University of Birmingham Mycobacterium tuberculosis complex genetic diversity

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. Background Each year, 9 million new cases of tuberculosis (TB) are recorded, of which 2 million result in fatality. Diagnostics, chemotherapy and vaccination are available, however, the disease is far from being eradicated [1]. Many genetic loci within the Mycobacterium tuberculosis complex (MTC) genomes are polymorphic and may be used for molecular evolutionary studies [2]. Among these, the Direct Repeat locus (DR), which consists of alternating identical DRs and variable spacers can be assessed using the "Spoligotyping" fingerprinting method thousands of different patterns [3]. DR loci are members of a universal family of sequences, designated as CRISPR [4], whose physiological role is poorly known [5,6]. Spoligotyping was previously shown to be useful for both clinical management and molecular epidemiology of MTC [7]. When used in association with variable-number of DNA tandem-repeat (VNTR) [8] or Mycobacterial-interspersed-repetitive-units (MIRU) [9], spoligotyping is a fast, robust, and cost effective genotyping technique, alternative to traditional IS6110-RFLP fingerprinting. These methods are also designated as MLVA (Multiple-locus variable number tandem repeats analysis) [10]. Since 1999, we have built and released genetic diversity databases of the MTC DR locus as an attempt to analyze MTC population structure, and to assess the complexity of global TB transmission and of the Published: 06 March 2006 BMC Microbiology2006, 6:23 doi:10.1186/1471-2180-6-23 Received: 08 November 2005 Accepted: 06 March 2006 This article is available from: http://www.biomedcentral.com/1471-2180/6/23 © 2006Brudey et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.