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Significance of the Identification in the Horn of Africa of an Exceptionally Deep Branching Mycobacterium tuberculosis Clade

Molecular and phylogeographic studies have led to the definition within the Mycobacterium tuberculosis complex (MTBC) of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and...

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Autores principales: Blouin, Yann, Hauck, Yolande, Soler, Charles, Fabre, Michel, Vong, Rithy, Dehan, Céline, Cazajous, Géraldine, Massoure, Pierre-Laurent, Kraemer, Philippe, Jenkins, Akinbowale, Garnotel, Eric, Pourcel, Christine, Vergnaud, Gilles
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531362/
https://www.ncbi.nlm.nih.gov/pubmed/23300794
http://dx.doi.org/10.1371/journal.pone.0052841
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author Blouin, Yann
Hauck, Yolande
Soler, Charles
Fabre, Michel
Vong, Rithy
Dehan, Céline
Cazajous, Géraldine
Massoure, Pierre-Laurent
Kraemer, Philippe
Jenkins, Akinbowale
Garnotel, Eric
Pourcel, Christine
Vergnaud, Gilles
author_facet Blouin, Yann
Hauck, Yolande
Soler, Charles
Fabre, Michel
Vong, Rithy
Dehan, Céline
Cazajous, Géraldine
Massoure, Pierre-Laurent
Kraemer, Philippe
Jenkins, Akinbowale
Garnotel, Eric
Pourcel, Christine
Vergnaud, Gilles
author_sort Blouin, Yann
collection PubMed
description Molecular and phylogeographic studies have led to the definition within the Mycobacterium tuberculosis complex (MTBC) of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and to have spread worldwide with human migrations. Under this assumption, there is a possibility that unknown deep branching lineages are present in this region. We genotyped by spoligotyping and multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) 435 MTBC isolates recovered from patients. Four hundred and eleven isolates were collected in the Republic of Djibouti over a 12 year period, with the other 24 isolates originating from neighbouring countries. All major M. tuberculosis lineages were identified, with only two M. africanum and one M. bovis isolates. Upon comparison with typing data of worldwide origin we observed that several isolates showed clustering characteristics compatible with new deep branching. Whole genome sequencing (WGS) of seven isolates and comparison with available WGS data from 38 genomes distributed in the different lineages confirms the identification of ancestral nodes for several clades and most importantly of one new lineage, here referred to as lineage 7. Investigation of specific deletions confirms the novelty of this lineage, and analysis of its precise phylogenetic position indicates that the other three superlineages constituting the MTBC emerged independently but within a relatively short timeframe from the Horn of Africa. The availability of such strains compared to the predominant lineages and sharing very ancient ancestry will open new avenues for identifying some of the genetic factors responsible for the success of the modern lineages. Additional deep branching lineages may be readily and efficiently identified by large-scale MLVA screening of isolates from sub-Saharan African countries followed by WGS analysis of a few selected isolates.
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spelling pubmed-35313622013-01-08 Significance of the Identification in the Horn of Africa of an Exceptionally Deep Branching Mycobacterium tuberculosis Clade Blouin, Yann Hauck, Yolande Soler, Charles Fabre, Michel Vong, Rithy Dehan, Céline Cazajous, Géraldine Massoure, Pierre-Laurent Kraemer, Philippe Jenkins, Akinbowale Garnotel, Eric Pourcel, Christine Vergnaud, Gilles PLoS One Research Article Molecular and phylogeographic studies have led to the definition within the Mycobacterium tuberculosis complex (MTBC) of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and to have spread worldwide with human migrations. Under this assumption, there is a possibility that unknown deep branching lineages are present in this region. We genotyped by spoligotyping and multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) 435 MTBC isolates recovered from patients. Four hundred and eleven isolates were collected in the Republic of Djibouti over a 12 year period, with the other 24 isolates originating from neighbouring countries. All major M. tuberculosis lineages were identified, with only two M. africanum and one M. bovis isolates. Upon comparison with typing data of worldwide origin we observed that several isolates showed clustering characteristics compatible with new deep branching. Whole genome sequencing (WGS) of seven isolates and comparison with available WGS data from 38 genomes distributed in the different lineages confirms the identification of ancestral nodes for several clades and most importantly of one new lineage, here referred to as lineage 7. Investigation of specific deletions confirms the novelty of this lineage, and analysis of its precise phylogenetic position indicates that the other three superlineages constituting the MTBC emerged independently but within a relatively short timeframe from the Horn of Africa. The availability of such strains compared to the predominant lineages and sharing very ancient ancestry will open new avenues for identifying some of the genetic factors responsible for the success of the modern lineages. Additional deep branching lineages may be readily and efficiently identified by large-scale MLVA screening of isolates from sub-Saharan African countries followed by WGS analysis of a few selected isolates. Public Library of Science 2012-12-27 /pmc/articles/PMC3531362/ /pubmed/23300794 http://dx.doi.org/10.1371/journal.pone.0052841 Text en © 2012 Blouin et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Blouin, Yann
Hauck, Yolande
Soler, Charles
Fabre, Michel
Vong, Rithy
Dehan, Céline
Cazajous, Géraldine
Massoure, Pierre-Laurent
Kraemer, Philippe
Jenkins, Akinbowale
Garnotel, Eric
Pourcel, Christine
Vergnaud, Gilles
Significance of the Identification in the Horn of Africa of an Exceptionally Deep Branching Mycobacterium tuberculosis Clade
title Significance of the Identification in the Horn of Africa of an Exceptionally Deep Branching Mycobacterium tuberculosis Clade
title_full Significance of the Identification in the Horn of Africa of an Exceptionally Deep Branching Mycobacterium tuberculosis Clade
title_fullStr Significance of the Identification in the Horn of Africa of an Exceptionally Deep Branching Mycobacterium tuberculosis Clade
title_full_unstemmed Significance of the Identification in the Horn of Africa of an Exceptionally Deep Branching Mycobacterium tuberculosis Clade
title_short Significance of the Identification in the Horn of Africa of an Exceptionally Deep Branching Mycobacterium tuberculosis Clade
title_sort significance of the identification in the horn of africa of an exceptionally deep branching mycobacterium tuberculosis clade
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531362/
https://www.ncbi.nlm.nih.gov/pubmed/23300794
http://dx.doi.org/10.1371/journal.pone.0052841
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