Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor

Handle URI:
http://hdl.handle.net/10754/621074
Title:
Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor
Authors:
Refregier, Guislaine; Abadia, Edgar; Matsumoto, Tomoshige; Ano, Hiromi; Takashima, Tetsuya; Tsuyuguchi, Izuo; Aktas, Elif; Cömert, Füsun; Gomgnimbou, Michel Kireopori; Panaiotov, Stefan; Phelan, Jody; Coll, Francesc; Mcnerney, Ruth; Pain, Arnab ( 0000-0002-1755-2819 ) ; Clark, Taane G.; Sola, Christophe
Abstract:
Two geographically distant M. tuberculosis sublineages, Tur from Turkey and T3-Osaka from Japan, exhibit partially identical genotypic signatures (identical 12-loci MIRU-VNTR profiles, distinct spoligotyping patterns). We investigated T3-Osaka and Tur sublineages characteristics and potential genetic relatedness, first using MIRU-VNTR locus analysis on 21 and 25 samples of each sublineage respectively, and second comparing Whole Genome Sequences of 8 new samples to public data from 45 samples uncovering human tuberculosis diversity. We then tried to date their Most Recent Common Ancestor (MRCA) using three calibrations of SNP accumulation rate (long-term = 0.03 SNP/genome/year, derived from a tuberculosis ancestor of around 70,000 years old; intermediate = 0.2 SNP/genome/year derived from a Peruvian mummy; short-term = 0.5 SNP/genome/year). To disentangle between these scenarios, we confronted the corresponding divergence times with major human history events and knowledge on human genetic divergence. We identified relatively high intrasublineage diversity for both T3-Osaka and Tur. We definitively proved their monophyly; the corresponding super-sublineage (referred to as “T3-Osa-Tur”) shares a common ancestor with T3-Ethiopia and Ural sublineages but is only remotely related to other Euro-American sublineages such as X, LAM, Haarlem and S. The evolutionary scenario based on long-term evolution rate being valid until T3-Osa-Tur MRCA was not supported by Japanese fossil data. The evolutionary scenario relying on short-term evolution rate since T3-Osa-Tur MRCA was contradicted by human history and potential traces of past epidemics. T3-Osaka and Tur sublineages were found likely to have diverged between 800 y and 2000 years ago, potentially at the time of Mongol Empire. Altogether, this study definitively proves a strong genetic link between Turkish and Japanese tuberculosis. It provides a first hypothesis for calibrating TB Euro-American lineage molecular clock; additional studies are needed to reliably date events corresponding to intermediate depths in tuberculosis phylogeny.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Pathogen Genomics Laboratory
Citation:
Refrégier G, Abadia E, Matsumoto T, Ano H, Takashima T, et al. (2016) Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor. Infection, Genetics and Evolution 45: 461–473. Available: http://dx.doi.org/10.1016/j.meegid.2016.10.009.
Publisher:
Elsevier BV
Journal:
Infection, Genetics and Evolution
Issue Date:
14-Oct-2016
DOI:
10.1016/j.meegid.2016.10.009
Type:
Article
ISSN:
1567-1348
Sponsors:
This work was initiated in 2005 in the Institut Pasteur of Guadeloupe, and Dr. Nalin Rastogi and Dr. Riza Durmaz are acknowledged for material support, stimulating discussions, and/or for having initiated long-term collaborative studies on MTBC DNA from Turkey. During the 2007–2008 period, T. Dos Vultos, J. Rauzier and B. Gicquel through the extensive 3R MTBC gene diversity study, provided an important advance to the T3-Osa-Tur hypothesis by providing confirmatory preliminary results. Technical support was provided by the Luminex Corp. (Austin, TX) for SNP genotyping, and by King Abdullah University of Science and Technology (KAUST) for Whole Genome Sequencing. GR and CS acknowledge recurrent support from CNRS-Univ. Paris-Sud.
