Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates

Abstract Tuberculosis (TB) is a severe infectious disease worldwide. Genetic variation of the causative agent, Mycobacterium tuberculosis (MTB), determines the outcomes of infection and anti-TB treatment. Until recently, there has been no effective and convenient way for classifying clinical isolate...

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Autores principales:	Horng-Yunn Dou, Chien-Hsing Lin, Yih-Yuan Chen, Shiu-Ju Yang, Jia-Ru Chang, Keh-Ming Wu, Ying-Tsong Chen, Pei-Ju Chin, Yen-Ming Liu, Ih-Jen Su, Shih-Feng Tsai
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fe2572729ff54903bb4f7b77362c096c
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spelling	oai:doaj.org-article:fe2572729ff54903bb4f7b77362c096c2021-12-02T15:05:44ZLineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates10.1038/s41598-017-01580-z2045-2322https://doaj.org/article/fe2572729ff54903bb4f7b77362c096c2017-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-01580-zhttps://doaj.org/toc/2045-2322Abstract Tuberculosis (TB) is a severe infectious disease worldwide. Genetic variation of the causative agent, Mycobacterium tuberculosis (MTB), determines the outcomes of infection and anti-TB treatment. Until recently, there has been no effective and convenient way for classifying clinical isolates based on the DNA sequences of the divergent lineages of MTB infecting human populations. Here, we identified single nucleotide polymorphisms (SNPs) of six representative strains from Taiwan by whole-genome sequencing and comparing the results to the sequence of the H37Rv reference strain. One hundred and ten SNPs, each unique to one of the six strains, were used to genotype 150 additional isolates by applying DNA mass spectrometry. Lineage-specific SNPs were identified that could distinguish the major lineages of the clinical isolates. A subset including 32 SNPs was found to be sufficient to type four major groups of MTB isolates in Taiwan (ancient Beijing, modern Beijing, East African–Indian, and Latin-American Mediterranean). However, there was high genetic homozygosity within the Euro-American lineage, which included spoligotype-classified Haarlem and T strains. By whole-genome sequencing of 12 representative Euro-American isolates, we identified multiple subtype-specific SNPs which allowed us to distinguish two major branches within the Euro-American lineage.Horng-Yunn DouChien-Hsing LinYih-Yuan ChenShiu-Ju YangJia-Ru ChangKeh-Ming WuYing-Tsong ChenPei-Ju ChinYen-Ming LiuIh-Jen SuShih-Feng TsaiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-9 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Horng-Yunn Dou Chien-Hsing Lin Yih-Yuan Chen Shiu-Ju Yang Jia-Ru Chang Keh-Ming Wu Ying-Tsong Chen Pei-Ju Chin Yen-Ming Liu Ih-Jen Su Shih-Feng Tsai Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates
description	Abstract Tuberculosis (TB) is a severe infectious disease worldwide. Genetic variation of the causative agent, Mycobacterium tuberculosis (MTB), determines the outcomes of infection and anti-TB treatment. Until recently, there has been no effective and convenient way for classifying clinical isolates based on the DNA sequences of the divergent lineages of MTB infecting human populations. Here, we identified single nucleotide polymorphisms (SNPs) of six representative strains from Taiwan by whole-genome sequencing and comparing the results to the sequence of the H37Rv reference strain. One hundred and ten SNPs, each unique to one of the six strains, were used to genotype 150 additional isolates by applying DNA mass spectrometry. Lineage-specific SNPs were identified that could distinguish the major lineages of the clinical isolates. A subset including 32 SNPs was found to be sufficient to type four major groups of MTB isolates in Taiwan (ancient Beijing, modern Beijing, East African–Indian, and Latin-American Mediterranean). However, there was high genetic homozygosity within the Euro-American lineage, which included spoligotype-classified Haarlem and T strains. By whole-genome sequencing of 12 representative Euro-American isolates, we identified multiple subtype-specific SNPs which allowed us to distinguish two major branches within the Euro-American lineage.
format	article
author	Horng-Yunn Dou Chien-Hsing Lin Yih-Yuan Chen Shiu-Ju Yang Jia-Ru Chang Keh-Ming Wu Ying-Tsong Chen Pei-Ju Chin Yen-Ming Liu Ih-Jen Su Shih-Feng Tsai
author_facet	Horng-Yunn Dou Chien-Hsing Lin Yih-Yuan Chen Shiu-Ju Yang Jia-Ru Chang Keh-Ming Wu Ying-Tsong Chen Pei-Ju Chin Yen-Ming Liu Ih-Jen Su Shih-Feng Tsai
author_sort	Horng-Yunn Dou
title	Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates
title_short	Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates
title_full	Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates
title_fullStr	Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates
title_full_unstemmed	Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates
title_sort	lineage-specific snps for genotyping of mycobacterium tuberculosis clinical isolates
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/fe2572729ff54903bb4f7b77362c096c
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Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates

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