The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes
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 E. Bentolila, Hafeza Aftab, Junko Akada, Takashi Matsumoto, Freddy Haesebrouck, Rony Colanzi, Thais Fernanda Bartelli, Diana Noronha Nunes, Adriane Pelosof, Cláudia Zitron, Emmanuel Dias‐Neto, Paulo Pimentel de Assumpção, Ivan Tishkov, Laure Brigitte Kouitcheu Mabeku, Karen J. Goodman, Janis Geary, Taylor Cromarty, Nancy L. Price, Douglas Quilty, Alejandro H. Corvalán, Carolina Serrano, Robinson González, Arnoldo Riquelme, Apolinaria García, Cristian Parra-Sepúlveda, Giuliano Bernal, Francisco Castillo, Alisa M. Goldstein, Nan Hu, Philip R. Taylor, María Mercedes Bravo, Alvaro J. Pazos, Luis Eduardo Bravo, Keith T. Wilson, James G. Fox, Vanessa Ramírez, 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 Bénéjat, Ousman Secka, Alexander Link, Peter Malfertheiner, Michael Buenor Adinortey, Ansumana Bockarie, Cynthia Ayefoumi Adinortey, Eric Gyamerah Ofori, Dionyssios N. Sgouras, Beatriz Martinez‐Gonzalez, Spyridon Michopoulos, Sotirios D. Georgopoulos, Elisa Hernández, Braulio Volga Tacatic, Mynor Aguilar, Ricardo L. Domínguez, Douglas R. Morgan, Hjördís Harðardóttir, Anna Ingibjörg Gunnarsdóttir, H Gudjónsson, Jón G. 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, Vallì De Re, Stefania Zanussi, Renato Cannizzaro
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.