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

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dc.contributor.author Brudey, Karine
dc.contributor.author Driscoll, Jeffrey R.
dc.contributor.author Rigouts, Leen
dc.contributor.author Prodinger, Wolfgang M.
dc.contributor.author Gori, Andrea
dc.contributor.author Al-Hajoj, Sahal A. M.
dc.contributor.author Allix, Caroline
dc.contributor.author Aristimuno, Liselotte
dc.contributor.author Arora, Jyoti
dc.contributor.author Baumanis, Viesturs
dc.contributor.author Binder, Lothar
dc.contributor.author Cafrune, Patricia
dc.contributor.author Cataldi, Angel
dc.contributor.author Cheong, Soonfatt
dc.contributor.author Diel, Roland
dc.contributor.author Ellermeier, Christopher
dc.contributor.author Evans, Jason T.
dc.contributor.author Fauville-Dufaux, Maryse
dc.contributor.author Ferdinand, Severine
dc.contributor.author Garcia de Viedma, Dario
dc.contributor.author Garzelli, Carlo
dc.contributor.author Gazzola, Lidia
dc.contributor.author Gomes, Harrison M.
dc.contributor.author Gutierrez, M. Cristina
dc.contributor.author Hawkey, Peter M.
dc.contributor.author van Helden, Paul D.
dc.contributor.author Kadival, Gurujaj V.
dc.contributor.author Kreiswirth, Barry N.
dc.contributor.author Kremer, Kristin
dc.contributor.author Kubin, Milan
dc.contributor.author Kulkarni, Savita P.
dc.contributor.author Liens, Benjamin
dc.contributor.author Lillebaek, Troels
dc.contributor.author Ly, Ho Minh
dc.contributor.author Martin, Carlos
dc.contributor.author Martin, Christian
dc.contributor.author Mokrousov, Igor
dc.contributor.author Narvskaia, Olga
dc.contributor.author Ngeow, Yun Fong
dc.contributor.author Naumann, Ludmilla
dc.contributor.author Niemann, Stefan
dc.contributor.author Parwati, Ida
dc.contributor.author Rahim, Mohammad Z.
dc.contributor.author Rasolofo-Razanamparany, Voahangy
dc.contributor.author Rasolonavalona, Tiana
dc.contributor.author Rossetti, M. Lucia
dc.contributor.author Rusch-Gerdes, Sabine
dc.contributor.author Sajduda, Anna
dc.contributor.author Samper, Sofia
dc.contributor.author Shemyakin, Igor
dc.contributor.author Singh, Urvashi B.
dc.contributor.author Somoskovi, Akos
dc.contributor.author Skuce, Robin
dc.contributor.author van Soolingen, Dick
dc.contributor.author Streicher, Elisabeth M.
dc.contributor.author Suffys, Philip N.
dc.contributor.author Tortoli, Enrico
dc.contributor.author Tracevska, Tatjana
dc.contributor.author Vincent, Veronique
dc.contributor.author Victor, Tommie C.
dc.contributor.author Warren, Robin
dc.contributor.author Yap, Sook Fan
dc.contributor.author Zaman, Kadiza
dc.contributor.author Portaels, Francoise
dc.contributor.author Rastogi, Nalin
dc.contributor.author Sola, Christophe
dc.date.accessioned 2010-12-10T13:54:39Z
dc.date.available 2010-12-10T13:54:39Z
dc.date.issued 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.identifier.other http://dx.doi.org/10.1186/1471-2180-6-23
dc.identifier.uri http://hdl.handle.net/10019.1/5050
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
dc.date.updated 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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