The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes
Year: 2023
Type: article
Abstract: Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics.
Source: Nature Communications
Authors: Kaisa Thorell, Zilia Y. Muñoz-Ramírez, Difei Wang, Santiago Sandoval-Motta, Rajiv Boscolo Agostini, Silvia Ghirotto, Roberto C. Torres, Judith Romero-Gallo, Uma Krishna, Richard M. Peek, M. Blanca Piazuelo, Naïma Raaf, Federico Bentolila, Hafeza Aftab, Junko Akada, Takashi Matsumoto, Freddy Haesebrouck, Rony P. Colanzi, Thais F. Bartelli, Diana Noronha Nunes, Adriane Pelosof, Claudia Zitron Sztokfisz, Emmanuel Dias-Neto, Paulo Pimentel Assumpção, Ivan Tishkov, Laure Brigitte Kouitcheu Mabeku, Karen J. Goodman, Janis Geary, Taylor J. Cromarty, Nancy L. Price, Douglas Quilty, Alejandro H. Corvalan, Carolina A. Serrano, Robinson Gonzalez, Arnoldo Riquelme, Apolinaria García-Cancino, Cristian Parra-Sepúlveda, Giuliano Bernal, Francisco Castillo, Alisa M. Goldstein, Nan Hu, Philip R. Taylor, Maria Mercedes Bravo, Alvaro Pazos, Luis E. Bravo, Keith T. Wilson, James G. Fox, Vanessa Ramírez-Mayorga, Silvia Molina-Castro, Sundry Durán-Bermúdez, Christian Campos-Núñez, Manuel Chaves-Cervantes, Evariste Tshibangu-Kabamba, Ghislain Disashi Tumba, Antoine Tshimpi-Wola, Patrick de Jesus Ngoma-Kisoko, Dieudonné Mumba Ngoyi, Modesto Cruz, Celso Hosking, José Jiménez Abreu, Christine Varon, Lucie Benejat, Ousman Secka, Alexander Link, Peter Malfertheiner, Michael Buenor Adinortey, Ansumana Sandy Bockarie, Cynthia Ayefoumi Adinortey, Eric Gyamerah Ofori, Dionyssios N. Sgouras, Beatriz Martinez-Gonzalez, Spyridon Michopoulos, Sotirios Georgopoulos, Elisa Hernandez, Braulio Volga Tacatic, Mynor Aguilar, Ricardo L. Dominguez, Douglas R. Morgan, Hjördís Harðardóttir, Anna Ingibjörg Gunnarsdóttir, Hallgrímur Guðjónsson, Jón Gunnlaugur Jónasson, Einar S. Björnsson, Mamatha Ballal, Vignesh Shetty, Muhammad Miftahussurur, Titong Sugihartono, Ricky Indra Alfaray, Langgeng Agung Waskito, Kartika Afrida Fauzia, Ari Fahrial Syam, Hasan Maulahela, Reza Malekzadeh, Masoud Sotoudeh, Avi Peretz, Maya Azrad, Avi On, Valli De Re, Stefania Zanussi, Renato Cannizzaro, Vincenzo Canzonieri, Takaya Shimura, Kengo Tokunaga, Takako Osaki, Shigeru Kamiya, Khaled Jadallah, Ismail Matalka, Nurbek Igissinov, Mariia Satarovna Moldobaeva, Attokurova Rakhat, Il Ju Choi, Jae Gyu Kim, Nayoung Kim, Minkyo Song, Mārcis Leja, Reinis Vangravs, Ģirts Šķenders, Dace Rudzīte, Aiga Rūdule, Aigars Vanags, Ilze Kikuste, Juozas Kupcinskas, Jurgita Skieceviciene, Laimas Jonaitis, Gediminas Kiudelis, Paulius Jonaitis, Vytautas Kiudelis, Greta Varkalaite, Jamuna Vadivelu, Mun Fai Loke, Kumutha Malar Vellasamy, Roberto Herrera-Goepfert, Juan Octavio Alonso-Larraga, Than Than Yee, Kyaw Htet, Takeshi Matsuhisa, Pradeep Krishna Shrestha, Shamshul Ansari, Olumide Abiodun, Christopher Jemilohun, Kolawole Oluseyi Akande, Oluwatosin Olu-Abiodun, Francis Ajang Magaji, Ayodele Omotoso, Chukwuemeka Chukwunwendu Osuagwu, Uchenna Okonkwo, Opeyemi O. Owoseni, Carlos Castaneda, Miluska Castillo, Billie Velapatino, Robert H. Gilman, Paweł Krzyżek, Grażyna Gościniak, Dorota Pawełka, Izabela Korona-Glowniak, Halina Cichoz-Lach, Monica Oleastro, Ceu Figueiredo, Jose C. Machado, Rui M. Ferreira, Dmitry S. Bordin, Maria A. Livzan, Vladislav V. Tsukanov, Patrick Tan, Khay Guan Yeoh, Feng Zhu, Reid Ally, Rainer Haas, Milagrosa Montes, María Fernández-Reyes, Esther Tamayo, Jacobo Lizasoain, Luis Bujanda, Sergio Lario, María José Ramírez-Lázaro, Xavier Calvet, Eduard Brunet-Mas, María José Domper-Arnal, Sandra García-Mateo, Daniel Abad-Baroja, Pedro Delgado-Guillena, Leticia Moreira, Josep Botargues, Isabel Pérez-Martínez, Eva Barreiro-Alonso, Virginia Flores, Javier P. Gisbert, Edurne Amorena