A 500-year tale of co-evolution, adaptation, and virulence: Helicobacter pylori in the Americas

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.

An American lineage of Helicobacter pylori prophages found in Colombia

“…These results are similar to those of the first studies of the Colombian strains and agree with the expected results based on migration involved in Spanish colonization 48,49 . It was recently demonstrated by studies that used the whole‐genome sequences, the existence of a specific population component in strains isolated from the Colombian mestizo population, 19‐21,25 suggesting that the H . pylori Colombian strains have followed unique evolutionary pathways 19 and have formed new subpopulations from a European source, 21 localized at the Iberian Peninsula.…”

“…The identification of a new population of prophages from the Americas is in agreement with other studies pointing to the existence of H . pylori subpopulations in Colombia 20,21 . We cannot affirm that the new subpopulation of prophages (hpColombia) described here is associated in the new subpopulation of Colombian strains, previously described.…”

“…pylori Colombian strains have followed unique evolutionary pathways 19 and have formed new subpopulations from a European source, 21 localized at the Iberian Peninsula. Thus, this Colombian subpopulation named hspSWEuropeColombia (previously reported as hspSEuropeColombia) showed hspSWEurope predominance 20 . Interestingly and opposing, for a new cluster of Colombia prophages (presented below), the closer population has hpNEurope predominance and not hpSWEurope, supporting that hpColombia diverges from hpNEurope population, whose prevalence is residual.…”

“…pylori genomes from Latin America reported the separation of American strains from those of European, African, Asian, and Amerindian origin. Moreover, frequent and recent recombination events have been detected in groups of exclusively Colombian, Mexican, and Nicaraguan strains 19,20 . H .…”

Molecular evidence for cross boundary spread ofSalmonellaspp. in meat sold at retail markets in the middle Mekong basin area

“…Increased population density strongly correlates with the risk of infectious disease, exponentially ( Wilkinson et al, 2018 ). Large scale population movement in specific geographical areas provide a pathway for disseminating and continuing to shape the epidemic of cross boundary disease ( Muñoz Ramirez et al, 2021 ). Volume, speed and reach of the movements have been considered as the potent force contribution ( Wilson, 1995 ).…”