The Forest behind the Tree: Phylogenetic Exploration of a Dominant Mycobacterium tuberculosis Strain Lineage from a High Tuberculosis Burden Country

Abstract

BackgroundGenotyping of Mycobacterium tuberculosis isolates is a powerful tool for epidemiological control of tuberculosis (TB) and phylogenetic exploration of the pathogen. Standardized PCR-based typing, based on 15 to 24 mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) loci combined with spoligotyping, has been shown to have adequate resolution power for tracing TB transmission and to be useful for predicting diverse strain lineages in European settings. Its informative value needs to be tested in high TB-burden countries, where the use of genotyping is often complicated by dominance of geographically specific, genetically homogeneous strain lineages.Methodology/Principal FindingsWe tested this genotyping system for molecular epidemiological analysis of 369 M. tuberculosis isolates from 3 regions of Brazil, a high TB-burden country. Deligotyping, targeting 43 large sequence polymorphisms (LSPs), and the MIRU-VNTRplus identification database were used to assess phylogenetic predictions. High congruence between the different typing results consistently revealed the countrywide supremacy of the Latin-American-Mediterranean (LAM) lineage, comprised of three main branches. In addition to an already known RDRio branch, at least one other branch characterized by a phylogenetically informative LAM3 spoligo-signature seems to be globally distributed beyond Brazil. Nevertheless, by distinguishing 321 genotypes in this strain population, combined MIRU-VNTR typing and spoligotyping demonstrated the presence of multiple distinct clones. The use of 15 to 24 loci discriminated 21 to 25% more strains within the LAM lineage, compared to a restricted lineage-specific locus set suggested to be used after SNP analysis. Noteworthy, 23 of the 28 molecular clusters identified were exclusively composed of patient isolates from a same region, consistent with expected patterns of mostly local TB transmission.Conclusions/SignificanceStandard MIRU-VNTR typing combined with spoligotyping can reveal epidemiologically meaningful clonal diversity behind a dominant M. tuberculosis strain lineage in a high TB-burden country and is useful to explore international phylogenetical ramifications.

Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria

“…Here, 43 genomic regions prone to LSPs among M. tuberculosis complex strains are interrogated. Deligotyping is an efficacious approach for the rapid screening of M. tuberculosis clinical isolates and, more importantly, a useful marker for delineating phylogenetic relationships (200,210).…”

“…A 24-locus format is more informative phylogenetically, and it can be used to trace transmission paths of TB (210,369,370). The discriminatory power of the 24-locus MIRU-VNTR typing system provides a resolution com-parable to that of IS6110-RFLP profiling (252,363,370,371).…”

Mycobacterium tuberculosis of the RD Rio Genotype Is the Predominant Cause of Tuberculosis and Associated with Multidrug Resistance in Porto Alegre City, South Brazil

“…An additional reason for studying the features of the spoligofamilies was the recent discovery of RD Rio , a subfamily inside the larger LAM spoligofamily, which seems to be prevalent in several places in Brazil (18)(19)(20)(21)(22)(23) but also in many other countries, particularly in Central and South America, Europe, and Africa (19 (24) as well as with drug resistance (24). To confirm and expand these findings, the present study was undertaken in Rio Grande do Sul (RS), the southernmost Brazilian state, for which no data on RD Rio status and characteristics exist.…”

Clustering of Tuberculosis Cases Based on Variable-Number Tandem-Repeat Typing in Relation to the Population Structure of Mycobacterium tuberculosis in the Netherlands

“…Moreover, epidemiological links have been found between cases caused by bacteria with slightly different DNA fingerprints (6). Clustering results among cases in the immigrant population especially should be interpreted with caution (7, 8), as isolates from these patients often belong to genetically compact strain lineages predominating in the countries of origin (9,10,11,12).In the Netherlands, more than 70% of all TB cases are found among foreign-born persons, and extensive information on each patient is stored in a national registry. We aimed to investigate the population structure of M. tuberculosis isolates among native and immigrant cases and to determine the consequences for the interpretation of recent transmission based on variable-number tandem-repeat (VNTR) typing results.…”

“…Moreover, epidemiological links have been found between cases caused by bacteria with slightly different DNA fingerprints (6). Clustering results among cases in the immigrant population especially should be interpreted with caution (7, 8), as isolates from these patients often belong to genetically compact strain lineages predominating in the countries of origin (9,10,11,12).…”