Muro, Pedro Linares, Vicente Martin, Laura Alcoba, Tania Fleitas-Kanonnikoff, Hisham N. Altayeb, Lars Engstrand, Helena Enroth, Peter M. Keller, Karoline Wagner, Daniel Pohl, Yi-Chia Lee, Jyh-Ming Liou, Ming-Shiang Wu, Bekir Kocazeybek, Suat Sarıbas, İhsan Tasçı, Süleyman Demiryas, Nuray Kepil, Luis Quiel, Miguel Villagra, Morgan Norton, Deborah Johnson, Robert J. Huang, Joo Ha Hwang, Wendy Szymczak, Saranathan Rajagopalan, Emmanuel Asare, William R. Jacobs, Haejin In, Roni Bollag, Aileen Lopez, Edward J. Kruse, Joseph White, David Y. Graham, Charlotte Lane, Yang Gao, Patricia I. Fields, Benjamin D. Gold, Marcia Cruz-Correa, María González-Pons, Luz M. Rodriguez, Vo Phuoc Tuan, Ho Dang Quy Dung, Tran Thanh Binh, Tran Thi Huyen Trang, Vu Van Khien, Xiongfong Chen, Castle Raley, Bailey Kessing, Yongmei Zhao, Bao Tran, Andrés J. Gutiérrez-Escobar, Yunhu Wan, Belynda Hicks, Bin Zhu, Kai Yu, Bin Zhu, Meredith Yeager, Amy Hutchinson, Kedest Teshome, Kristie Jones, Wen Luo, Quentin Jehanne, Yukako Katsura, Patricio Gonzalez-Hormazabal, Xavier Didelot, Sam Sheppard, Eduardo Tarazona-Santos, Leonardo Mariño-Ramírez, John T. Loh, Steffen Backert, Michael Naumann, Christian C. Abnet, Annemieke Smet, Douglas E. Berg, Álvaro Chiner-Oms, Iñaki Comas, Francisco José Martínez-Martínez, Roxana Zamudio, Philippe Lehours, Francis Megraud, Koji Yahara, Martin J. Blaser, Tamas Vincze, Richard D. Morgan, Richard J. Roberts, Stephen J. Chanock, John P. Dekker, Javier Torres, Timothy L. Cover, Mehwish Noureen, Wolfgang Fischer, Filipa F. Vale, Joshua L. Cherry, Naoki Osada, Masaki Fukuyo, Masanori Arita, Yoshio Yamaoka, Ichizo Kobayashi, Ikuo Uchiyama, Daniel Falush, M. Constanza Camargo, Charles S. Rabkin
Institutions: University of Gothenburg, Autonomous University of Chihuahua, Frederick National Laboratory for Cancer Research, Division of Cancer Epidemiology and Genetics, National Institute of Genomic Medicine, Secretaría de Ciencia, Humanidades, Tecnología e Innovación, Universidad Nacional Autónoma de México, University of Ferrara, Institut Pasteur of Shanghai, Vanderbilt University Medical Center, University of Algiers Benyoucef Benkhedda, Hospital Alemán, Dhaka Medical College and Hospital, Oita University, Ghent University, AC Camargo Hospital, Universidade Federal do Pará, Medical University of Sofia, Université de Dschang, University of Alberta, Queen's University, Pontificia Universidad Católica de Chile, University of Concepción, Universidad Católica del Norte, Instituto Nacional de Cancerología, University of Nariño, Universidad del Valle, Massachusetts Institute of Technology, Universidad de Costa Rica, University of Mbuji Mayi, Osaka Metropolitan University, University of Kinshasa, National Institute of Biomedical Research, Universidad Autónoma de Santo Domingo, Inserm, Centre Hospitalier Universitaire de Bordeaux, BoRdeaux Institute of onCology, London School of Hygiene & Tropical Medicine, MRC Unit the Gambia, Medical Research Council, Otto-von-Guericke-Universität Magdeburg, University of Cape Coast, University of Education, Winneba, Pasteur Hellenic Institute, Alexandra Hospital, Universidad de San Carlos de Guatemala, Roosevelt Hospital, Galileo University, Hospital Regional de Occidente, University of Alabama at Birmingham, National University Hospital of Iceland, University of Iceland, Manipal Academy of Higher Education, Kasturba Medical College, Manipal, University of Cambridge, Universitas Airlangga, University of Indonesia, Digestive Disease Research Institute, Tehran University of Medical Sciences, Bar-Ilan University, Poriya Medical Center, Centro di Riferimento Oncologico, Nagoya City University, Kyorin University, Jordan University of Science and Technology, Astana Medical University, Kyrgyz