Cargando…
Whole-genome sequencing-based epidemiological analysis of anti-tuberculosis drug resistance genes in Japan in 2007: Application of the Genome Research for Asian Tuberculosis (GReAT) database
We investigated the lineages of Mycobacterium tuberculosis (Mtb) isolates from the RYOKEN study in Japan in 2007 and the usefulness of genotypic drug susceptibility testing (DST) using the Genome Research for Asian Tuberculosis (GReAT) database. In total, 667 isolates were classified into lineage 1...
Autores principales: | , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731343/ https://www.ncbi.nlm.nih.gov/pubmed/31492902 http://dx.doi.org/10.1038/s41598-019-49219-5 |
_version_ | 1783449672593965056 |
---|---|
author | Takii, Takemasa Seki, Kouhei Wakabayashi, Yasutaka Morishige, Yuta Sekizuka, Tsuyoshi Yamashita, Akifumi Kato, Kengo Uchimura, Kazuhiro Ohkado, Akihiro Keicho, Naoto Mitarai, Satoshi Kuroda, Makoto Kato, Seiya |
author_facet | Takii, Takemasa Seki, Kouhei Wakabayashi, Yasutaka Morishige, Yuta Sekizuka, Tsuyoshi Yamashita, Akifumi Kato, Kengo Uchimura, Kazuhiro Ohkado, Akihiro Keicho, Naoto Mitarai, Satoshi Kuroda, Makoto Kato, Seiya |
author_sort | Takii, Takemasa |
collection | PubMed |
description | We investigated the lineages of Mycobacterium tuberculosis (Mtb) isolates from the RYOKEN study in Japan in 2007 and the usefulness of genotypic drug susceptibility testing (DST) using the Genome Research for Asian Tuberculosis (GReAT) database. In total, 667 isolates were classified into lineage 1 (4.6%), lineage 2 (0.8%), lineage 2/Beijing (72.1%), lineage 3 (0.5%), and lineage 4 (22.0%). The nationality, gender, and age groups associated with the isolates assigned to lineage 1 were significantly different from those associated with other lineages. In particular, isolates of lineage 1.2.1 (EAI2) formed sub-clusters and included a 2,316-bp deletion in the genome. The proportion of the isolates resistant to at least one anti-tuberculosis (TB) drug was 10.8%, as determined by either the genotypic or phenotypic method of DST. However, the sensitivities to isoniazid, streptomycin, and ethambutol determined by the genotypic method were low. Thus, unidentified mutations in the genome responsible for drug resistance were explored, revealing previously unreported mutations in the katG, gid, and embB genes. This is the first nationwide report of whole-genome analysis of TB in Japan. |
format | Online Article Text |
id | pubmed-6731343 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-67313432019-09-18 Whole-genome sequencing-based epidemiological analysis of anti-tuberculosis drug resistance genes in Japan in 2007: Application of the Genome Research for Asian Tuberculosis (GReAT) database Takii, Takemasa Seki, Kouhei Wakabayashi, Yasutaka Morishige, Yuta Sekizuka, Tsuyoshi Yamashita, Akifumi Kato, Kengo Uchimura, Kazuhiro Ohkado, Akihiro Keicho, Naoto Mitarai, Satoshi Kuroda, Makoto Kato, Seiya Sci Rep Article We investigated the lineages of Mycobacterium tuberculosis (Mtb) isolates from the RYOKEN study in Japan in 2007 and the usefulness of genotypic drug susceptibility testing (DST) using the Genome Research for Asian Tuberculosis (GReAT) database. In total, 667 isolates were classified into lineage 1 (4.6%), lineage 2 (0.8%), lineage 2/Beijing (72.1%), lineage 3 (0.5%), and lineage 4 (22.0%). The nationality, gender, and age groups associated with the isolates assigned to lineage 1 were significantly different from those associated with other lineages. In particular, isolates of lineage 1.2.1 (EAI2) formed sub-clusters and included a 2,316-bp deletion in the genome. The proportion of the isolates resistant to at least one anti-tuberculosis (TB) drug was 10.8%, as determined by either the genotypic or phenotypic method of DST. However, the sensitivities to isoniazid, streptomycin, and ethambutol determined by the genotypic method were low. Thus, unidentified mutations in the genome responsible for drug resistance were explored, revealing previously unreported mutations in the katG, gid, and embB genes. This is the first nationwide report of whole-genome analysis of TB in Japan. Nature Publishing Group UK 2019-09-06 /pmc/articles/PMC6731343/ /pubmed/31492902 http://dx.doi.org/10.1038/s41598-019-49219-5 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Takii, Takemasa Seki, Kouhei Wakabayashi, Yasutaka Morishige, Yuta Sekizuka, Tsuyoshi Yamashita, Akifumi Kato, Kengo Uchimura, Kazuhiro Ohkado, Akihiro Keicho, Naoto Mitarai, Satoshi Kuroda, Makoto Kato, Seiya Whole-genome sequencing-based epidemiological analysis of anti-tuberculosis drug resistance genes in Japan in 2007: Application of the Genome Research for Asian Tuberculosis (GReAT) database |
