Genomic analysis of Latin American-Mediterranean family of Mycobacterium tuberculosis clinical strains from Kazakhstan

Tarlykov, Pavel; Atavliyeva, Sabina; Alenova, Arike; Ramankulov, Yerlan

doi:10.1590/0074-02760200215

Cited by 5 publications

(5 citation statements)

References 38 publications

(49 reference statements)

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“…Among the rifampicin-resistant isolates, the LAM genotype was associated with the His526Leu mutation of the rpoB gene (p < 0.0001; OR = 141.3333; 95%CI: 15.9020-1256.1369). This mutation of the rpoB gene was also identified in the genomes of drug-resistant LAM isolates (66.7%; 2/3) from Kazakhstan [34].…”

Section: Discussionmentioning

confidence: 70%

Prevalence of Beijing Central Asian/Russian Cluster 94-32 among Multidrug-Resistant M. tuberculosis in Kazakhstan

Akhmetova,

Bismilda,

Chingissova

et al. 2023

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The Beijing genotype is the most distributed M. tuberculosis family in Kazakhstan. In this study, we identified dominant Beijing clusters in Kazakhstan and assessed their drug susceptibility profiles and association with the most widely spread mutation Ser531Leu of the rpoB gene and the mutation Ser315Thr of the katG gene associated with resistance to rifampicin and isoniazid, respectively. M. tuberculosis isolates (n = 540) from new TB cases were included in the study. MIRU-VNTR genotyping was performed for 540 clinical isolates to determine M. tuberculosis families using 24 loci. RD analysis was additionally performed for the Beijing isolates. The identification of mutations in the drug-resistance genes of M. tuberculosis was performed with allele-specific real-time PCR and Sanger sequencing. The Beijing genotype was identified in 60% (324/540) of the clinical isolates. Central Asian/Russian cluster 94-32 was the most distributed cluster among the Beijing isolates (50.3%; 163/324). Three other dominant Beijing clusters were identified as 94-33 (3.4%; 11/324), 100-32 (3.1%; 10/324) and 99-32 (3.1%; 10/324). The Beijing genotype was associated with drug-resistant TB (p < 0.0001), including multidrug-resistant TB (p < 0.0001), in our study. An association of the mutation Ser531Leu of the rpoB gene with the Beijing genotype was found (p < 0.0001; OR = 16.0000; 95%CI: 4.9161–52.0740). Among the Beijing isolates, cluster 94-32 showed an association with MDR-TB (p = 0.021). This is why the evaluation of the Beijing genotype and its clusters is needed to control MDR-TB in Kazakhstan.

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Section: Discussionmentioning

confidence: 70%

Prevalence of Beijing Central Asian/Russian Cluster 94-32 among Multidrug-Resistant M. tuberculosis in Kazakhstan

Akhmetova,

Bismilda,

Chingissova

et al. 2023

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“…Only some publications relate to preliminary data and reported several genome sequences of DR (including one XDR and several MDR) clinical isolates of M. tuberculosis isolated in Kazakhstan performed by using a next-generation sequencing platform [ 24 , 25 , 26 , 27 , 28 , 29 ]. Drafts of complete genome sequences of two Kazakhstani isolates [ 24 ] and one isolate with extensive drug resistance [ 26 , 27 ] were published by our group.…”

Section: Discussionmentioning

confidence: 99%

“…Drug resistance mutations in the genome were reported as a part of the study of the mechanisms of Reversion of Antibiotic Resistance in MDR Mycobacterium tuberculosis induced by a Nanomolecular Iodine-Containing Complex FS-1 [ 25 ]. The genomes of three drug-resistant clinical isolates of the Latin American-Mediterranean (LAM) family collected in Kazakhstan were reported by Tarlykov et al [ 28 ]. A last study of ours concentrated on WGS MDR-TB isolates from Kazakhstan [ 29 ] and identified Lineage 2 East-Asia (Beijing) as a major contributor to the genetic diversity of MTB in the region.…”

