Molecular snapshot of Mycobacterium tuberculosis population in Kazakhstan: A country-wide study

Skiba, Yuriy A.; Mokrousov, Igor; Ismagulova, Gulnara; Maltseva, Elina R.; Yurkevich, Nadezhda; Bismilda, Venera; Chingissova, Lyailya; Abildaev, T.; Аitkhozhinа, N. А.

doi:10.1016/j.tube.2015.04.012

Cited by 42 publications

(38 citation statements)

References 21 publications

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“…Asian/Russian type Beijing 94–32 is highly prevalent in the former Soviet Central Asia 39 40 41 42 and is one of the two largest and significant Beijing subtypes in Russia 4 18 38 . Indeed it is SLV derived from the strain from Qinghai, a neighbor province of Xinjiang-Uyghur, and of Central Asia as a whole ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Evolutionary History and Ongoing Transmission of Phylogenetic Sublineages of Mycobacterium tuberculosis Beijing Genotype in China

Yin

Liu

Jiao

et al. 2016

Sci Rep

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Mycobacterium tuberculosis Beijing genotype originated in China and has undergone a dramatic population growth and global spread in the last century. Here, a collection of M. tuberculosis Beijing family isolates from different provinces across all China was genotyped by high-resolution (24-MIRU-VNTR) and lowresolution, high-rank (modern and ancient sublineages) markers. The molecular profiles and global and local phylogenies were compared to the strain phenotype and patient data. The phylogeographic patterns observed in the studied collection demonstrate that large-scale (but not middle/small-scale) distance remains one of the decisive factors of the genetic divergence of M. tuberculosis populations. Analysis of diversity and network topology of the local collections appears to corroborate a recent intriguing hypothesis about Beijing genotype originating in South China. Placing our results within the Eurasian context suggested that important Russian B0/W148 and Asian/Russian A0/94-32 epidemic clones of the Beijing genotype could trace their origins to the northeastern and northwestern regions of China, respectively. The higher clustering of the modern isolates in children and lack of increased MDR rate in any sublineage suggest that not association with drug resistance but other (e.g., speculatively, virulencerelated) properties underlie an enhanced dissemination of the evolutionarily recent, modern sublineage of the Beijing genotype in China.The advent of next-generation sequencing technologies for whole genome analysis of bacterial pathogens opened a new perspective to the more robust and more meaningful reconstructions. Nonetheless, a new technology is not a magic wand in itself since bioinformatics tools and algorithms do not always permit to achieve an unambiguous interpretation 1 . In the field of molecular evolution and phylogenetics of Mycobacterium tuberculosis, a consensus view on many issues is yet to be reached. Perhaps, the most controversial topics with contrasting opinions concern the location and dating of the origin of M. tuberculosis species and its lineages and reasons underlying the evolutionary success of certain strains [2][3][4] .M. tuberculosis is a clonal species and its different lineages are marked with clearly different "curricula vitae", some having declined even in the areas of their origin (M. africanum in West Africa being the most remarkable example), others having undergone a dramatic increase in effective population size and global dispersal. The latter may be exemplified by the Beijing family and its particular sublineages and clonal clusters.

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Section: Resultsmentioning

confidence: 99%

Evolutionary History and Ongoing Transmission of Phylogenetic Sublineages of Mycobacterium tuberculosis Beijing Genotype in China

Yin

Liu

Jiao

et al. 2016

Sci Rep

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“…A comparative genotypic profile analysis was carried out including a total of 5482 isolates and 24-loci MIRU-VNTR profiles assembled from three large global studies, along with publicly available metadata [16][17][18]. Hierarchical clustering analysis was conducted in R statistical software using the hclust function and clusters defined as groups of two or more isolates sharing identical 24-loci MIRU-VNTR profiles.…”

Section: Genotyping and Cluster Identificationmentioning

confidence: 99%

“…Except for cases directly linked with immigrants, which is not relevant in the Guinea-Bissau dataset since all patients were of Guinean nationality, the absence of additional transmission clusters with established epidemiological links render unknown the routes by which MDR-TB Beijing strains are being introduced. To identify links with other Beijing clusters, we compared the genotypic profiles of all seventeen clinical isolates included in this study against a global dataset of 5,482 isolates assembled from three large studies [16][17][18]. The comparison against this dataset yielded a total of 1,848 distinct profiles (Hunter-Gaston Index of Diversity, h = 0.9812).…”

Section: Emergence Of Beijing Family Mdr-tb In Portugal and Guinea-bimentioning

confidence: 99%

Emergence of multidrug-resistant Mycobacterium tuberculosis of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing

