Abstract
Helicobacter pylori is a common component of the human stomach microbiota, possibly dating back to the speciation of Homo sapiens. A history of pathogen evolution in allopatry has led to the development of genetically distinct H. pylori subpopulations, associated with different human populations, and more recent admixture among H. pylori subpopulations can provide information about human migrations. However, little is known about the degree to which some H. pylori genes are conserved in the face of admixture, potentially indicating host adaptation, or how virulence genes spread among different populations. We analyzed H. pylori genomes from 14 countries in the Americas, strains from the Iberian Peninsula, and public genomes from Europe, Africa, and Asia, to investigate how admixture varies across different regions and gene families. Whole-genome analyses of 723 H. pylori strains from around the world showed evidence of frequent admixture in the American strains with a complex mosaic of contributions from H. pylori populations originating in the Americas as well as other continents. Despite the complex admixture, distinctive genomic fingerprints were identified for each region, revealing novel American H. pylori subpopulations. A pan-genome Fst analysis showed that variation in virulence genes had the strongest fixation in America, compared with non-American populations, and that much of the variation constituted non-synonymous substitutions in functional domains. Network analyses suggest that these virulence genes have followed unique evolutionary paths in the American populations, spreading into different genetic backgrounds, potentially contributing to the high risk of gastric cancer in the region.
Highlights
IntroductionThe arrival of the conquistadors in the Americas more than 500 years ago was a major event in human evolution.Extended author information available on the last page of the articleColonialism connected human European and African newcomers with Indigenous people (we capitalize Indigenous to respect the preference of some Indigenous research partners who contributed samples for this work) living in the Americas in the precolonial era [1]
The arrival of the conquistadors in the Americas more than 500 years ago was a major event in human evolution.Extended author information available on the last page of the articleColonialism connected human European and African newcomers with Indigenous people living in the Americas in the precolonial era [1]
Genomic variation among H. pylori subpopulations in the Americas reflects the ongoing adaption and admixture among strains originating in the Americas and other continents
Summary
The arrival of the conquistadors in the Americas more than 500 years ago was a major event in human evolution.Extended author information available on the last page of the articleColonialism connected human European and African newcomers with Indigenous people (we capitalize Indigenous to respect the preference of some Indigenous research partners who contributed samples for this work) living in the Americas in the precolonial era [1]. The mode of transmission of H. pylori, thought to occur principally from human-tohuman through close personal contact within families and communities [5], may have led to a degree of genetic isolation and the emergence of H. pylori subpopulations that are geographically stratified in different human populations [6, 7]. This has allowed the study of recent human migrations by quantifying changes in the patterns of admixture between historically isolated H. pylori populations [8, 9]
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