Mycobacterium tuberculosis Latin American-Mediterranean family and its sublineages in the light of robust evolutionary markers

Abstract

Mycobacterium tuberculosis has a clonal population structure, and the Latin American-Mediterranean (LAM) family is one of the largest and most widespread within this species, showing evidence for remarkable pathobiology and a confusing phylogeny. Here, we applied robust phylogenetic markers to study the evolution of the LAM family and its major sublineages circulating in Russia and neighboring countries. A total of 250 M. tuberculosis isolates were confirmed to belong to the LAM family based on the analysis of the LAM-specific single-nucleotide polymorphisms (SNPs) in the Rv3062 and Rv0129c genes. At this stage, the family status was rectified for 121 isolates misleadingly assigned by CRISPR spoligotyping to non-LAM families (T1- or T5-RUS1). Consequently, the reestimated LAM prevalence rate increased 2-fold in Russia and Kazakhstan and 4-fold in Belarus. The majority (91.8 to 98.7%) of the LAM isolates from all three countries belonged to the LAM-RUS sublineage. In contrast, the Ibero-American LAM RD-Rio sublineage was identified in only 7 Russian isolates. Taken together, our findings and further analyses suggest a monophyletic origin of LAM-RUS: at a historically distant time, in Russia, in a small founding bacterial/human population. Its dissemination pattern and high prevalence rate in Northern Eurasia may indicate a long-term coexistence of the LAM-RUS sublineage and local human populations hypothetically leading to coadaptation and reduced pathogenicity of the relatively more ancient clones, such as spoligotype international type 254 (SIT254), compared to the more recent SIT252 and SIT266 clones. In contrast, rare LAM RD-Rio isolates were likely brought to Russia through occasional human contact. The spread of RD-Rio strains is not as global as commonly claimed and is determined largely by human migration flows (rather than by pathobiological properties of these strains). Consequently, a host population factor appears to play a major role in shaping the in situ dissemination pattern of the imported strains in an autochthonous population.

FIG 1

Relationships of the spoligotypes identified in this study in LAM isolates, within the RD framework, evaluated as a forest graph. Binary spoligoprofiles are shown schematically for some major types in the bottom right inset. Numbers in italics in country-specific segments of the pie charts show percentages of the strains of this particular type in the total collection of a given country. The “spoligoforest” burst output was generated with the SpolTools program. Solid edges are unique relationships between spoligotypes. Dotted lines have a probability of <0.5, while dashed lines have a probability of >0.5 (see Table 1 for types and profiles used).

FIG 2

Geographic distribution of the LAM family and its sublineages and major spoligotypes. Numbers in italics show percentages of LAM isolates in the local population of M. tuberculosis (also roughly reflected by the circle size). The prevalence of LAM isolates in St. Petersburg was estimated to be 25% based on an analysis of the IS6110-RFLP database of our laboratory in the light of previously reported LAM-RUS IS6110-RFLP profiles (23). Data on Tula were reported previously (8, 23). Map source, Free World Maps (http://www.freeworldmaps.net/pdf/world/ApianGlobular1.pdf).