Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor

Autor: Christophe Sola, Elif Aktaş, Michel K. Gomgnimbou, Füsun Cömert, Francesc Coll, Arnab Pain, Stefan Panaiotov, Hiromi Ano, Guislaine Refrégier, Ruth McNerney, Taane G. Clark, Tomoshige Matsumoto, Izuo Tsuyuguchi, Tetsuya Takashima, Edgar Abadia, Jody Phelan
Přispěvatelé: Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Instituto Venezolano de Investigaciones Cientificas ( IVIC ), Department of Clinical Research and Development, Osaka Prefectural Hospital Organization, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases, Habikino-city, Şişli Etfal Research and Training Hopital, Faculty of Medicine, Bülent Ecevit University, Zonguldak, National Center of Parasitic and Infectious Diseases, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine ( LSHTM ), Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, King Abdullah University of Science and Technology ( KAUST ), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Instituto Venezolano de Investigaciones Cientificas (IVIC), London School of Hygiene and Tropical Medicine (LSHTM), King Abdullah University of Science and Technology (KAUST), Zonguldak Bülent Ecevit Üniversitesi
Jazyk: angličtina
Rok vydání: 2016
Předmět:
Zdroj: Infection, Genetics and Evolution
Infection, Genetics and Evolution, Elsevier, 2016, 45, pp.461-473. 〈10.1016/j.meegid.2016.10.009〉
Infection, Genetics and Evolution, 2016, 45, pp.461-473. ⟨10.1016/j.meegid.2016.10.009⟩
Infection, Genetics and Evolution, Elsevier, 2016, 45, pp.461-473. ⟨10.1016/j.meegid.2016.10.009⟩
ISSN: 1567-1348
1567-7257
Popis: 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. © 2016 Elsevier B.V.
Research Councils UK King Abdullah University of Science and Technology
This study was financed by UMR9198, CEA-CNRS-UPS, Institut de Biologie Intégrative de la Cellule, Gif-sur-Yvette, France . GR and CS hold respectively an assistant professorship and a full professorship position at University Paris-Sud. No competitive interest is to be declared. JP is supported by a BBSRC UK PhD studentship. TGC is funded by the Medical Research Council UK (Grant no. MR/K000551/1 , MR/M01360X/1 , MR/N010469/1 ).
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.
Databáze: OpenAIRE
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