A new evolutionary scenario for the Mycobacterium tuberculosis complex

Abstract

The distribution of 20 variable regions resulting from insertiondeletion events in the genomes of the tubercle bacilli has been evaluated in a total of 100 strains of Mycobacterium tuberculosis, Mycobacterium africanum, Mycobacterium canettii, Mycobacterium microti, and Mycobacterium bovis. This approach showed that the majority of these polymorphisms did not occur independently in the different strains of the M. tuberculosis complex but, rather, resulted from ancient, irreversible genetic events in common progenitor strains. Based on the presence or absence of an M. tuberculosis specific deletion (TbD1), M. tuberculosis strains can be divided into ancestral and ''modern'' strains, the latter comprising representatives of major epidemics like the Beijing, Haarlem, and African M. tuberculosis clusters. Furthermore, successive loss of DNA, reflected by region of difference 9 and other subsequent deletions, was identified for an evolutionary lineage represented by M. africanum, M. microti, and M. bovis that diverged from the progenitor of the present M. tuberculosis strains before TbD1 occurred. These findings contradict the often-presented hypothesis that M. tuberculosis, the etiological agent of human tuberculosis evolved from M. bovis, the agent of bovine disease. M. canettii and ancestral M. tuberculosis strains lack none of these deleted regions, and, therefore, seem to be direct descendants of tubercle bacilli that existed before the M. africanum3 M. bovis lineage separated from the M. tuberculosis lineage. This observation suggests that the common ancestor of the tubercle bacilli resembled M. tuberculosis or M. canettii and could well have been a human pathogen already.evolution ͉ diagnostic ͉ identification T he mycobacteria grouped in the Mycobacterium tuberculosis complex are characterized by 99.9% similarity at the nucleotide level and identical 16S rRNA sequences (1, 2) but differ widely in terms of their host tropisms, phenotypes, and pathogenicity. Assuming that they all are derived from a common ancestor, it is intriguing that some are exclusively human (M. tuberculosis, Mycobacterium africanum, Mycobacterium canettii) or rodent pathogens (Mycobacterium microti), whereas others have a wide host spectrum (Mycobacterium bovis). What was the genetic organization of the last common ancestor of the tubercle bacilli, and in which host did it live? Which genetic events may have contributed to the fact that the host spectrum is so different and often specific? Where and when did M. tuberculosis evolve? Answers to these questions are important for a better understanding of the pathogenicity and the global epidemiology of tuberculosis and may help to anticipate future trends in the spread of the disease.Because of the unusually high degree of conservation in their housekeeping genes, it has been suggested that the members of the M. tuberculosis complex underwent an evolutionary bottleneck at the time of speciation, estimated to have occurred roughly 15,000-20,000 years ago (2). Also, it has been speculated tha...

Bracken: estimating species abundance in metagenomics data

“…Their high sequence identity indicates that they should be considered as two strains of a single species, but they retain different species names. As a compromise, taxonomists have created the category Mycobacterium tuberculosis complex (Brosch et al, 2002) to represent a collection of taxa that now includes more than 100 strains of five different species. This category sits above the species level but below the genus level in the current microbial taxonomy, but it can best be described as a species.…”

Bovine Tuberculosis in the Republic of Macedonia: Postmortem, Microbiological and Molecular Study in Slaughtered Reactor Cattle

“…The RDs or large sequence polymorphisms (LSP) are conserved in the mycobacteria belonging to the MTBC and due to their irrevocable character and intra-lineage consistency are widely used for construction of evolutionary schemes of the complex. (4,26). The evolutionary scenarios suggest that the modern MTBC species evolved from a common ancestor through gaining these irreversible genomic deletions i.e RDs.…”

“…The evolutionary scenarios suggest that the modern MTBC species evolved from a common ancestor through gaining these irreversible genomic deletions i.e RDs. (4,27). The absence or presence of these genomic deletions can act as a discrimination tool for identification of the MTBC members -fact that has been used for designing and development of variety of PCR assays targeting the RDs.…”

“…Although the disease in cattle is mainly caused by Mycobacterium bovis (M. bovis) and to a lesser extent by Mycobacterium caprae (M. caprae) (2), according to the Task Force Bovine Tuberculosis Subgroup (3), bovine tuberculosis is the "Infection in cattle with any of the disease causing mycobacterial species within the Mycobacterium tuberculosis complex". Despite the differences in host specificity, the members of the Mycobacterium tuberculosis complex (MTBC) have 99.9% similarity at a nucleotide level and an identical 16s rRNA sequence (4).…”

Defining mycobacteria: Shared and specific genome features for different lifestyles

“…• Recent examples of evolutionary studies in mycobacteria include evidence for the descent of M. bovis from M. tuberculosis rather than in the reverse direction [37]; the combined downsizing of the M. marinum genome and the acquisition of a plasmid bearing virulence gene clusters to generate a new species, M. ulcerans, a human host-adapted Mycobacterium sp. associated in the environment with the aquatic insect Naucoris cimicoides [38] and also snails [39] and plants [40.] Similarly, strains within and outside the M. avium complex (MAC) have been studied to address evolution, strain differentiation, differential growth niches and replication rates [7,32,41].…”