Socio-demographic characteristics of participants in the epidemiological survey, in total sample and stratified by H. pylori serostatus.

Distribution of pepsinogen I (A), pepsinogen II (B) and of the ratio pepsinogen I/pepsinogen II (PgI/PgII) (C) stratified by serostatus.

with 6 supplements Population structure and ancestry of H. pylori strains involved in the Trans-Atlantic Slave Trade.

(A) Coancestry PCA analysis of 1165 H. pylori strains from Europe, Africa, multiple American populations and Cabo Verde. (B) Unsupervised ADMIXTURE Clustering at K=2 and K=7. Only European and African population groups with n > 10 are included. Cabo Verdean samples are subdivided according to within-population structure (see Figure 3; hspEuropeCV-C1 - hspEuropeCV-Clonal1; hspEuropeCV-C2 - hspEuropeCV-Clonal2). American populations are assigned to either hspEurope or hspAfrica1 based on their proportion of European and African ancestry. Accordingly, strains from the USA, Brazil, Colombia, Honduras, Mexico, Nicaragua, and Peru are classified, from left to right, hspAfrica1USA, hspEuropeUSA, hspAfrica1Brazil, hspEuropeBrazil, hspAfrica1Colombia, hspEuropeColombia, hspAfrica1Honduras, hspEuropeHonduras, hspAfrica1Mexico, hspEuropeMexico, hspAfrica1Nicaragua, hspEuropeNicaragua, hspAfrica1Peru, hspEuropePeru. (C) Same PCA as in (A), but showing only the Cabo Verdean sample. (D) Same PCA as in (A), but showing only the USA population.

with 5 supplements Population Structure of H. pylori strain in Cabo Verde.

(A) Maximum likelihood unrooted phylogenetic tree of Cabo Verdean strains. Colour code is in (B) and (D). (B) PCA of Cabo Verdean strains. (C) ChromoPainter co-ancestry matrix with each cell indicating the proportion of DNA chunks that each genome copies from all other genomes (see Figure 3 – data source 1 for SOURCEFIND self-and between group copy fraction estimates). The colour bar on the left is repeated in the bottom of the matrix and denotes the Cabo Verdean population groups (with colour code in B and (D)), hspSWEurope (light blue) and hspAfrica1WAfrica (red). (D) Folded site frequency spectrum (fSFS) of synonymous variants in Cabo Verdean population groups. To get a comparable result, the fSFS was calculated based on the same sample size for all population groups.

with 5 supplements Genomic composition of Cabo Verdean H. pylori population groups.

(A) Forest plots showing odds ratios and 95% confidence intervals for the top three genomic annotations in the core and accessory genomes, derived from a fold enrichment analysis of hspEuropeCV–Clonal1. (B) Forest plots showing odds ratios and 95% confidence intervals for the top three genomic annotations in the core and accessory genomes, derived from a fold enrichment analysis of hspEuropeCV–Clonal2. (C) Hierarchical clustering based on the accessory genomes’ presence (burgundy)/absence (white) for the whole Cabo Verdean sample. Strains are coloured based on their population group on the top of the chart. Boxed region corresponds to cagPAI. Core genetic variants were called via mapping to the reference sequence 26695 and correspond to those present in ≥95% of the total sample. Accessory genes were obtained through pangenome alignment and correspond to genes present in 5-95% of the total sample. COG category descriptions are in Figure 4 – source data 1-2.

Host-H. pylori codiversification in Cabo Verde.

Host west African (YRI) ancestry (X-axis) is plotted against H .pylori African (hpAfrica1WestAfrica) ancestry (Y-axis).