Evaluation of different genotyping schemes M.tuberculosis isolates from Kazakhstan by 24 MIRU-VNTR loci based on number of tandem repeats analysis
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Keywords:
Tuberculosis, genotyping, MIRU-VNTR analysis, genotyping schemes, mycobacterium tuberculosis,Abstract
Molecular genetic MIRU-VNTR typing is simple and fast method seems to be interesting and promising for the study of the genetic diversity of M.tuberculosis, also using as instrument of studying modern clinical TB microbiology and epidemiology. The results of genotyping of 81 clinical isolates of M. tuberculosis collected from 7 different regions of Kazakhstan by 12, 15 and 24 loci based on MIRU-VNTR analysis are represented in this article. Polymorphic and informative loci were determined, different genotyping schemes were evaluated that allowed to choose optimal scheme of genotyping based on MIRU-VNTR analysis Most discriminatory power of the genotyping scheme has the full set of 24 M.tuberculosis loci (HGDI = 0,88), the smallest discriminatory power of the combination scheme has 12MIRU loci (HGDI = 0,73), roughly the same discriminatory power showed schemes of 15 loci (HGDI = 0.84 and 0.81).References
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10 Frothingham R., Meeker-O’Connell W.A. Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats // Microbiol. – 1998. – Vol. 144. – P. 1189-1196.
11 Mazars E., Lesjean S., Banuls A.L., Gilbert M., Vincent V., Gicquel B., Tibayrenc M., Locht C., and Supply P. High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology // Proc. Nat. Acad. Sci. USA. – 2001. – Vol. 98(4). – P. 1901–1906.
12 Supply P., Mazars E., Lesjean S., Vincent V., Gicquel B. and Locht C. Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome // Molecular Microbiology. – 2000. – 36(3). – Р. 762-771.
13 Allix-Béguec C., Supply P., and Fauville-Dufaux M. Utility of fast mycobacterial interspersed repetitive unit-variable number tandem repeat genotyping in clinical mycobacteriological analysis // Clin. Infect. Dis. – 2004. – Vol. 39. – P. 783–789.
14 Supply P., Allix C., Lesjean S., Cardoso-Oelemann M., Rusch-Gerdes, S., Willery E., Savine E., de Haas P., van Deutekom H., Roring S., Bifani P., Kurepina N., Kreiswirth B., Sola C., Rastogi N., Vatin V., Gutierrez M. C., Fauville M., Niemann S., Skuce R., Kremer K., Locht C., D. van Soolingen. Proposal for Standardization of Optimized Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing of Mycobacterium tuberculosis // J. Clin. Microbiol. – 2006. – Vol. 44. –P. 4498-4510.
15 Jiao W., Mokrousov I., Sun G., Guo Y., Vyazovaya A., Narvskaya O. and Shen A. Evaluation of New Variable-Number Tandem-Repeat Systems for Typing Mycobacterium tuberculosis with Beijing Genotype Isolates from Beijing, China // J. Clin. Microbiol. – 2008. – Vol. 46(3). – P. 1045–1049.
2 Абильдаев Т.Ш. Статический обзор по туберкулезу в Республике Казахстан. – Алматы, 2014. – 68c.
3 Groenen P. M., Bunschoten A. E., van Soolingen D., and van Embden J. D. Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method // Mol. Microbiol. – 1993. – Vol.10. – P. 1057–1065.
4 Brudey K., Driscoll J. R., Rigouts L. et. al. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology // BMC Microbiol. – 2006. – Vol. 6. – P. 23.
5 Kremer K., Glynn J. R., Lillebaek T., Niemann S., Kurepina N. E., Kreiswirth B. N., Bifani P. J., and van Soolingen D.. Definition of the Beijing/W lineage of Mycobacterium tuberculosison the basis of genetic markers // J. Clin. Microbiol. – 2004. – Vol. 42. – P. 4040–4049.
6 Suresh N., Arora J., Pant H., Rana T. and Singh U. B. Spoligotyping of Mycobacterium tuberculosi sDNA from Archival Ziehl–Neelsen -stained sputum smears // J. Microbiol. Meth. -2007. – Vol. 68(2). – P. 291-295.
7 Hawkey P.M., Smith E.G., Evans J.T., Monk P., Bryan G., Mohamed H.H., Bardhan M. and Pugh R.N.. Mycobacterial Interspersed Repetitive Unit Typing of Mycobacterium tuberculosis Compared to IS6110-Based Restriction Fragment Length Polymorphism Analysis for Investigation of Apparently Clustered Cases of Tuberculosis // J. Clin. Microbiol. – 2003. – Vol. 41. – P. 3514-3520.
8 Poynten M., Andresen D. N., Gottlieb T. Laboratory cross-contamination of Mycobacterium tuberculosis: an investigation and analysis of causes and consequences // Intern. Med. J. – 2002. – Vol. 32. – P. 511-512.
9 Allix-Béguec C., Supply P., and Fauville-Dufaux M. Utility of fast mycobacterial interspersed repetitive unit-variable number tandem repeat genotyping in clinical mycobacteriological analysis // Clin. Infect. Dis. – 2004. – Vol. 39. – P. 783–789.
10 Frothingham R., Meeker-O’Connell W.A. Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats // Microbiol. – 1998. – Vol. 144. – P. 1189-1196.
11 Mazars E., Lesjean S., Banuls A.L., Gilbert M., Vincent V., Gicquel B., Tibayrenc M., Locht C., and Supply P. High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology // Proc. Nat. Acad. Sci. USA. – 2001. – Vol. 98(4). – P. 1901–1906.
12 Supply P., Mazars E., Lesjean S., Vincent V., Gicquel B. and Locht C. Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome // Molecular Microbiology. – 2000. – 36(3). – Р. 762-771.
13 Allix-Béguec C., Supply P., and Fauville-Dufaux M. Utility of fast mycobacterial interspersed repetitive unit-variable number tandem repeat genotyping in clinical mycobacteriological analysis // Clin. Infect. Dis. – 2004. – Vol. 39. – P. 783–789.
14 Supply P., Allix C., Lesjean S., Cardoso-Oelemann M., Rusch-Gerdes, S., Willery E., Savine E., de Haas P., van Deutekom H., Roring S., Bifani P., Kurepina N., Kreiswirth B., Sola C., Rastogi N., Vatin V., Gutierrez M. C., Fauville M., Niemann S., Skuce R., Kremer K., Locht C., D. van Soolingen. Proposal for Standardization of Optimized Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing of Mycobacterium tuberculosis // J. Clin. Microbiol. – 2006. – Vol. 44. –P. 4498-4510.
15 Jiao W., Mokrousov I., Sun G., Guo Y., Vyazovaya A., Narvskaya O. and Shen A. Evaluation of New Variable-Number Tandem-Repeat Systems for Typing Mycobacterium tuberculosis with Beijing Genotype Isolates from Beijing, China // J. Clin. Microbiol. – 2008. – Vol. 46(3). – P. 1045–1049.
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Kozhamkulov, U., Аkhmetova А., Bismilda, V., Chingissova, L., Zholdybayeva Е., & Akilzhanova А. (2015). Evaluation of different genotyping schemes M.tuberculosis isolates from Kazakhstan by 24 MIRU-VNTR loci based on number of tandem repeats analysis. Experimental Biology, 62(3), 55–60. Retrieved from https://bb.kaznu.kz/index.php/biology/article/view/367
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MICROBIOLOGY
