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The establishment of databases on circulating genotypes of Mycobacterium tuberculosis complex and web tools for an effective response to better monitor, understand and control the tuberculosis epidemic worldwide.

Abstract : In this paper we will briefly review various Mycobacterium tuberculosis complex (MTBC) genotyping databases developed over last fifteen years at the Institut Pasteur de la Guadeloupe, which represent a great concerted initiative and effort to control the tuberculosis epidemic. Starting from the initial excel-based version in 1999 (SpolDB1; n=610 clinical isolates) to the fourth MySQL-based version in 2006 (SpolDB4; n=39,295 clinical isolates), these databases permitted to have a first phylogeographical snapshot of circulating MTBC genotypic lineages based on spacer oligonucleotide typing (spoligotyping) which allows to study the polymorphism of the Direct Repeat (DR) locus. The two most recent MySQL-based multimarker versions concern the 5th version SITVITWEB released in 2012 (n=62,582 clinical isolates) with both spoligotyping and 12-loci Mycobacterial Interspersed Repetitive Units - Variable Number of Tandem Repeats (MIRU-VNTRs); and the 6th version named SITVIT2 that will be released in 2014 (n= 111,635 clinical isolates) with spoligotyping and 12-, 15- or 24-loci MIRUVNTR data. In these recent versions, a web-based interface allows the user to search for strains through the database by criteria, such as the year, the isolation country, the country of origin, the investigator’s name. It further facilitates to perform combined searches in SITVIT2, making it possible to get the genotyping data on selected strains in conjunction with their geographical distribution, as well as available data on drug resistance, demographic and epidemiologic characteristics. Our research initiative is thus focused to further improve in depth phylogenetic characterization of MTBC lineages in conjunction with epidemiological analysis of circulating clones to generate evidence-based geographical mapping of predominant clinical isolates of tubercle bacilli causing the bulk of the disease both at country and regional level. Further superimposition of these maps with socio-political, economical, and demographical characteristics available through Geographic Information Systems (GIS) allows to have a precise view of prevailing disparities as seen at the level of United Nation’s sub-regional stratification. An in-depth comprehension of these disparities and drawbacks is important to take appropriate actions by decision-makers and public health authorities alike, in order to better monitor, understand and control the tuberculosis epidemic worldwide.
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David Couvin, Nalin Rastogi. The establishment of databases on circulating genotypes of Mycobacterium tuberculosis complex and web tools for an effective response to better monitor, understand and control the tuberculosis epidemic worldwide.. EuroReference - Les Cahiers de la Référence, ANSES - Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (France), 2014, 2014 (12), pp.36-48. ⟨pasteur-02954167⟩

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