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Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage

By gathering 680 publicly available Sequence Read Archives from isolates of Mycobacterium tuberculosis complex (MTBC) including 190 belonging to the lineage 2 Beijing, and using an in-house bioinformatical pipeline, the TB-Annotator, that analyses more than 50 000 characters, we describe herein a ne...

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Autores principales: Guyeux, Christophe, Senelle, Gaetan, Refrégier, Guislaine, Bretelle-Establet, Florence, Cambau, Emmanuelle, Sola, Christophe
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cambridge University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8931808/
https://www.ncbi.nlm.nih.gov/pubmed/35042579
http://dx.doi.org/10.1017/S0950268822000048
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author Guyeux, Christophe
Senelle, Gaetan
Refrégier, Guislaine
Bretelle-Establet, Florence
Cambau, Emmanuelle
Sola, Christophe
author_facet Guyeux, Christophe
Senelle, Gaetan
Refrégier, Guislaine
Bretelle-Establet, Florence
Cambau, Emmanuelle
Sola, Christophe
author_sort Guyeux, Christophe
collection PubMed
description By gathering 680 publicly available Sequence Read Archives from isolates of Mycobacterium tuberculosis complex (MTBC) including 190 belonging to the lineage 2 Beijing, and using an in-house bioinformatical pipeline, the TB-Annotator, that analyses more than 50 000 characters, we describe herein a new L2 sublineage from 20 isolates found in the Tochigi province, (Japan), that we designate as asia ancestral 5 (AAnc5). These isolates harbour a number of specific criteria (42 SNPs) and their intra-cluster pairwise distance suggests historical and not epidemiological transmission. These isolates harbour a mutation in rpoC, and do not fulfil, any of the modern Beijing lineage criteria, nor any of the other ancestral Beijing lineages described so far. Asia ancestral 5 isolates do not possess mutT2 58 and ogt 12 characteristics of modern Beijing, but possess ancestral Beijing SNPs characteristics. By looking into the literature, we found a reference isolate ID381, described in Kobe and Osaka belonging to the ‘G3’ group, sharing 36 out of the 42 specific SNPs found in AAnc5. We also assessed the intermediate position of the asia ancestral 4 (AAnc4) sublineage recently described in Thailand and propose an improved classification of the L2 that now includes AAnc4 and AAnc5. By increasing the recruitment into TB-Annotator to around 3000 genomes (including 642 belonging to L2), we confirmed our results and discovered additional historical ancestral L2 branches that remain to be investigated in more detail. We also present, in addition, some anthropological and historical data from Chinese and Japan history of tuberculosis, as well as from Korea, that could support our results on L2 evolution. This study shows that the reconstruction of the early history of tuberculosis in Asia is likely to reveal complex patterns since its emergence.
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spelling pubmed-89318082022-03-31 Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage Guyeux, Christophe Senelle, Gaetan Refrégier, Guislaine Bretelle-Establet, Florence Cambau, Emmanuelle Sola, Christophe Epidemiol Infect Original Paper By gathering 680 publicly available Sequence Read Archives from isolates of Mycobacterium tuberculosis complex (MTBC) including 190 belonging to the lineage 2 Beijing, and using an in-house bioinformatical pipeline, the TB-Annotator, that analyses more than 50 000 characters, we describe herein a new L2 sublineage from 20 isolates found in the Tochigi province, (Japan), that we designate as asia ancestral 5 (AAnc5). These isolates harbour a number of specific criteria (42 SNPs) and their intra-cluster pairwise distance suggests historical and not epidemiological transmission. These isolates harbour a mutation in rpoC, and do not fulfil, any of the modern Beijing lineage criteria, nor any of the other ancestral Beijing lineages described so far. Asia ancestral 5 isolates do not possess mutT2 58 and ogt 12 characteristics of modern Beijing, but possess ancestral Beijing SNPs characteristics. By looking into the literature, we found a reference isolate ID381, described in Kobe and Osaka belonging to the ‘G3’ group, sharing 36 out of the 42 specific SNPs found in AAnc5. We also assessed the intermediate position of the asia ancestral 4 (AAnc4) sublineage recently described in Thailand and propose an improved classification of the L2 that now includes AAnc4 and AAnc5. By increasing the recruitment into TB-Annotator to around 3000 genomes (including 642 belonging to L2), we confirmed our results and discovered additional historical ancestral L2 branches that remain to be investigated in more detail. We also present, in addition, some anthropological and historical data from Chinese and Japan history of tuberculosis, as well as from Korea, that could support our results on L2 evolution. This study shows that the reconstruction of the early history of tuberculosis in Asia is likely to reveal complex patterns since its emergence. Cambridge University Press 2022-01-19 /pmc/articles/PMC8931808/ /pubmed/35042579 http://dx.doi.org/10.1017/S0950268822000048 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited.
spellingShingle Original Paper
Guyeux, Christophe
Senelle, Gaetan
Refrégier, Guislaine
Bretelle-Establet, Florence
Cambau, Emmanuelle
Sola, Christophe
Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage
title Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage
title_full Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage
title_fullStr Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage
title_full_unstemmed Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage
title_short Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage
title_sort connection between two historical tuberculosis outbreak sites in japan, honshu, by a new ancestral mycobacterium tuberculosis l2 sublineage
topic Original Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8931808/
https://www.ncbi.nlm.nih.gov/pubmed/35042579
http://dx.doi.org/10.1017/S0950268822000048
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