Development of a hierarchical variable-number tandem repeat typing scheme for Mycobacterium tuberculosis in China.

Molecular typing based on variable-number tandem repeats (VNTR) analysis is a promising tool for identifying transmission of Mycobacterium tuberculosis. However, the currently proposed 15- and 24-locus VNTR sets (VNTR-15/24) only have limited resolution and contain too many loci for large-scale typi...

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Autores principales:	Tao Luo, Chongguang Yang, Yu Pang, Yanlin Zhao, Jian Mei, Qian Gao
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/de5cd13e849a43599b4c854dc728b7ed
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spelling	oai:doaj.org-article:de5cd13e849a43599b4c854dc728b7ed2021-11-18T08:31:06ZDevelopment of a hierarchical variable-number tandem repeat typing scheme for Mycobacterium tuberculosis in China.1932-620310.1371/journal.pone.0089726https://doaj.org/article/de5cd13e849a43599b4c854dc728b7ed2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24586989/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Molecular typing based on variable-number tandem repeats (VNTR) analysis is a promising tool for identifying transmission of Mycobacterium tuberculosis. However, the currently proposed 15- and 24-locus VNTR sets (VNTR-15/24) only have limited resolution and contain too many loci for large-scale typing in high burden countries. To develop an optimal typing scheme in China, we evaluated the resolution and robustness of 25 VNTR loci, using population-based collections of 1362 clinical isolates from six provinces across the country. The resolution of most loci showed considerable variations among regions. By calculating the average resolution of all possible combinations of 20 robust loci, we identified an optimal locus set with a minimum of 9 loci (VNTR-9) that could achieve comparable resolution of the standard VNTR-15. The VNTR-9 had consistently high resolutions in all six regions, and it was highly concordant with VNTR-15 for defining both clustered and unique genotypes. Furthermore, VNTR-9 was phylogenetically informative for classifying lineages/sublineages of M. tuberculosis. Three hypervariable loci (HV-3), VNTR 3232, VNTR 3820 and VNTR 4120, were proved important for further differentiating unrelated clustered strains based on VNTR-9. We propose the optimized VNTR-9 as first-line method and the HV-3 as second-line method for molecular typing of M. tuberculosis in China and surrounding countries. The development of hierarchical VNTR typing methods that can achieve high resolution with a small number of loci could be suitable for molecular epidemiology study in other high burden countries.Tao LuoChongguang YangYu PangYanlin ZhaoJian MeiQian GaoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 2, p e89726 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tao Luo Chongguang Yang Yu Pang Yanlin Zhao Jian Mei Qian Gao Development of a hierarchical variable-number tandem repeat typing scheme for Mycobacterium tuberculosis in China.
description	Molecular typing based on variable-number tandem repeats (VNTR) analysis is a promising tool for identifying transmission of Mycobacterium tuberculosis. However, the currently proposed 15- and 24-locus VNTR sets (VNTR-15/24) only have limited resolution and contain too many loci for large-scale typing in high burden countries. To develop an optimal typing scheme in China, we evaluated the resolution and robustness of 25 VNTR loci, using population-based collections of 1362 clinical isolates from six provinces across the country. The resolution of most loci showed considerable variations among regions. By calculating the average resolution of all possible combinations of 20 robust loci, we identified an optimal locus set with a minimum of 9 loci (VNTR-9) that could achieve comparable resolution of the standard VNTR-15. The VNTR-9 had consistently high resolutions in all six regions, and it was highly concordant with VNTR-15 for defining both clustered and unique genotypes. Furthermore, VNTR-9 was phylogenetically informative for classifying lineages/sublineages of M. tuberculosis. Three hypervariable loci (HV-3), VNTR 3232, VNTR 3820 and VNTR 4120, were proved important for further differentiating unrelated clustered strains based on VNTR-9. We propose the optimized VNTR-9 as first-line method and the HV-3 as second-line method for molecular typing of M. tuberculosis in China and surrounding countries. The development of hierarchical VNTR typing methods that can achieve high resolution with a small number of loci could be suitable for molecular epidemiology study in other high burden countries.
format	article
author	Tao Luo Chongguang Yang Yu Pang Yanlin Zhao Jian Mei Qian Gao
author_facet	Tao Luo Chongguang Yang Yu Pang Yanlin Zhao Jian Mei Qian Gao
author_sort	Tao Luo
title	Development of a hierarchical variable-number tandem repeat typing scheme for Mycobacterium tuberculosis in China.
title_short	Development of a hierarchical variable-number tandem repeat typing scheme for Mycobacterium tuberculosis in China.
title_full	Development of a hierarchical variable-number tandem repeat typing scheme for Mycobacterium tuberculosis in China.
title_fullStr	Development of a hierarchical variable-number tandem repeat typing scheme for Mycobacterium tuberculosis in China.
title_full_unstemmed	Development of a hierarchical variable-number tandem repeat typing scheme for Mycobacterium tuberculosis in China.
title_sort	development of a hierarchical variable-number tandem repeat typing scheme for mycobacterium tuberculosis in china.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/de5cd13e849a43599b4c854dc728b7ed
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Development of a hierarchical variable-number tandem repeat typing scheme for Mycobacterium tuberculosis in China.

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