Additional Links:
http://www.sciencedirect.com/science/article/pii/S156713481630418X
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorRefregier, Guislaineen
dc.contributor.authorAbadia, Edgaren
dc.contributor.authorMatsumoto, Tomoshigeen
dc.contributor.authorAno, Hiromien
dc.contributor.authorTakashima, Tetsuyaen
dc.contributor.authorTsuyuguchi, Izuoen
dc.contributor.authorAktas, Elifen
dc.contributor.authorCömert, Füsunen
dc.contributor.authorGomgnimbou, Michel Kireoporien
dc.contributor.authorPanaiotov, Stefanen
dc.contributor.authorPhelan, Jodyen
dc.contributor.authorColl, Francescen
dc.contributor.authorMcnerney, Ruthen
dc.contributor.authorPain, Arnaben
dc.contributor.authorClark, Taane G.en
dc.contributor.authorSola, Christopheen
dc.date.accessioned2016-10-19T07:57:09Z-
dc.date.available2016-10-19T07:57:09Z-
dc.date.issued2016-10-14en
dc.identifier.citationRefrégier G, Abadia E, Matsumoto T, Ano H, Takashima T, et al. (2016) Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor. Infection, Genetics and Evolution 45: 461–473. Available: http://dx.doi.org/10.1016/j.meegid.2016.10.009.en
dc.identifier.issn1567-1348en
dc.identifier.doi10.1016/j.meegid.2016.10.009en
dc.identifier.urihttp://hdl.handle.net/10754/621074-
dc.description.abstractTwo geographically distant M. tuberculosis sublineages, Tur from Turkey and T3-Osaka from Japan, exhibit partially identical genotypic signatures (identical 12-loci MIRU-VNTR profiles, distinct spoligotyping patterns). We investigated T3-Osaka and Tur sublineages characteristics and potential genetic relatedness, first using MIRU-VNTR locus analysis on 21 and 25 samples of each sublineage respectively, and second comparing Whole Genome Sequences of 8 new samples to public data from 45 samples uncovering human tuberculosis diversity. We then tried to date their Most Recent Common Ancestor (MRCA) using three calibrations of SNP accumulation rate (long-term = 0.03 SNP/genome/year, derived from a tuberculosis ancestor of around 70,000 years old; intermediate = 0.2 SNP/genome/year derived from a Peruvian mummy; short-term = 0.5 SNP/genome/year). To disentangle between these scenarios, we confronted the corresponding divergence times with major human history events and knowledge on human genetic divergence. We identified relatively high intrasublineage diversity for both T3-Osaka and Tur. We definitively proved their monophyly; the corresponding super-sublineage (referred to as “T3-Osa-Tur”) shares a common ancestor with T3-Ethiopia and Ural sublineages but is only remotely related to other Euro-American sublineages such as X, LAM, Haarlem and S. The evolutionary scenario based on long-term evolution rate being valid until T3-Osa-Tur MRCA was not supported by Japanese fossil data. The evolutionary scenario relying on short-term evolution rate since T3-Osa-Tur MRCA was contradicted by human history and potential traces of past epidemics. T3-Osaka and Tur sublineages were found likely to have diverged between 800 y and 2000 years ago, potentially at the time of Mongol Empire. Altogether, this study definitively proves a strong genetic link between Turkish and Japanese tuberculosis. It provides a first hypothesis for calibrating TB Euro-American lineage molecular clock; additional studies are needed to reliably date events corresponding to intermediate depths in tuberculosis phylogeny.en
dc.description.sponsorshipThis work was initiated in 2005 in the Institut Pasteur of Guadeloupe, and Dr. Nalin Rastogi and Dr. Riza Durmaz are acknowledged for material support, stimulating discussions, and/or for having initiated long-term collaborative studies on MTBC DNA from Turkey. During the 2007–2008 period, T. Dos Vultos, J. Rauzier and B. Gicquel through the extensive 3R MTBC gene diversity study, provided an important advance to the T3-Osa-Tur hypothesis by providing confirmatory preliminary results. Technical support was provided by the Luminex Corp. (Austin, TX) for SNP genotyping, and by King Abdullah University of Science and Technology (KAUST) for Whole Genome Sequencing. GR and CS acknowledge recurrent support from CNRS-Univ. Paris-Sud.en
dc.publisherElsevier BVen
dc.relation.urlhttp://www.sciencedirect.com/science/article/pii/S156713481630418Xen
dc.rights© 2016. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.subjectPhylogeographyen
dc.subjectMolecular clocken
dc.subjectPhylogeneticsen
dc.subjectPathogen evolutionen
dc.titleTurkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestoren
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentPathogen Genomics Laboratoryen
dc.identifier.journalInfection, Genetics and Evolutionen
dc.eprint.versionPost-printen
dc.contributor.institutionInstitute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, Franceen
dc.contributor.institutionInstituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuelaen
dc.contributor.institutionDepartment of Clinical Research and Development, Osaka Prefectural Hospital Organization, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases, Habikino-city, Japanen
dc.contributor.institutionŞişli Etfal Research and Training Hopital, Istanbul, Turkeyen
dc.contributor.institutionNational Center of Parasitic and Infectious Diseases, Sofia, Bulgariaen
dc.contributor.institutionFaculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UKen
dc.contributor.institutionInfection and Immunity Unit, UCT Lung Institute, University of Cape Town, Old Main Building, Groote Schuur Hospital, Cape Town,South Africaen
kaust.authorPain, Arnaben
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