Whole-Genome Sequence-Based Characterization of Pre-XDR <i>M. tuberculosis</i> Clinical Isolates Collected in Kazakhstan
Background: Kazakhstan has a high burden of multidrug-resistant tuberculosis in the Central Asian region. This study aimed to perform genomic characterization of <i>Mycobacterium tuberculosis</i> strains obtained from Kazakhstani patients with pre-extensively drug-resistant tuberculosis...
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| Format: | Article |
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MDPI AG
2023-06-01
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| Series: | Diagnostics |
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| Online Access: | https://www.mdpi.com/2075-4418/13/12/2005 |
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| author | Asset Daniyarov Ainur Akhmetova Saule Rakhimova Zhannur Abilova Dauren Yerezhepov Lyailya Chingissova Venera Bismilda Nurlan Takenov Ainur Akilzhanova Ulykbek Kairov Ulan Kozhamkulov |
| author_facet | Asset Daniyarov Ainur Akhmetova Saule Rakhimova Zhannur Abilova Dauren Yerezhepov Lyailya Chingissova Venera Bismilda Nurlan Takenov Ainur Akilzhanova Ulykbek Kairov Ulan Kozhamkulov |
| author_sort | Asset Daniyarov |
| collection | DOAJ |
| description | Background: Kazakhstan has a high burden of multidrug-resistant tuberculosis in the Central Asian region. This study aimed to perform genomic characterization of <i>Mycobacterium tuberculosis</i> 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 <i>M. tuberculosis</i> 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. |
| first_indexed | 2024-03-11T02:34:48Z |
| format | Article |
| id | doaj.art-7dbd93897a8848ab90c0e617bae1926d |
| institution | Directory Open Access Journal |
| issn | 2075-4418 |
| language | English |
| last_indexed | 2024-03-11T02:34:48Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diagnostics |
| spelling | doaj.art-7dbd93897a8848ab90c0e617bae1926d2023-11-18T09:59:47ZengMDPI AGDiagnostics2075-44182023-06-011312200510.3390/diagnostics13122005Whole-Genome Sequence-Based Characterization of Pre-XDR <i>M. tuberculosis</i> Clinical Isolates Collected in KazakhstanAsset Daniyarov0Ainur Akhmetova1Saule Rakhimova2Zhannur Abilova3Dauren Yerezhepov4Lyailya Chingissova5Venera Bismilda6Nurlan Takenov7Ainur Akilzhanova8Ulykbek Kairov9Ulan Kozhamkulov10Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, KazakhstanLaboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, KazakhstanLaboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, KazakhstanLaboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, KazakhstanLaboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, KazakhstanNational Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty 050000, KazakhstanNational Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty 050000, KazakhstanNational Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty 050000, KazakhstanLaboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, KazakhstanLaboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, KazakhstanLaboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, KazakhstanBackground: Kazakhstan has a high burden of multidrug-resistant tuberculosis in the Central Asian region. This study aimed to perform genomic characterization of <i>Mycobacterium tuberculosis</i> 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 <i>M. tuberculosis</i> 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.https://www.mdpi.com/2075-4418/13/12/2005tuberculosisnext-generation sequencingbioinformatics analysis<i>Mycobacterium tuberculosis</i>pre-extensively drug-resistant |
| spellingShingle | Asset Daniyarov Ainur Akhmetova Saule Rakhimova Zhannur Abilova Dauren Yerezhepov Lyailya Chingissova Venera Bismilda Nurlan Takenov Ainur Akilzhanova Ulykbek Kairov Ulan Kozhamkulov Whole-Genome Sequence-Based Characterization of Pre-XDR <i>M. tuberculosis</i> Clinical Isolates Collected in Kazakhstan Diagnostics tuberculosis next-generation sequencing bioinformatics analysis <i>Mycobacterium tuberculosis</i> pre-extensively drug-resistant |
| title | Whole-Genome Sequence-Based Characterization of Pre-XDR <i>M. tuberculosis</i> Clinical Isolates Collected in Kazakhstan |
| title_full | Whole-Genome Sequence-Based Characterization of Pre-XDR <i>M. tuberculosis</i> Clinical Isolates Collected in Kazakhstan |
| title_fullStr | Whole-Genome Sequence-Based Characterization of Pre-XDR <i>M. tuberculosis</i> Clinical Isolates Collected in Kazakhstan |
| title_full_unstemmed | Whole-Genome Sequence-Based Characterization of Pre-XDR <i>M. tuberculosis</i> Clinical Isolates Collected in Kazakhstan |
| title_short | Whole-Genome Sequence-Based Characterization of Pre-XDR <i>M. tuberculosis</i> Clinical Isolates Collected in Kazakhstan |
| title_sort | whole genome sequence based characterization of pre xdr i m tuberculosis i clinical isolates collected in kazakhstan |
| topic | tuberculosis next-generation sequencing bioinformatics analysis <i>Mycobacterium tuberculosis</i> pre-extensively drug-resistant |
| url | https://www.mdpi.com/2075-4418/13/12/2005 |
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