The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes
Authors: Thorell Kaisa , Muñoz-Ramírez Zilia Y. , Wang Difei , Sandoval-Motta Santiago , Boscolo Agostini Rajiv , Ghirotto Silvia , Torres Roberto C. ,   HpGP Research Network, Romero-Gallo Judith , Krishna Uma , Peek Richard M. , Piazuelo M. Blanca , Raaf Naïma , Bentolila Federico , Aftab Hafeza , Akada Junko , Matsumoto Takashi , Haesebrouck Freddy , Colanzi Rony P. , Bartelli Thais F. , Nunes Diana Noronha , Pelosof Adriane , Sztokfisz Claudia Zitron , Dias-Neto Emmanuel , Assumpção Paulo Pimentel , Tishkov Ivan , Mabeku Laure Brigitte Kouitcheu , Goodman Karen J. , Geary Janis , Cromarty Taylor J. , Price Nancy L. , Quilty Douglas , Corvalan Alejandro H. , Serrano Carolina A. , Gonzalez Robinson , Riquelme Arnoldo , García-Cancino Apolinaria , Parra-Sepúlveda Cristian , Bernal Giuliano , Castillo Francisco , Goldstein Alisa M. , Hu Nan , Taylor Philip R. , Bravo Maria Mercedes , Pazos Alvaro , Bravo Luis E. , Wilson Keith T. , Fox James G. , Ramírez-Mayorga Vanessa , Molina-Castro Silvia , Durán-Bermúdez Sundry , Campos-Núñez Christian , Chaves-Cervantes Manuel , Tshibangu-Kabamba Evariste , Tumba Ghislain Disashi , Tshimpi-Wola Antoine , de Jesus Ngoma-Kisoko Patrick , Ngoyi Dieudonné Mumba , Cruz Modesto , Hosking Celso , Abreu José Jiménez , Varon Christine , Benejat Lucie , Secka Ousman , Link Alexander , Malfertheiner Peter , Adinortey Michael Buenor , Bockarie Ansumana Sandy , Adinortey Cynthia Ayefoumi , Ofori Eric Gyamerah , Sgouras Dionyssios N. , Martinez-Gonzalez Beatriz , Michopoulos Spyridon , Georgopoulos Sotirios , Hernandez Elisa , Tacatic Braulio Volga , Aguilar Mynor , Dominguez Ricardo L. , Morgan Douglas R. , Harðardóttir Hjördís , Gunnarsdóttir Anna Ingibjörg , Guðjónsson Hallgrímur , Jónasson Jón Gunnlaugur , Björnsson Einar S. , Ballal Mamatha , Shetty Vignesh , Miftahussurur Muhammad , Sugihartono Titong , Alfaray Ricky Indra , Waskito Langgeng Agung , Fauzia Kartika Afrida , Syam Ari Fahrial , Maulahela Hasan , Malekzadeh Reza , Sotoudeh Masoud , Peretz Avi , Azrad Maya , On Avi , De Re Valli , Zanussi Stefania , Cannizzaro Renato , Canzonieri Vincenzo , Shimura Takaya , Tokunaga Kengo , Osaki Takako , Kamiya Shigeru , Jadallah Khaled , Matalka Ismail , Igissinov Nurbek , Moldobaeva Mariia Satarovna , Rakhat Attokurova , Choi Il Ju , Kim Jae Gyu , Kim Nayoung , Song Minkyo , Leja Mārcis , Vangravs Reinis , Šķenders Ģirts , Rudzīte Dace , Rūdule Aiga , Vanags Aigars , Kikuste Ilze , Kupcinskas Juozas , Skieceviciene Jurgita , Jonaitis Laimas , Kiudelis Gediminas , Jonaitis Paulius , Kiudelis Vytautas , Varkalaite Greta , Vadivelu Jamuna , Loke Mun Fai , Vellasamy Kumutha Malar , Herrera-Goepfert Roberto , Alonso-Larraga Juan Octavio , Yee Than Than , Htet Kyaw , Matsuhisa Takeshi , Shrestha Pradeep Krishna , Ansari Shamshul , Abiodun