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Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations

2022-11-11Journal article Open access
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dc.contributor.authorThorpe, Harry A
dc.contributor.authorTourrette, Elise
dc.contributor.authorYahara, Koji
dc.contributor.authorVale, Filipa F.
dc.contributor.authorLiu, Siqi
dc.contributor.authorOleastro, Mónica
dc.contributor.authorAlarcon, Teresa
dc.contributor.authorPerets, Tsachi-Tsadok
dc.contributor.authorLatifi-Navid, Saeid
dc.contributor.authorYamaoka, Yoshio
dc.contributor.authorMartinez-Gonzalez, Beatriz
dc.contributor.authorKarayiannis, Ioannis
dc.contributor.authorKaramitros, Timokratis
dc.contributor.authorSgouras, Dionyssios N.
dc.contributor.authorElamin, Wael
dc.contributor.authorPascoe, Ben
dc.contributor.authorSheppard, Samuel K.
dc.contributor.authorRonkainen, Jukka
dc.contributor.authorAro, Pertti
dc.contributor.authorEngstrand, Lars
dc.contributor.authorAgreus, Lars
dc.contributor.authorSuerbaum, Sebastian
dc.contributor.authorThorell, Kaisa
dc.contributor.authorFalush, Daniel
dc.date.accessioned2023-09-01T11:10:22Z
dc.date.available2023-09-01T11:10:22Z
dc.date.issued2022-11-11
dc.date.updated2023-03-07T14:42:48Z
dc.description.abstractHelicobacter pylori lives in the human stomach and has a population structure resembling that of its host. However, H. pylori from Europe and the Middle East trace substantially more ancestry from modern African populations than the humans that carry them. Here, we use a collection of Afro-Eurasian H. pylori genomes to show that this African ancestry is due to at least three distinct admixture events. H. pylori from East Asia, which have undergone little admixture, have accumulated many more non-synonymous mutations than African strains. European and Middle Eastern bacteria have elevated African ancestry at the sites of these mutations, implying selection to remove them during admixture. Simulations show that population fitness can be restored after bottlenecks by migration and subsequent admixture of small numbers of bacteria from non-bottlenecked populations. We conclude that recent spread of African DNA has been driven by deleterious mutations accumulated during the original out-of-Africa bottleneck.pt_PT
dc.description.sponsorshipThe authors thank Sabrina Woltemate for technical assistance. This work was supported by Sequencing Grants-in-aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan (221S0002, 18KK0266, 19H03473, 21H00346 and 22H02871) to Y.Y. F.F.V. is financed by FCT through Assistant Researcher grant CEECIND/03023/2017 and a project grant PTDC/BTM-TEC/3238/2020. I.K. studentship was funded by the National Strategic Reference Framework Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014-2020, project No. MIS5002486) and sequencing of strains was supported by the InfeNeutra Project (NSRF 2007-2013, project no. MIS450598) of the Ministry of Culture and Education, Greece. K.T. and the sequencing of KI isolates was supported by Erik Philip-Sörensen Foundation grant G2016-08, and Swedish Society for Medical research (SSMF). All primary bioinformatics and parts of the comparative genomics were performed on resources provided by Swedish National Infrastructure for Computing (SNIC) through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) under projects snic2018-8-24 and uppstore2017270, and those provided by the National Institute of Genetics and the Human Genome Center at the Institute of Medical Science (University of Tokyo). Work by S.S. was supported by the German Research Foundation (DFG, project number 158 989 968–SFB 900/A1) and by the Bavarian Ministry of Science and the Arts in the framework of the Bavarian Research Network “New Strategies Against Multi-Resistant Pathogens by Means of Digital Networking—bayresq.net”. D.F. was supported by Shanghai Municipal Science and Technology Major Project No. 2019SHZDZX02.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationThorpe HA, Tourrette E, Yahara K, Vale FF, Liu S, Oleastro M, et al. Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations. Nat Commun [Internet]. 11 de novembro de 2022;13(1):6842. Disponível em: https://www.nature.com/articles/s41467-022-34475-3pt_PT
dc.identifier.doi10.1038/s41467-022-34475-3pt_PT
dc.identifier.slugcv-prod-3158715
dc.identifier.urihttp://hdl.handle.net/10451/59116
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherSpringer Naturept_PT
dc.relationNot Available
dc.relation.publisherversionhttps://www.nature.com/articles/s41467-022-34475-3pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.titleRepeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutationspt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleNot Available
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/CEEC IND 2017/CEECIND%2F03023%2F2017%2FCP1476%2FCT0004/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FBTM-TEC%2F3238%2F2020/PT
oaire.citation.issue1pt_PT
oaire.citation.startPage6842pt_PT
oaire.citation.titleNature Communicationspt_PT
oaire.citation.volume13pt_PT
oaire.fundingStreamCEEC IND 2017
oaire.fundingStream3599-PPCDT
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project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.cv.cienciaid4718-00EF-4BF0 | Ana Filipa Ferreira do Vale
rcaap.rightsopenAccesspt_PT
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