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

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dc.contributor.authorBrudey, Karine
dc.contributor.authorDriscoll, Jeffrey R.
dc.contributor.authorRigouts, Leen
dc.contributor.authorProdinger, Wolfgang M.
dc.contributor.authorGori, Andrea
dc.contributor.authorAl-Hajoj, Sahal A. M.
dc.contributor.authorAllix, Caroline
dc.contributor.authorAristimuno, Liselotte
dc.contributor.authorArora, Jyoti
dc.contributor.authorBaumanis, Viesturs
dc.contributor.authorBinder, Lothar
dc.contributor.authorCafrune, Patricia
dc.contributor.authorCataldi, Angel
dc.contributor.authorCheong, Soonfatt
dc.contributor.authorDiel, Roland
dc.contributor.authorEllermeier, Christopher
dc.contributor.authorEvans, Jason T.
dc.contributor.authorFauville-Dufaux, Maryse
dc.contributor.authorFerdinand, Severine
dc.contributor.authorGarcia de Viedma, Dario
dc.contributor.authorGarzelli, Carlo
dc.contributor.authorGazzola, Lidia
dc.contributor.authorGomes, Harrison M.
dc.contributor.authorGutierrez, M. Cristina
dc.contributor.authorHawkey, Peter M.
dc.contributor.authorVan Helden, Paul D.
dc.contributor.authorKadival, Gurujaj V.
dc.contributor.authorKreiswirth, Barry N.
dc.contributor.authorKremer, Kristin
dc.contributor.authorKubin, Milan
dc.contributor.authorKulkarni, Savita P.
dc.contributor.authorLiens, Benjamin
dc.contributor.authorLillebaek, Troels
dc.contributor.authorLy, Ho Minh
dc.contributor.authorMartin, Carlos
dc.contributor.authorMartin, Christian
dc.contributor.authorMokrousov, Igor
dc.contributor.authorNarvskaia, Olga
dc.contributor.authorNgeow, Yun Fong
dc.contributor.authorNaumann, Ludmilla
dc.contributor.authorNiemann, Stefan
dc.contributor.authorParwati, Ida
dc.contributor.authorRahim, Mohammad Z.
dc.contributor.authorRasolofo-Razanamparany, Voahangy
dc.contributor.authorRasolonavalona, Tiana
dc.contributor.authorRossetti, M. Lucia
dc.contributor.authorRusch-Gerdes, Sabine
dc.contributor.authorSajduda, Anna
dc.contributor.authorSamper, Sofia
dc.contributor.authorShemyakin, Igor
dc.contributor.authorSingh, Urvashi B.
dc.contributor.authorSomoskovi, Akos
dc.contributor.authorSkuce, Robin
dc.contributor.authorVan Soolingen, Dick
dc.contributor.authorStreicher, Elizabeth M.en_ZA
dc.contributor.authorSuffys, Philip N.
dc.contributor.authorTortoli, Enrico
dc.contributor.authorTracevska, Tatjana
dc.contributor.authorVincent, Veronique
dc.contributor.authorVictor, Tommie C.
dc.contributor.authorWarren, Robin
dc.contributor.authorYap, Sook Fan
dc.contributor.authorZaman, Kadiza
dc.contributor.authorPortaels, Francoise
dc.contributor.authorRastogi, Nalin
dc.contributor.authorSola, Christophe
dc.date.accessioned2010-12-10T13:54:39Z
dc.date.available2010-12-10T13:54:39Z
dc.date.issued2006-03
dc.date.updated2010-11-30T19:04:10Z
dc.descriptionIncludes bibliography
dc.description.abstractBackground: 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.description.versionPeer reviewed
dc.format.extent17 p. : ill.
dc.identifier.citationBrudey, 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.issn1471-2180
dc.identifier.otherhttp://dx.doi.org/10.1186/1471-2180-6-23
dc.identifier.urihttp://hdl.handle.net/10019.1/5050
dc.language.isoen_ZAen_ZA
dc.language.rfc3066en
dc.rights.holderBrudey et al.; licensee BioMed Central Ltd.en_ZA
dc.subjectMycobacterium tuberculosis complex (MTC)en_ZA
dc.subjectCRISPR (Clustered regularly interspaced short palindromic repeats)en_ZA
dc.subjectSpoligotypingen_ZA
dc.subject.lcshMycobacterium tuberculosis -- Genetic aspectsen_ZA
dc.titleMycobacterium tuberculosis complex genetic diversity : mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiologyen_ZA
dc.typeArticleen_ZA
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