扩展的MTC多态性遗传数据库的建立和挖掘正在进行中。
The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network. Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.
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影响因子：
9.4
作者：
Fabre, M;Koeck, JL;Pourcel, C
通讯作者：
Pourcel, C
DOI：
10.1099/00221287-144-5-1189
发表时间：
1998-05-01
期刊：
MICROBIOLOGY-UK
影响因子：
--
作者：
Frothingham, R;Meeker-O'Connell, WA
通讯作者：
Meeker-O'Connell, WA
影响因子：
11.8
作者：
Filliol I;Driscoll JR;Van Soolingen D;Kreiswirth BN;Kremer K;Valétudie G;Anh DD;Barlow R;Banerjee D;Bifani PJ;Brudey K;Cataldi A;Cooksey RC;Cousins DV;Dale JW;Dellagostin OA;Drobniewski F;Engelmann G;Ferdinand S;Gascoyne-Binzi D;Gordon M;Gutierrez MC;Haas WH;Heersma H;Källenius G;Kassa-Kelembho E;Koivula T;Ly HM;Makristathis A;Mammina C;Martin G;Moström P;Mokrousov I;Narbonne V;Narvskaya O;Nastasi A;Niobe-Eyangoh SN;Pape JW;Rasolofo-Razanamparany V;Ridell M;Rossetti ML;Stauffer F;Suffys PN;Takiff H;Texier-Maugein J;Vincent V;De Waard JH;Sola C;Rastogi N
通讯作者：
Rastogi N
影响因子：
3.2
作者：
Dale, JW;Al-Ghusein, H;Yesilkaya, H
通讯作者：
Yesilkaya, H
影响因子：
11.8
作者：
Baker L;Brown T;Maiden MC;Drobniewski F
通讯作者：
Drobniewski F