Genomic variation and ancestry of Helicobacter pylori in the admixed population of Cabo Verde reveal host adaptation, limited host-pathogen ancestry concordance, and signatures of trans-Atlantic slave trade migrations
- 1Division of Microbiology and Infection, University of Leicester, Leicester LE1 9HN, UK
Abstract
The genomic structure of the stomach-colonising, gastric cancer-associated bacterium Helicobacter pylori mirrors human evolutionary history, making it difficult to disentangle shared ancestry from true host-pathogen interactions driving disease risk between populations. Recently admixed populations offer opportunities for new coevolutionary trajectories between H. pylori and its host that may disrupt parallel evolution. Here, we analyse host H. pylori IgG, blood serum biomarkers, and paired host-bacterial genomic data from the general population (independent of dyspepsia symptoms) of Cabo Verde. Seropositivity is high (82.8%), as in neighbouring African populations. Serum biomarkers indicate that this unique cohort mainly comprises hosts with limited evidence of atrophic gastritis. Genomic analyses show that Cabo Verdean H. pylori derive European (hspSWeurope) and West African (hspAfrica1WAfrica) ancestry. The delineation of a reference dataset that includes new strains from Ghana, uncovered a distinct West-Central African cluster (hspAfrica1WCAfrica). This dataset allowed inference of within Africa and within Europe ancestries in Cabo Verdean and American strains that reflect historical migrations since European colonisation and the trans-Atlantic Slave Trade. European strains in Cabo Verde show additional population structure, including two low-diversity clusters. Approximate Bayesian Computation (ABC) inference indicates that the most common cluster represents a clonal expansion. Notably, these strains lack known virulence genes and show significant divergence from gastric cancer strains. The genomic signatures of this expanded group are compatible with founder effects and/or genetic adaptation, and new methods are needed to distinguish between these processes in highly recombining bacteria. Finally, host and bacterial ancestry are uncoupled, indicating disruption of ancestral parallel evolution. Cabo Verde, therefore, provides a unique natural model for studying host-pathogen interactions underlying susceptibility to H. pylori.
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BibTeX
@misc{archampong2026genomic,
title = {{Genomic variation and ancestry of Helicobacter pylori in the admixed population of Cabo Verde reveal host adaptation, limited host-pathogen ancestry concordance, and signatures of trans-Atlantic slave trade migrations}},
author = {T. Archampong and Y. L. Tam and C. Davison and I. Boughanmi and S. Tallman and M. Rodrigues and N. Tavares and K. S. Santos and F. Barbosa Amado and I. Ramos and A. Martins and R. Haigh and M. R. Oggioni and R. M. Ferreira and C. Figueiredo and F. Freund and I. I. Araujo and S. Beleza},
howpublished = {bioRxiv},
year = {2026},
month = jun,
doi = {10.64898/2026.06.05.730320},
url = {https://www.biorxiv.org/content/10.64898/2026.06.05.730320v2},
note = {CC BY},
}
RIS
TY - UNPB
TI - Genomic variation and ancestry of Helicobacter pylori in the admixed population of Cabo Verde reveal host adaptation, limited host-pathogen ancestry concordance, and signatures of trans-Atlantic slave trade migrations
AU - T. Archampong
AU - Y. L. Tam
AU - C. Davison
AU - I. Boughanmi
AU - S. Tallman
AU - M. Rodrigues
AU - N. Tavares
AU - K. S. Santos
AU - F. Barbosa Amado
AU - I. Ramos
AU - A. Martins
AU - R. Haigh
AU - M. R. Oggioni
AU - R. M. Ferreira
AU - C. Figueiredo
AU - F. Freund
AU - I. I. Araujo
AU - S. Beleza
PY - 2026
DA - 2026/06/05
PB - bioRxiv
DO - 10.64898/2026.06.05.730320
UR - https://www.biorxiv.org/content/10.64898/2026.06.05.730320v2
AB - The genomic structure of the stomach-colonising, gastric cancer-associated bacterium Helicobacter pylori mirrors human evolutionary history, making it difficult to disentangle shared ancestry from true host-pathogen interactions driving disease risk between populations. Recently admixed populations offer opportunities for new coevolutionary trajectories between H. pylori and its host that may disrupt parallel evolution. Here, we analyse host H. pylori IgG, blood serum biomarkers, and paired host-bacterial genomic data from the general population (independent of dyspepsia symptoms) of Cabo Verde. Seropositivity is high (82.8%), as in neighbouring African populations. Serum biomarkers indicate that this unique cohort mainly comprises hosts with limited evidence of atrophic gastritis. Genomic analyses show that Cabo Verdean H. pylori derive European (hspSWeurope) and West African (hspAfrica1WAfrica) ancestry. The delineation of a reference dataset that includes new strains from Ghana, uncovered a distinct West-Central African cluster (hspAfrica1WCAfrica). This dataset allowed inference of within Africa and within Europe ancestries in Cabo Verdean and American strains that reflect historical migrations since European colonisation and the trans-Atlantic Slave Trade. European strains in Cabo Verde show additional population structure, including two low-diversity clusters. Approximate Bayesian Computation (ABC) inference indicates that the most common cluster represents a clonal expansion. Notably, these strains lack known virulence genes and show significant divergence from gastric cancer strains. The genomic signatures of this expanded group are compatible with founder effects and/or genetic adaptation, and new methods are needed to distinguish between these processes in highly recombining bacteria. Finally, host and bacterial ancestry are uncoupled, indicating disruption of ancestral parallel evolution. Cabo Verde, therefore, provides a unique natural model for studying host-pathogen interactions underlying susceptibility to H. pylori.
ER -