Olumide , Jemilohun Christopher , Akande Kolawole Oluseyi , Olu-Abiodun Oluwatosin , Magaji Francis Ajang , Omotoso Ayodele , Osuagwu Chukwuemeka Chukwunwendu , Okonkwo Uchenna , Owoseni Opeyemi O. , Castaneda Carlos , Castillo Miluska , Velapatino Billie , Gilman Robert H. , Krzyżek Paweł , Gościniak Grażyna , Pawełka Dorota , Korona-Glowniak Izabela , Cichoz-Lach Halina , Oleastro Monica , Figueiredo Ceu , Machado Jose C. , Ferreira Rui M. , Bordin Dmitry S. , Livzan Maria A. , Tsukanov Vladislav V. , Tan Patrick , Yeoh Khay Guan , Zhu Feng , Ally Reid , Haas Rainer , Montes Milagrosa , Fernández-Reyes María , Tamayo Esther , Lizasoain Jacobo , Bujanda Luis , Lario Sergio , Ramírez-Lázaro María José , Calvet Xavier , Brunet-Mas Eduard , Domper-Arnal María José , García-Mateo Sandra , Abad-Baroja Daniel , Delgado-Guillena Pedro , Moreira Leticia , Botargues Josep , Pérez-Martínez Isabel , Barreiro-Alonso Eva , Flores Virginia , Gisbert Javier P. , Muro Edurne Amorena , Linares Pedro , Martin Vicente , Alcoba Laura , Fleitas-Kanonnikoff Tania , Altayeb Hisham N. , Engstrand Lars , Enroth Helena , Keller Peter M. , Wagner Karoline , Pohl Daniel , Lee Yi-Chia , Liou Jyh-Ming , Wu Ming-Shiang , Kocazeybek Bekir , Sarıbas Suat , Tasçı İhsan , Demiryas Süleyman , Kepil Nuray , Quiel Luis , Villagra Miguel , Norton Morgan , Johnson Deborah , Huang Robert J. , Hwang Joo Ha , Szymczak Wendy , Rajagopalan Saranathan , Asare Emmanuel , Jacobs William R. , In Haejin , Bollag Roni , Lopez Aileen , Kruse Edward J. , White Joseph , Graham David Y. , Lane Charlotte , Gao Yang , Fields Patricia I. , Gold Benjamin D. , Cruz-Correa Marcia , González-Pons María , Rodriguez Luz M. , Tuan Vo Phuoc , Dung Ho Dang Quy , Binh Tran Thanh , Trang Tran Thi Huyen , Van Khien Vu , Chen Xiongfong , Raley Castle , Kessing Bailey , Zhao Yongmei , Tran Bao , Gutiérrez-Escobar Andrés J. , Wan Yunhu , Hicks Belynda , Zhu Bin , Yu Kai , Zhu Bin , Yeager Meredith , Hutchinson Amy , Teshome Kedest , Jones Kristie , Luo Wen , Jehanne Quentin , Katsura Yukako , Gonzalez-Hormazabal Patricio , Didelot Xavier , Sheppard Sam , Tarazona-Santos Eduardo , Mariño-Ramírez Leonardo , Loh John T. , Backert Steffen , Naumann Michael , Abnet Christian C. , Smet Annemieke , Berg Douglas E. , Chiner-Oms Álvaro , Comas Iñaki , Martínez-Martínez Francisco José , Zamudio Roxana , Lehours Philippe , Megraud Francis , Yahara Koji , Blaser Martin J. , Vincze Tamas , Morgan Richard D. , Roberts Richard J. , Chanock Stephen J. , Dekker John P. , Torres Javier , Cover Timothy L. , Noureen Mehwish , Fischer Wolfgang , Vale Filipa F. , Cherry Joshua L. , Osada Naoki , Fukuyo Masaki , Arita Masanori , Yamaoka Yoshio , Kobayashi Ichizo , Uchiyama Ikuo , Falush Daniel , Camargo M. Constanza , Rabkin Charles S. 
Published: December 2023

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.