Brudey, Karine and Driscoll, Jeffrey R. and Rigouts, Leen and Prodinger, Wolfgang M. and Gori, Andrea and Al-Hajoj, Sahal A. and Allix, Caroline and Aristimuno, Liselotte and Arora, Jyoti and Baumanis, Viesturs and Binder, Lothar and Cafrune, Patricia and Cataldi, Angel and Cheong, Soonfatt and Diel, Roland and Ellermeier, Christopher and Evans, Jason T. and Fauville-Dufaux, Maryse and Ferdinand, Severine and Garcia de Viedma, Dario and Garzelli, Carlo and Gazzola, Lidia and Gomes, Harrison M. and Guttierez, M. Cristina and Hawkey, Peter M. and van Helden, Paul D. and Kadival, Gurujaj V. and Kreiswirth, Barry N. and Kremer, Kristin and Kubin, Milan and Kulkarni, Savita P. and Liens, Benjamin and Lillebaek, Troels and Ly, Ho Minh and Martin, Carlos and Martin, Christian and Mokrousov, Igor and Narvskaia, Olga and Ngeow, Yun Fong and Naumann, Ludmilla and Niemann, Stefan and Parwati, Ida and Rahim, Zeaur and Rasolofo-Razanamparany, Voahangy and Rasolonavalona, Tiana and Rossetti, M. Lucia and Ruesch-Gerdes, Sabine and Sajduda, Anna and Samper, Sofia and Shemyakin, Igor G. and Singh, Urvashi B. and Somoskovi, Akos and Skuce, Robin A. and van Soolingen, Dick and Streicher, Elisabeth M. and Suffys, Philip N. and Tortoli, Enrico and Tracevska, Tatjana and Vincent, Veronique and Victor, Tommie C. and Warren, Robin M. and Yap, Sook Fan and Zaman, Khadiza and Portaels, Francoise and Rastogi, Nalin and Sola, Christophe (2006) Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpoIDB4) for classification, population genetics and epidemiology. BMC MICROBIOLOGY, 6: 23. ISSN 1471-2180,
Full text not available from this repository.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, SpoIDB4, 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 SpoIDB4 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 Naive-Bayes mixture-model analysis has validated main of the previous supervised SpoIDB3 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. SpoIDB4 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.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | DIRECT REPEAT LOCUS; TANDEM DNA REPEATS; VARIABLE-NUMBER; NUCLEOTIDE POLYMORPHISMS; SPACER OLIGONUCLEOTIDES; MOLECULAR EPIDEMIOLOGY; PULMONARY TUBERCULOSIS; STRAIN DIFFERENTIATION; GLOBAL DISTRIBUTION; COPY NUMBERS; |
| Subjects: | 600 Technology > 610 Medical sciences Medicine |
| Divisions: | Medicine > Lehrstuhl für Innere Medizin II |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 17 Feb 2021 12:24 |
| Last Modified: | 17 Feb 2021 12:24 |
| URI: | https://pred.uni-regensburg.de/id/eprint/34778 |
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