Implication of the RDRio Mycobacterium tuberculosis sublineage in multidrug resistant tuberculosis in Portugal

David, Susana; Duarte, E.L.; Leite, Clarice Q. F.; Ribeiro, João-Nuno; Maio, José-Nuno; Paixão, Eleonora; Portugal, Clara; Sancho, Luísa; Sousa, José Germano de

doi:10.1016/j.meegid.2012.04.021

Cited by 20 publications

(30 citation statements)

References 28 publications

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“…LAM isolates bearing the RD174 deletion were also tested for the RD Rio deletion that it is known to co-segregate with the RD174 deletion [24]–[25].…”

Section: Resultsmentioning

confidence: 99%

“…The Euro-American lineage consists of 10 distinct sublineages, each defined by a large sequence deletion, named RD115, RD122, RD174 (that recently has been demonstrated to co-segregate with the so-called deletion RD Rio [24]–[25]), RD182, RD183, RD193, RD219, RD724, RD726 and RD761, and an 11 th group including strains with no RD deletion (the so-called H37Rv-like) [5]. By spoligotyping, the Euro-American lineage, is characterized by deletion of spacers 33–36 in the DR locus [17], [26] and consists of the major families T, Haarlem (H), Latin American-Mediterranean (LAM), S and X, including a total of 34 subfamilies.…”

Section: Introductionmentioning

confidence: 99%

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Genomic Variability of Mycobacterium tuberculosis Strains of the Euro-American Lineage Based on Large Sequence Deletions and 15-Locus MIRU-VNTR Polymorphism

et al. 2014

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A sample of 260 Mycobacterium tuberculosis strains assigned to the Euro-American family was studied to identify phylogenetically informative genomic regions of difference (RD). Mutually exclusive deletions of regions RD115, RD122, RD174, RD182, RD183, RD193, RD219, RD726 and RD761 were found in 202 strains; the RDRio deletion was detected exclusively among the RD174-deleted strains. Although certain deletions were found more frequently in certain spoligotype families (i.e., deletion RD115 in T and LAM, RD174 in LAM, RD182 in Haarlem, RD219 in T and RD726 in the “Cameroon” family), the RD-defined sublineages did not specifically match with spoligotype-defined families, thus arguing against the use of spoligotyping for establishing exact phylogenetic relationships between strains. Notably, when tested for katG463/gyrA95 polymorphism, all the RD-defined sublineages belonged to Principal Genotypic Group (PGG) 2, except sublineage RD219 exclusively belonging to PGG3; the 58 Euro-American strains with no deletion were of either PGG2 or 3. A representative sample of 197 isolates was then analyzed by standard 15-locus MIRU-VNTR typing, a suitable approach to independently assess genetic relationships among the strains. Analysis of the MIRU-VNTR typing results by using a minimum spanning tree (MST) and a classical dendrogram showed groupings that were largely concordant with those obtained by RD-based analysis. Isolates of a given RD profile show, in addition to closely related MIRU-VNTR profiles, related spoligotype profiles that can serve as a basis for better spoligotype-based classification.

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“…LAM isolates bearing the RD174 deletion were also tested for the RD Rio deletion that it is known to co-segregate with the RD174 deletion [24]–[25].…”

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genomic Variability of Mycobacterium tuberculosis Strains of the Euro-American Lineage Based on Large Sequence Deletions and 15-Locus MIRU-VNTR Polymorphism

et al. 2014

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“…), rare stranger. While the LAM-RUS branch was studied only by one Russian group, the RD-Rio sublineage has attracted much more attention since its discovery (5)(6)(7)29), but evidence of its increased virulence and transmissibility appears controversial (30,31). In this study, only a few isolates belonged to RD-Rio (7 such isolates) (Fig.…”

Section: Figmentioning

confidence: 82%

“…This LAM sublineage was a major focus of studies carried out in different settings across the Americas, Europe, and Africa (6,7), and its global spread has been suggested (6); we discuss this issue of "global spread" below.…”

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confidence: 99%

Mycobacterium tuberculosis Latin American-Mediterranean Family and Its Sublineages in the Light of Robust Evolutionary Markers

2014

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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.Nothing in biology makes sense except in the light of evolution.-Theodosius Dobzhansky (32) M ycobacterium tuberculosis is doubtless an important pathogen from a human health viewpoint. Per se, it is also an interesting biological species. Under the umbrella name M. tuberculosis complex, it encompasses different ecotypes, its niches expanding well beyond that of the human host. It has long been a common yet true saying that M. tuberculosis is marked by a high level of genetic homogeneity (1). Over the past decade, an expansion of knowledge, greatly aided by whole-genome sequencing, has demonstrated a higher level of genetic variation than initially thought. On the other hand, notwithstanding the excellent added value of new-generation technologies, the previous use of the much simpler molecular typing methods more than 10 years ago delineated the phylogenetic structure of M. tuberculosis and identified most of its major families/genotypes (2). A Latin AmericanMediterranean ...

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“…A number of studies demonstrated an association with drug resistance of the Latin-American-Mediterranean (LAM) family [2][3][4]. On the other hand, other studies have shown high transmissibility of this strain, but not a significant association with increased virulence [5,6].…”

Section: Introductionmentioning

confidence: 99%

Prevalence of Latin-American-Mediterranean genetic family in population structure of Mycobacterium tuberculosis in Bulgaria

Valcheva¹,

Rastogi²,

Mokrousov³

2015

International Journal of Mycobacteriology

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Tuberculosis (TB) control remains an important public health priority for Bulgaria. The population structure of Mycobacterium tuberculosis is clonal and certain genetic families of this species (e.g., Latin-American-Mediterranean [LAM]) have attracted more attention due to their global dissemination and/or particular pathogenic properties, e.g., association with multidrug resistance (MDR). The aim of this study was to evaluate the prevalence of the M. tuberculosis LAM family in Bulgaria based on the use of different molecular markers. A total of 101 previously spoligotyped M. tuberculosis strains were studied by LAM-specific PCR assay to detect an insertion of IS6110 in the specific genome region. On the whole, clear-cut results were obtained for most strains; spoligotype-based family was reassigned in some of them. At the same time, double bands were amplified in some cases and warrant further validation studies of this method. The higher MDR rate among LAM versus other genotype isolates was observed (P=0.04). In conclusion, these results suggest a low (<4%) prevalence rate of LAM in Bulgaria (that is similar to its Balkan neighbors) and highlight the importance of using robust markers for correct detection of the LAM family.

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Implication of the RDRio Mycobacterium tuberculosis sublineage in multidrug resistant tuberculosis in Portugal

Cited by 20 publications

References 28 publications

Genomic Variability of Mycobacterium tuberculosis Strains of the Euro-American Lineage Based on Large Sequence Deletions and 15-Locus MIRU-VNTR Polymorphism

Genomic Variability of Mycobacterium tuberculosis Strains of the Euro-American Lineage Based on Large Sequence Deletions and 15-Locus MIRU-VNTR Polymorphism

Mycobacterium tuberculosis Latin American-Mediterranean Family and Its Sublineages in the Light of Robust Evolutionary Markers

Prevalence of Latin-American-Mediterranean genetic family in population structure of Mycobacterium tuberculosis in Bulgaria

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