Journal Article

The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

Falush, Daniel, Wang, Difei, Camargo, M. Constanza, Muñoz-Ramírez, Zilia Y., Torres, Roberto C., Rabkin, Charles S., Thorell, Kaisa, Ghirotto, Silvia, Boscolo Agostini, Rajiv, Sandoval-Motta, Santiago

2023

Overview

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 ( Hp GP), 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 Hp GP 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 Hp GP dataset and the corresponding strains to become a major asset for H. pylori genomics. The bacterium Helicobacter pylori , often found in the human stomach, can be classified into distinct subpopulations associated with the geographic origin of the host. Here, the authors provide insights into H. pylori population structure by collecting over 1,000 clinical strains from 50 countries and generating and analyzing high-quality bacterial genome sequences.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 45/23 / 631/208/457 / 631/326/325/2482 / 631/326/41/2530 / 631/326/421 / Bacteria / Base Sequence / Datasets / Evolutionary genetics / Gene sequencing / Genome, Bacterial - genetics / Genomes / Genomics / Health risks / Helicobacter Infections - microbiology / Helicobacter pylori / Humanities and Social Sciences / Humans / Indigenous peoples / Microbiology in the Medical Area / Mikrobiologi inom det medicinska området / multidisciplinary / Pathogenesis / Pathogenicity / Pathogens / Population Groups / Population structure / Science / Science (multidisciplinary) / Strains (organisms) / Subpopulations / Therapeutic targets / Trinucleotide repeats