State Medical Academy, National Cancer Center, Chung-Ang University Hospital, Seoul National University, Riga East University Hospital, University of Latvia, Lithuanian University of Health Sciences, University of Malaya, Instituto Nacional de Cancerología, Nippon Medical School, Tribhuvan University, Tribhuvan University Teaching Hospital, Maharajgunj Medical Campus, Higher Colleges of Technology, Babcock University, University of Ibadan, Crescent University, University of Jos, Jos University Teaching Hospital, University Of Calabar Teaching Hospital, University of Nigeria Teaching Hospital, Federal Medical Centre, Universidad Científica del Sur, Instituto Nacional de Enfermedades Neoplásicas, Universidad Peruana Cayetano Heredia, Johns Hopkins University, Wroclaw Medical University, Medical University of Lublin, National Institute of Health Dr. Ricardo Jorge, Universidade do Porto, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Russian University of Medicine, Moscow Clinical Scientific Center, Tver State Medical University, Omsk State Medical University, Russian Academy of Sciences, Krasnoyarsk Scientific Center, Research Institute of Medical Problems of the North, Agency for Science, Technology and Research, National University of Singapore, Duke-NUS Medical School, Cancer Science Institute of Singapore, Genome Institute of Singapore, National University Health System, University of the Witwatersrand, Chris Hani Baragwanath Hospital, Max-von-Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universität München, Donostiako Unibertsitate Ospitalea, University of the Basque Country, Biogipuzkoa Health Research Institute, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Universitat Autònoma de Barcelona, Instituto de Salud Carlos III, Corporació Sanitària Parc Taulí, Institute of Research and Innovation Parc Tauli, Hospital Clínico Universitario Lozano Blesa, Hospital Universitario Miguel Servet, Hospital General de Granollers, Hospital Clínic de Barcelona, Universitat de Barcelona, Bellvitge University Hospital, Hospital Universitario Central de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias, Hospital General Universitario Gregorio Marañón, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa, Universidad Autónoma de Madrid, Hospital Universitario de León, Universidad de León, Hospital Clínico Universitario de Valencia, INCLIVA Health Research Institute, King Abdulaziz University, Sudan University of Science and Technology, Karolinska Institutet, University of Skövde, University of Bern, University Hospital of Basel, University of Zurich, University Hospital Zurich, National Taiwan University, Istanbul University-Cerrahpaşa, Istanbul University, Lawrence General Hospital, Carson Tahoe Regional Medical Center, Stanford Medicine, Stanford University, Albert Einstein College of Medicine, Rutgers Cancer Institute, Augusta University, Augusta University Health, Baylor College of Medicine, Centers for Disease Control and Prevention, GI Care for Kids, University of Puerto Rico, Medical Sciences Campus, University of Puerto Rico System, National Cancer Institute, Cho Ray Hospital, 108 Military Central Hospital, Institute for the Evolutionary Origins of Human Behavior, Kyoto University, University of Chile, University of Warwick, University of Bath, Universidade Federal de Minas Gerais, National Institute on Minority Health and Health Disparities, Friedrich-Alexander-Universität Erlangen-Nürnberg, University of Antwerp, Washington University in St. Louis, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Consejo Superior de Investigaciones Científicas, Instituto de Biomedicina de Valencia, Quadram Institute, National Institute of Infectious Diseases, Rutgers, The State University of New Jersey, New England Biolabs (United States), National Institute of Allergy and Infectious Diseases, Mexican Social Security Institute, VA Tennessee Valley Healthcare System, The Graduate University for Advanced Studies, SOKENDAI, University of Lisbon, National Institutes of Health, National Center for Biotechnology Information, Fogarty International Center, Hokkaido University, Chiba University, National Institute of Genetics, Hosei University, National Institute for Basic Biology, National Institutes of Natural Sciences