title | Whole-genome sequencing-based epidemiological analysis of anti-tuberculosis drug resistance genes in Japan in 2007: Application of the Genome Research for Asian Tuberculosis (GReAT) database |
title_full | Whole-genome sequencing-based epidemiological analysis of anti-tuberculosis drug resistance genes in Japan in 2007: Application of the Genome Research for Asian Tuberculosis (GReAT) database |
title_fullStr | Whole-genome sequencing-based epidemiological analysis of anti-tuberculosis drug resistance genes in Japan in 2007: Application of the Genome Research for Asian Tuberculosis (GReAT) database |
title_full_unstemmed | Whole-genome sequencing-based epidemiological analysis of anti-tuberculosis drug resistance genes in Japan in 2007: Application of the Genome Research for Asian Tuberculosis (GReAT) database |
title_short | Whole-genome sequencing-based epidemiological analysis of anti-tuberculosis drug resistance genes in Japan in 2007: Application of the Genome Research for Asian Tuberculosis (GReAT) database |
title_sort | whole-genome sequencing-based epidemiological analysis of anti-tuberculosis drug resistance genes in japan in 2007: application of the genome research for asian tuberculosis (great) database |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731343/ https://www.ncbi.nlm.nih.gov/pubmed/31492902 http://dx.doi.org/10.1038/s41598-019-49219-5 |
work_keys_str_mv | AT takiitakemasa wholegenomesequencingbasedepidemiologicalanalysisofantituberculosisdrugresistancegenesinjapanin2007applicationofthegenomeresearchforasiantuberculosisgreatdatabase AT sekikouhei wholegenomesequencingbasedepidemiologicalanalysisofantituberculosisdrugresistancegenesinjapanin2007applicationofthegenomeresearchforasiantuberculosisgreatdatabase AT wakabayashiyasutaka wholegenomesequencingbasedepidemiologicalanalysisofantituberculosisdrugresistancegenesinjapanin2007applicationofthegenomeresearchforasiantuberculosisgreatdatabase AT morishigeyuta wholegenomesequencingbasedepidemiologicalanalysisofantituberculosisdrugresistancegenesinjapanin2007applicationofthegenomeresearchforasiantuberculosisgreatdatabase AT sekizukatsuyoshi wholegenomesequencingbasedepidemiologicalanalysisofantituberculosisdrugresistancegenesinjapanin2007applicationofthegenomeresearchforasiantuberculosisgreatdatabase AT yamashitaakifumi wholegenomesequencingbasedepidemiologicalanalysisofantituberculosisdrugresistancegenesinjapanin2007applicationofthegenomeresearchforasiantuberculosisgreatdatabase AT katokengo wholegenomesequencingbasedepidemiologicalanalysisofantituberculosisdrugresistancegenesinjapanin2007applicationofthegenomeresearchforasiantuberculosisgreatdatabase AT uchimurakazuhiro wholegenomesequencingbasedepidemiologicalanalysisofantituberculosisdrugresistancegenesinjapanin2007applicationofthegenomeresearchforasiantuberculosisgreatdatabase AT ohkadoakihiro wholegenomesequencingbasedepidemiologicalanalysisofantituberculosisdrugresistancegenesinjapanin2007applicationofthegenomeresearchforasiantuberculosisgreatdatabase AT keichonaoto wholegenomesequencingbasedepidemiologicalanalysisofantituberculosisdrugresistancegenesinjapanin2007applicationofthegenomeresearchforasiantuberculosisgreatdatabase AT mitaraisatoshi wholegenomesequencingbasedepidemiologicalanalysisofantituberculosisdrugresistancegenesinjapanin2007applicationofthegenomeresearchforasiantuberculosisgreatdatabase AT kurodamakoto wholegenomesequencingbasedepidemiologicalanalysisofantituberculosisdrugresistancegenesinjapanin2007applicationofthegenomeresearchforasiantuberculosisgreatdatabase AT katoseiya wholegenomesequencingbasedepidemiologicalanalysisofantituberculosisdrugresistancegenesinjapanin2007applicationofthegenomeresearchforasiantuberculosisgreatdatabase |