Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology
Authors: Brudey Karine , Driscoll Jeffrey R , Rigouts Leen , Prodinger Wolfgang M , Gori Andrea , Al-Hajoj Sahal A , Allix Caroline , Aristimuño Liselotte , Arora Jyoti , Baumanis Viesturs , Binder Lothar , Cafrune Patricia , Cataldi Angel , Cheong Soonfatt , Diel Roland , Ellermeier Christopher , Evans Jason T , Fauville-Dufaux Maryse , Ferdinand Séverine , de Viedma Dario Garcia , Garzelli Carlo , Gazzola Lidia , Gomes Harrison M , Guttierez 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 , Narvskaïa Olga , Ngeow Yun Fong , Naumann Ludmilla , Niemann Stefan , Parwati Ida , Rahim Zeaur , Rasolofo-Razanamparany Voahangy , Rasolonavalona Tiana , Rossetti M Lucia , Rüsch-Gerdes Sabine , Sajduda Anna , Samper Sofia , Shemyakin Igor G , Singh Urvashi B , Somoskovi Akos , Skuce Robin A , van Soolingen Dick , Streicher Elisabeth M , Suffys Philip N , Tortoli Enrico , Tracevska Tatjana , Vincent Véronique , Victor Tommie C , Warren Robin M , Yap Sook Fan , Zaman Khadiza , Portaels Françoise , Rastogi Nalin , Sola Christophe 
Published: March 2006

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.