Section: Discussionmentioning

confidence: 99%

Whole-Genome Sequence-Based Characterization of Pre-XDR M. tuberculosis Clinical Isolates Collected in Kazakhstan

et al. 2023

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Background: Kazakhstan has a high burden of multidrug-resistant tuberculosis in the Central Asian region. This study aimed to perform genomic characterization of Mycobacterium tuberculosis strains obtained from Kazakhstani patients with pre-extensively drug-resistant tuberculosis diagnosed in Kazakhstan. Methods: Whole-genome sequencing was performed on 10 pre-extensively drug-resistant M. tuberculosis strains from different regions of Kazakhstan. All strains had high-confidence resistance mutations according to the resistance grading system previously established by the World Health Organization. The genome analysis was performed using TB-Profiler, Mykrobe, CASTB, and ResFinder. Results: Valuable information for understanding the genetic diversity of tuberculosis in Kazakhstan can also be obtained from whole-genome sequencing. The results from the Phenotypic Drug Susceptibility Testing (DST) of bacterial strains were found to be consistent with the drug resistance information obtained from genomic data that characterized all isolates as pre-XDR. This information can help in developing targeted prevention and control strategies based on the local epidemiology of tuberculosis. Furthermore, the data obtained from whole-genome sequencing can help in tracing the transmission pathways of tuberculosis and facilitating early detection of outbreaks. Conclusions: The results from whole-genome sequencing of tuberculosis clinical samples in Kazakhstan provide important insights into the drug resistance patterns and genetic diversity of tuberculosis in the country. These results can contribute to the improvement of tuberculosis control and management programs in Kazakhstan.

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“…Only a handful of regional studies have used the WGS approach to characterize the MTBC population in Kazakhstan. The sample size in these studies usually does not exceed 10 isolates due to budget constraints and/or lack of funding [8,9,11,12,28,29]. As a result, WGS technology has not been widely adopted in Kazakhstan in clinical or other settings.…”

Section: Discussionmentioning

confidence: 99%

“…A PubMed search using the terms "whole-genome sequencing", "Kazakhstan", and "tuberculosis" found only six publications, describing a total of 97 Sequence Read Archive (SRA) whole-genome sequences of local Mtb isolates. This suggests that the use of WGS in TB research and surveillance is not yet widespread in Kazakhstan [8][9][10][11][12][13].…”

Section: Introductionmentioning

confidence: 99%

Genomic Characterization of Drug-Resistant Mycobacterium tuberculosis L2/Beijing Isolates from Astana, Kazakhstan

Auganova,

Atavliyeva,

Amirgazin

et al. 2023

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Kazakhstan ranks among the countries with the highest number of MDR-TB patients per 100,000 population worldwide. The successful transmission of local MDR strains of Mycobacterium tuberculosis (Mtb) poses a significant threat to disease control. In this study, we employed whole-genome sequencing to examine drug resistance, compensatory mutations, population structure, and transmission patterns in a sample of 24 clinical isolates of L2/Beijing Mtb collected in Astana, Kazakhstan between 2021 and 2022. The genotypic prediction of Mtb susceptibility to anti-TB agents was consistent with the phenotypic susceptibility, except for bedaquiline. An analysis of resistance-associated genes characterized most of the isolates as pre-extensively drug-resistant tuberculosis (pre-XDR-TB) (n = 15; 62.5%). The phylogenetic analysis grouped the isolates into four transmission clusters; the dominant cluster was assigned to the “aggressive” Central Asia outbreak (CAO) clade of L2/Beijing (n = 15; 62.5%). Thirteen mutations with putative compensatory effects were observed exclusively in Mtb isolates containing the rpoB S450L mutation. The putative compensatory mutations had a stabilizing effect on RpoABC protein stability and dynamics. The high prevalence of the CAO clade in the population structure of Mtb may explain the rapid spread of MDR-TB in Kazakhstan.

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Genomic analysis of Latin American-Mediterranean family of Mycobacterium tuberculosis clinical strains from Kazakhstan

Cited by 5 publications

References 38 publications

Prevalence of Beijing Central Asian/Russian Cluster 94-32 among Multidrug-Resistant M. tuberculosis in Kazakhstan

Prevalence of Beijing Central Asian/Russian Cluster 94-32 among Multidrug-Resistant M. tuberculosis in Kazakhstan

Whole-Genome Sequence-Based Characterization of Pre-XDR M. tuberculosis Clinical Isolates Collected in Kazakhstan

Genomic Characterization of Drug-Resistant Mycobacterium tuberculosis L2/Beijing Isolates from Astana, Kazakhstan

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