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: Yann Blouin, Yolande Hauck, Charles Soler, Michel Fabre, Rithy Vong, Céline Dehan, Géraldine Cazajous, Pierre-Laurent Massoure, Philippe Kraemer, Akinbowale Jenkins, Eric Garnotel, Christine Pourcel, Gilles Vergnaud
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spelling oai:doaj.org-article:8fe6911c62ca4abeaefbf6dee99da6922021-11-18T08:03:27ZSignificance of the identification in the Horn of Africa of an exceptionally deep branching Mycobacterium tuberculosis clade.1932-620310.1371/journal.pone.0052841https://doaj.org/article/8fe6911c62ca4abeaefbf6dee99da6922012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23300794/?tool=EBIhttps://doaj.org/toc/1932-6203Molecular 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.Yann BlouinYolande HauckCharles SolerMichel FabreRithy VongCéline DehanGéraldine CazajousPierre-Laurent MassourePhilippe KraemerAkinbowale JenkinsEric GarnotelChristine PourcelGilles VergnaudPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 12, p e52841 (2012)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Yann Blouin
Yolande Hauck
Charles Soler
Michel Fabre
Rithy Vong
Céline Dehan
Géraldine Cazajous
Pierre-Laurent Massoure
Philippe Kraemer
Akinbowale Jenkins
Eric Garnotel
Christine Pourcel
Gilles Vergnaud
Significance of the identification in the Horn of Africa of an exceptionally deep branching Mycobacterium tuberculosis clade.
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.
format article
author Yann Blouin
Yolande Hauck
Charles Soler
Michel Fabre
Rithy Vong
Céline Dehan
Géraldine Cazajous
Pierre-Laurent Massoure
Philippe Kraemer
Akinbowale Jenkins
Eric Garnotel
Christine Pourcel
Gilles Vergnaud
author_facet Yann Blouin
Yolande Hauck
Charles Soler
Michel Fabre
Rithy Vong
Céline Dehan
Géraldine Cazajous
Pierre-Laurent Massoure
Philippe Kraemer
Akinbowale Jenkins
Eric Garnotel
Christine Pourcel
Gilles Vergnaud
author_sort Yann Blouin
title 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_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_sort significance of the identification in the horn of africa of an exceptionally deep branching mycobacterium tuberculosis clade.
publisher Public Library of Science (PLoS)
publishDate 2012
url https://doaj.org/article/8fe6911c62ca4abeaefbf6dee99da692
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