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 approximately 6,000 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.

Figures

Figure 1

Broad evolutionary scenario for M. tuberculosis complex organisms. The precursor of M. tuberculosis complex organisms was characterized by KatG codon 463 (Leu) and GyrA codon 95 (Thr). Strain Ravenal is a typical M. bovis isolate; New York City IS6110 type strain W and Houston IS6110 types 002, 003, 007, 015, and 033 are group 1 organisms; Erdman, Oshkosh, New York City strain C, and Houston IS6110 types 004, 006, 016, 020, and 030 are group 2; and H37Ra, H37Rv, and Houston IS6110 type 001 are group 3.

Figure 2

Distribution of IS6110 copy number with respect to three genotypic groups of M. tuberculosis. The data are based on analysis of 427 isolates recovered from patients in Houston, TX. To avoid bias caused by redundant sampling of recent derivatives of epidemiologically linked isolates, only one isolate per distinct IS6110 subtype was used in the analysis. This resulted in a data set composed of 213 distinct IS6110 subtypes, of which 21% were group 1, 62% group 2, and 18% group 3.