Phylogenetic structure of the global population of Helicobacter Pylori

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Abstract

Helicobacter pylori (H. pylori) is widely considered to be one of the oldest bacteria in the human microbiome. During the co-evolutionary relationships between humans and H. pylori bacterium, spanning at least 100 000 years, a high rate of mutation and recombination events led to extremely high genomic polymorphism of the H. pylori species. Despite this, the large diversity of H. pylori genomes is very well structured, allowing to divide it into different populations associated with the geographic location of H. pylori strains. To date, seven modern H. pylori populations have been determined globally: hpAfrica1, hpAfrica2, hpEastAsia, hpEurope, hpAsia2, hpNEAfrica and hspSahul originated from at least six ancestral populations (ancestral European 1, ancestral European 2, ancestral EastAsia, ancestral Africa1, ancestral Africa2, ancestral Sahul). The global phylogenetic analysis showed that H. pylori is organized into two superlineages: one containing hpAfrica2 and the other containing all other populations in a single monophyletic clade. This indicates that, hpAfrica2 is the most ancient of all H. pylori populations, while the others continued evolutionary development along as mankind spread beyond the African continent. Thus, the H. pylori species populational diversification, which occurred in parallel with paired hosts, allowed us to use H. pylori genetic variants as biological markers, reflecting ethnogeographic migration processes in human history. Moreover, the rapid and dynamic evolution of H. pylori informs about ongoing recombination events enabling use H. pylori as a model both for the co-evolution of pathogenic bacteria and humans as well as for within-individual host pathogen microevolution. This review summarized developments from numerous studies on coevolution process and phylogenetic pattern of the global H. pylori population. The relationships between currently known bacterial populations and subpopulations, related geographical distribution, reconstruction of evolutionary pathway for ancestral and recent populations are detailed. New data on the H. pylori strain populational pattern in Russia, as well as strains circulating in the Northern, Central and South America, are presented. Phylogenetic analysis of the H. pylori population pattern permitted to reconstruct both prehistoric and recent human migrations, demographic processes as well as multilayered evolutionary pathways of H. pylori population.

About the authors

Daria A. Starkova

St. Petersburg Pasteur Institute

Email: dariastarkova13@gmail.com
ORCID iD: 0000-0003-3199-8689

PhD (Biology), Senior Researcher of the Pathogens Identification Laboratory, Senior Researcher of the Laboratory of Molecular Epidemiology and Evolutionary Genetics

Russian Federation, 197101, St. Petersburg, Mira str., 14

A. V. Svarval

St. Petersburg Pasteur Institute

Author for correspondence.
Email: alena.svarval@mail.ru
ORCID iD: 0000-0001-9340-4132

PhD (Medicine), Senior Researcher, Head of the Pathogens Identification Laboratory

Russian Federation, 197101, St. Petersburg, Mira str., 14

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