Perdigão

Silva

Maltêz

et al. 2020

Emerging Microbes & Infections

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The Beijing genotype comprises a highly disseminated strain type that is frequently associated with multidrug resistant (MDR) tuberculosis (TB) and increased transmissibility but, countries such as Portugal and Guinea-Bissau fall outside the regions phylogeographically associated with this specific genotype. Nevertheless, recent data shows that this genotype might be gradually emerging in these two countries as an underlying cause of primary MDR-TB. Here, we describe the emergence of Mycobacterium tuberculosis Beijing strains associated with MDR-TB in Portugal and Guinea-Bissau demonstrating the presence of the well described superclusters 100-32 and 94-32 in Portugal and Guinea-Bissau, respectively. Genome-wide analysis and comparison with a global genomic dataset of M. tuberculosis Beijing strains, revealed the presence of two genomic clusters encompassing isolates from Portugal and Guinea-Bissau, GC1 (n = 121) and GC2 (n = 39), both of which bore SNP signatures compatible with the 100-32/B0/W148 and 94-32/Central Asia Outbreak clades, respectively. Moreover, GC2 encompasses a cross-border cluster between Portugal, Guinea-Bissau and Brazil thus supporting migration-associated introduction of MDR-TB and subsequent clonal expansion at the community-level. The comparison with global Beijing datasets demonstrates the global reach of the disease and its complex dissemination across multiple countries while in parallel there are clear microevolutionary trajectories towards extensively drug resistant TB.

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“…Molecular tools can positively impact on earlier detection of Mtb and identification of drug resistance (3, 4). Genotyping of Mtb isolates has revealed associations between drug resistance and Mtb lineage (5–8), identified routes of transmission (9, 10) and described the dynamics of epidemic clones (3, 11–14). Further developments in multiplex assays as well as the expanded use of next generation sequencing assays will increasingly allow Mtb strains to be simultaneously screened for resistance associated mutations and the bacterial lineage they represent.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of SNP-based genotyping to monitor tuberculosis control in a high MDR-TB setting

Tukvadze

Bergval²,

Bablishvili

et al. 2016

Preprint

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25 26 Mycobacterium tuberculosis (Mtb) lineage identification and typing of clinical isolates in 27 general is performed only retrospectively. The results are rarely linked to drug susceptibility 28 testing (DST) or patient data. Consequently, the association between Mtb lineage, (multi)drug 29 resistance and treatment history is not fully explored at the local level. Here we evaluated a 30 new SNP based typing assay. We furthermore assessed the added value of genotyping of Mtb 31 isolates for epidemiological purposes and guidance of tuberculosis (TB) control. Mtb lineage, 32 DST profile and treatment history were determined for 399 samples at the National TB 33 Reference Laboratory (NRL) in Tbilisi, Georgia by local staff. Data was shared electronically 34 and analysis was performed remotely. Out of 399 isolates, 74 (74/399, 18.5%) were at least 35 multidrug resistant (MDR)-TB, of which 63 (63/74, 85.1%) were members of three different 36 Mtb Beijing lineages. Previous treatment was reported in 38/74 (51.4%) MDR(+) patients. The 37 availability of this data allows associations with lineages. Notably, multidrug resistant TB was 38 more strongly associated with the Beijing lineage than treatment history. Of all MDR-TB 39Beijing strains 56.7% (42/74) were members of a genetic cluster. This is most easily explained 40 by (ongoing) MDR-TB transmission rather than drug resistance amplification. This knowledge 41 is useful when designing intervention strategies for MDR-TB. Our study provides an example 42 that on-site integrated Mtb genotyping is realistic and could support TB control activities. 43 44 48 TB control activities (1, 2). Justifying investment in effective TB control strategies in a 49 country can be achieved in part by defining and monitoring the (MDR) TB epidemic to 50 identify appropriate interventions. 51 52 Molecular tools can positively impact on earlier detection of Mtb and identification of drug 53 resistance (3, 4). Genotyping of Mtb isolates has revealed associations between drug 54resistance and Mtb lineage (5-8), identified routes of transmission (9, 10) and described the 55 dynamics of epidemic clones (3,(11)(12)(13)(14). Further developments in multiplex assays as well as 56 the expanded use of next generation sequencing assays will increasingly allow Mtb strains to 57 be simultaneously screened for resistance associated mutations and the bacterial lineage they 58 represent. 60A robust link has been found between previous treatment for TB and multidrug resistance 61 (15), and is identified as a risk factor for MDR-TB by the WHO (16) but other factors are 62 also important, for example the bacterial lineage. This is especially true when transmission of 63 resistant strains is more common than the acquisition of resistance during treatment. 64 Members of the East Asia lineage (Mtb lineage 2) (17, 18) have repeatedly been associated 65 with multidrug resistance in high burden MDR-TB countries (11, 19) but less so in low 66 burden (MDR)-TB countries (20-22). The relative importance and interdepen...

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Molecular snapshot of Mycobacterium tuberculosis population in Kazakhstan: A country-wide study

Cited by 42 publications

References 21 publications

Evolutionary History and Ongoing Transmission of Phylogenetic Sublineages of Mycobacterium tuberculosis Beijing Genotype in China

Evolutionary History and Ongoing Transmission of Phylogenetic Sublineages of Mycobacterium tuberculosis Beijing Genotype in China

Emergence of multidrug-resistant Mycobacterium tuberculosis of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing

Evaluation of SNP-based genotyping to monitor tuberculosis control in a high MDR-TB setting

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