University of Oulu

Thorpe, H.A., Tourrette, E., Yahara, K. et al. Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations. Nat Commun 13, 6842 (2022).

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

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Author: Thorpe, Harry A.1; Tourrette, Elise2; Yahara, Koji3;
Organizations: 1Department of Biostatistics, University of Oslo, Oslo, Norway
2CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
3Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
4Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
5University of Chinese Academy of Sciences, Beijing, China
6National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal
7Department of Microbiology, Hospital Universitario La Princesa, Instituto de Investigación Sanitaria Princesa, Madrid, Spain
8Gastroenterology Laboratory, Rabin Medical Center, Petah Tikva, Israel
9Department of Digital Medical Technologies, Holon Institute of Technology, Holon, Israel
10Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
11Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
12Department of Medicine-Gastroenterology, Baylor College of Medicine, Houston, TX, USA
13Laboratory of Medical Microbiology, Hellenic Pasteur Institute, Athens, Greece
14G42 Healthcare, Abu Dhabi, UAE
15Elrazi University, Khartoum, Sudan
16Department of Biology, University of Oxford, Oxford, UK
17Ineos Oxford Institute, Department of Biology, University of Oxford, Oxford, UK
18Center for Life Course Health Research, University of Oulu, Oulu, Finland
19Primary Health Care Center, Tornio, Finland
20Arokero Oy, Tornio, Finland
21Center for Translational Microbiome Research, Department for Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Stockholm, Sweden
22Division of Family Medicine, Karolinska Institutet, Stockholm, Sweden
23Department of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
24Department of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
25DZIF German Center for Infection Research, Hannover-Braunschweig and Munich Partner Sites, Munich, Germany
26Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
27Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1.7 MB)
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Language: English
Published: Springer Nature, 2022
Publish Date: 2023-06-29


Helicobacter 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.

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Series: Nature communications
ISSN: 2041-1723
ISSN-E: 2041-1723
ISSN-L: 2041-1723
Volume: 13
Issue: 1
Article number: 6842
DOI: 10.1038/s41467-022-34475-3
Type of Publication: A1 Journal article – refereed
Field of Science: 3121 General medicine, internal medicine and other clinical medicine
Funding: 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. 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—”. D.F. was supported by Shanghai Municipal Science and Technology Major Project No. 2019SHZDZX02.
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