Language: English
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $6,290
Funders: U.S. Department of Veterans Affairs, Universidad Científica del Sur, ArcticNet, European Commission, National Research Foundation, National Research Foundation Singapore, Fundação de Amparo à Pesquisa do Estado de São Paulo, Bundesministerium für Bildung und Forschung, Ministero della Salute, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Svenska Sällskapet för Medicinsk Forskning, Universiti Malaya, Stiftelsen Assar Gabrielssons Fond, Universidad de Costa Rica, Göteborgs Universitet, Magnus Bergvalls Stiftelse, Institut National Du Cancer, Alberta Innovates, Hellenic Society of Gastroenterology, Agencia Nacional de Investigación y Desarrollo, National Institutes of Health, Centers for Disease Control and Prevention, Medical Research Council, National Medical Research Council, Japan Society for the Promotion of Science, Comisión Nacional de Investigación Científica y Tecnológica, National Cancer Institute, National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Environmental Health Sciences, U.S. National Library of Medicine, National Institute on Minority Health and Health Disparities, Fondo Nacional de Desarrollo Científico y Tecnológico, Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias
Awards: G1046522931, G1173929046, A DUAL ROLE FOR KCNQ1OT1 IN THE INDUCTION AND DISRUPTION OF SENESCENCE IN THE PREMALIGNANCY OF GASTRIC CANCER, G1337233005, Thousands of adaptive changes emerging from thousands of genomes within a species, G1788375732, G1908682455, G1953887145, G1986623869, G2076520454, Helicobacter Pylori and Gastrointestinal Biology, G2677070840, G2734939043, CeLac and European consortium for a personalized medicine approach to Gastric Cancer, G3207356259, Platform for Advanced Genome Science, G3572101131, G3706700131, G400951311, G4049090479, Chronic respiratory effects of early life PM exposure, G434337789, G4370016789, G4628183745, G4665397411, G48435065, CENTER FOR CANCER PREVENTION AND CONTROL (CECAN), G551219040, G5513958502, G5844820580, ROLE OF THE GENOMIC AND MICROBIOME PROFILE IN GASTRIC CARCINOGENESIS A PROSPECTIVE ENDOSCOPIC FOLLOW-UP, G6438247056, G652983587, G725763919, REGULATION OF CXC CHEMOKINE EXPRESSION BY H. PYLORI, Hispanic Alliance for Clinical and Translational Research (Alliance), G7420761326, G749189708, G7517881220, Elucidation of cancer mutagen by novel signature analysis, Establishing a low-cost next-generation sequencing platform for on-site real-time surveillance of SARS-CoV-2 and other viruses in an unreached community from the Democratic Republic of Congo, G7997921828, G8379432780, Gastric Cancer Epidemiology Initiative in Central America, CENTRO DE ESTUDIOS AVANZADOS DE ENFERMEDADES CRONICAS (ACCDIS), G8473455870, G8495673431, Pathological analysis of Helicobacter suis and gastric microbiome in gastric MALT lymphoma, Gastric cancer and duodenal ulcer - two different mechanisms of gastric disease onset based on Helicobacter pylori infection, G9000023350, G9000040438, G9000042956, G9000064184, G9000080324, G9000175371, Molecular and Cellular Basis for Digestive Diseases, G94614213, G951791973, G99091514
OpenAlex ID: W4389546256