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

Asset Daniyarov; Ainur Akhmetova; Saule Rakhimova; Zhannur Abilova; Dauren Yerezhepov; Lyailya Chingissova; Venera Bismilda; Nurlan Takenov; Ainur Akilzhanova; Ulykbek Kairov; Ulan Kozhamkulov

doi:10.3390/diagnostics13122005

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

Department of General Biology and Genomics
L.N. Gumilyov Eurasian National University
National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan
Center for Life Sciences

Research output: Contribution to journal › Article › peer-review

7 Citations (Scopus)

Abstract

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.

Original language	English
Article number	2005
Journal	Diagnostics
Volume	13
Issue number	12
DOIs	https://doi.org/10.3390/diagnostics13122005
Publication status	Published - Jun 8 2023

Funding

This research was funded by a grant from the Ministry of Education and Science of the Republic of Kazakhstan AP09259750 and Nazarbayev University under Collaborative Research Program Grant No11022021CRP1511.

Funders	Funder number
Ministry of Education and Science of the Republic of Kazakhstan	AP09259750
Nazarbayev University

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Mycobacterium tuberculosis
bioinformatics analysis
next-generation sequencing
pre-extensively drug-resistant
tuberculosis

ASJC Scopus subject areas

Clinical Biochemistry

Access to Document

10.3390/diagnostics13122005

Cite this

Daniyarov, A., Akhmetova, A., Rakhimova, S., Abilova, Z., Yerezhepov, D., Chingissova, L., Bismilda, V., Takenov, N., Akilzhanova, A., Kairov, U., & Kozhamkulov, U. (2023). Whole-Genome Sequence-Based Characterization of Pre-XDR M. tuberculosis Clinical Isolates Collected in Kazakhstan. Diagnostics, 13(12), Article 2005. https://doi.org/10.3390/diagnostics13122005

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abstract = "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.",

keywords = "Mycobacterium tuberculosis, bioinformatics analysis, next-generation sequencing, pre-extensively drug-resistant, tuberculosis",

author = "Asset Daniyarov and Ainur Akhmetova and Saule Rakhimova and Zhannur Abilova and Dauren Yerezhepov and Lyailya Chingissova and Venera Bismilda and Nurlan Takenov and Ainur Akilzhanova and Ulykbek Kairov and Ulan Kozhamkulov",

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AU - Akhmetova, Ainur

AU - Rakhimova, Saule

AU - Abilova, Zhannur

AU - Yerezhepov, Dauren

AU - Chingissova, Lyailya

AU - Bismilda, Venera

AU - Takenov, Nurlan

AU - Akilzhanova, Ainur

AU - Kairov, Ulykbek

AU - Kozhamkulov, Ulan

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N2 - 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.

AB - 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.

KW - Mycobacterium tuberculosis

KW - bioinformatics analysis

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