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

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.

Extremely high prevalence of multidrug resistant tuberculosis in Murmansk, Russia: a population-based study

“…Thus, introduction of molecular methods suitable for rapid detection of MDR-TB could improve disease management and decrease the transmission rate in this area. [8].…”

“…The Beijing strains have also been associated with TB treatment failures and relapse cases [7]. It has been further proposed that Beijing strains have some selective advantage over others [8].…”

Molecular epidemiology of human and animal tuberculosis in Ibadan, Southwestern Nigeria

“…This is the second time M. tuberculosis has been reported in animal isolates from Nigeria, strongly supporting the possibility of human to livestock transmission (Cadmus et al, 2006). We isolated three such strains in this study, including an isolate of the EAI clade (Brudey et al, 2006) recovered from a goat (g49). EAI strains represent the most ancestral clade of the M. tuberculosis complex (except the M. canettii ancestor) (Fabre et al, 2004).…”

Spoligotyping of clinical Mycobacterium tuberculosis isolates from the state of Minas Gerais, Brazil

“…Further, spoligotyping has gained increased international acceptance as a rapid, first line and discriminatory test (Sola et al 2001, Filliol et al 2002, Brudey et al 2006. The spoligotyping method was also the basis for the creation of the largest genotype database for M. tuberculosis, containing a global distribution and phylogenetic analysis for worldwide spoligotypes (Brudey et al 2006). This database provides information that is useful for comparing the patterns found within different world regions, enhancing our understanding of disease distribution dynamics.…”

“…Spoligotyping is based on a polymorphism in the chromosomal direct repeat locus (Kamerbeek et al 1997) and has been applied to the characterization of the Mtb complex. Further, spoligotyping has gained increased international acceptance as a rapid, first line and discriminatory test (Sola et al 2001, Filliol et al 2002, Brudey et al 2006. The spoligotyping method was also the basis for the creation of the largest genotype database for M. tuberculosis, containing a global distribution and phylogenetic analysis for worldwide spoligotypes (Brudey et al 2006).…”