Mycobacterium tuberculosis complex genetic diversity : mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology

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Show simple item record Brudey, Karine Driscoll, Jeffrey R. Rigouts, Leen Prodinger, Wolfgang M. Gori, Andrea Al-Hajoj, Sahal A. M. Allix, Caroline Aristimuno, Liselotte Arora, Jyoti Baumanis, Viesturs Binder, Lothar Cafrune, Patricia Cataldi, Angel Cheong, Soonfatt Diel, Roland Ellermeier, Christopher Evans, Jason T. Fauville-Dufaux, Maryse Ferdinand, Severine Garcia de Viedma, Dario Garzelli, Carlo Gazzola, Lidia Gomes, Harrison M. Gutierrez, M. Cristina Hawkey, Peter M. van Helden, Paul D. Kadival, Gurujaj V. Kreiswirth, Barry N. Kremer, Kristin Kubin, Milan Kulkarni, Savita P. Liens, Benjamin Lillebaek, Troels Ly, Ho Minh Martin, Carlos Martin, Christian Mokrousov, Igor Narvskaia, Olga Ngeow, Yun Fong Naumann, Ludmilla Niemann, Stefan Parwati, Ida Rahim, Mohammad Z. Rasolofo-Razanamparany, Voahangy Rasolonavalona, Tiana Rossetti, M. Lucia Rusch-Gerdes, Sabine Sajduda, Anna Samper, Sofia Shemyakin, Igor Singh, Urvashi B. Somoskovi, Akos Skuce, Robin van Soolingen, Dick Streicher, Elisabeth M. Suffys, Philip N. Tortoli, Enrico Tracevska, Tatjana Vincent, Veronique Victor, Tommie C. Warren, Robin Yap, Sook Fan Zaman, Kadiza Portaels, Francoise Rastogi, Nalin Sola, Christophe 2010-12-10T13:54:39Z 2010-12-10T13:54:39Z 2006-03
dc.identifier.citation Brudey, K 2006, 'Mycobacterium tuberculosiscomplex genetic diversity : mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology', BMC Microbiology, 6(1):23. en_ZA
dc.identifier.issn 1471-2180
dc.description Includes bibliography
dc.description.abstract Background: 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. Results: 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. Conclusion: 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. en_ZA
dc.format.extent 17 p. : ill.
dc.language.iso en_ZA en_ZA
dc.subject Mycobacterium tuberculosis complex (MTC) en_ZA
dc.subject CRISPR (Clustered regularly interspaced short palindromic repeats) en_ZA
dc.subject Spoligotyping en_ZA
dc.subject.lcsh Mycobacterium tuberculosis -- Genetic aspects en_ZA
dc.title Mycobacterium tuberculosis complex genetic diversity : mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology en_ZA
dc.type Article en_ZA 2010-11-30T19:04:10Z
dc.description.version Peer reviewed
dc.language.rfc3066 en
dc.rights.holder Brudey et al.; licensee BioMed Central Ltd. en_ZA
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