Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination

Abstract

One-third of humans are infected with Mycobacterium tuberculosis, the causative agent of tuberculosis. Sequence analysis of two megabases in 26 structural genes or loci in strains recovered globally discovered a striking reduction of silent nucleotide substitutions compared with other human bacterial pathogens. The lack of neutral mutations in structural genes indicates that M. tuberculosis is evolutionarily young and has recently spread globally. Species diversity is largely caused by rapidly evolving insertion sequences, which means that mobile element movement is a fundamental process generating genomic variation in this pathogen. Three genetic groups of M. tuberculosis were identified based on two polymorphisms that occur at high frequency in the genes encoding catalase-peroxidase and the A subunit of gyrase. Group 1 organisms are evolutionarily old and allied with M. bovis, the cause of bovine tuberculosis. A subset of several distinct insertion sequence IS6110 subtypes of this genetic group have IS6110 integrated at the identical chromosomal insertion site, located between dnaA and dnaN in the region containing the origin of replication. Remarkably, study of Ϸ6,000 isolates from patients in Houston and the New York City area discovered that 47 of 48 relatively large case clusters were caused by genotypic group 1 and 2 but not group 3 organisms. The observation that the newly emergent group 3 organisms are associated with sporadic rather than clustered cases suggests that the pathogen is evolving toward a state of reduced transmissability or virulence.One-third of the world's population is infected with Mycobacterium tuberculosis, and 3 million human deaths annually are attributed to the organism (1, 2). Although there is a very large global pool of infected individuals and considerable chromosomal heterogeneity based on restriction fragment length polymorphism (RFLP) patterns generated by probing with mobile insertion elements (3, 4), studies of drug resistance and pathogenesis have raised the possibility that synonymous (silent) nucleotide substitutions in structural genes may be limited (5). To investigate this apparent discrepancy from the perspective of molecular population genetics, we sequenced two megabases in 26 structural genes or loci in strains of M. tuberculosis and the three closely related members of the M. tuberculosis complex (M. africanum, M. bovis, and M. microti) collected worldwide. MATERIALS AND METHODSBacterial Isolates. The study is based on a sample of 842 M. tuberculosis complex isolates recovered from diverse geographic localities. The organisms include M. tuberculosis (n ϭ 715), M. bovis (n ϭ 109), and M. africanum and M. microti (n ϭ 9 each). M. tuberculosis isolates were recovered from diseased patients in the United States (five states), Latin America (Mexico, Honduras, Ecuador, Peru, Venezuela, Brazil, and Chile), Europe (Portugal, Spain, The Netherlands, Belgium, Germany, Switzerland, Italy, former Yugoslavia, and Romania), Africa (Kenya, Rwanda, Guinea, Algeria, Som...

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

“…All the Beijing SIT1 and SIT255 isolates (n=92) contained katG Arg463Leu (CGG→CTG) single nucleotide polymorphism (SNP). This SNP is characteristic of isolates belonging to the principal genetic grouping 1 (PPG1) [17]. Two phenotypically isoniazid resistant isolates encoded a wild type katG gene and one Beijing isolate had only the Arg463Leu SNP in the katG.…”

Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India

“…The remaining 24.8% (25/101) of isolates belonged to the following clades: T (7/101), Beijing (6/101), LAM (3/101), H (3/101) and unknown (6/101). These observations emphasise the complex diversity of the phylogenetically coherent M. tuberculosis in our study sample from North Delhi, an observation that was further corroborated by the MST illustrated in A in Figure. Indeed, as many as 82/101 (81.2%) strains from our study belonged to Principal Genetic Group (PGG) 1, according to the katG-gyrA polymorphism-based classification of Sreevatsan et al (1997), and these strains represented all of the known lineages associated with PGG1 isolates, i.e., EAI 26.7%, CAS 43.6%, Beijing 5.94% and Manu 4.95%. However, evolutionarily modern PGG2/3 strains were limited to LAM, H and T; these strains accounted for only 12.9% (13) of the 101 strains studied.…”

“…The colours of the circles in the tree indicate the number of clinical isolates represented by each circle, i.e., unique isolates (sky blue) vs. clustered isolates (deep blue: 2-5 strains; red: 6 strains or more). Principal genetic groups in the present study were described based on spoligodefined lineages (Brudey et al 2006), which have previously been correlated with the katG-gyrA-based classification of Sreevatsan et al (1997).…”

Evaluation of Two Molecular Assays for Rapid Detection of Mycobacterium tuberculosis Resistance to Fluoroquinolones in High-Tuberculosis and -Multidrug-Resistance Settings

“…The vast majority (49 isolates, 96.0%) of tested MDRTB strains were identified as belonging to the Beijing genotype family using spoligotyping; two other strains (4.0%) belonged to the T1 genotype family. All Beijing family strains had the natural mutation 95 (AGC-ACC) in the gyrA gene associated with the Beijing genotype and the principal genetic group 1 (12,40). Genotyping using 28-locus VNTR, followed by cluster analysis, allowed identification of four clusters with cluster sizes varying from 2 to 25 strains and 10 unique profiles.…”