Genomes ofHelicobacter pylorifrom native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island

Background:Helicobacter pyloriis presumed to be co-evolved with its human host and is a highly
diverse gastric pathogen at genetic levels. Ancient origins ofH. pyloriin the New World are still
debatable. It is not clear how different waves of human migrations in South America contributed
to the evolution of strain diversity ofH. pylori. The objective of our 'phylogeographic' study was to
gain fresh insights into these issues through mapping genetic origins of H. pylori of native Peruvians
(of Amerindian ancestry) and their genomic comparison with isolates from Spain, and Japan.Results: For this purpose, we attempted to dissect genetic identity of strains by fluorescent
amplified fragment length polymorphism (FAFLP) analysis, multilocus sequence typing (MLST) of
the 7 housekeeping genes (atpA, efp, ureI, ppa, mutY, trpC, yphC) and the sequence analyses of the
babB adhesin and oipA genes. The whole cag pathogenicity-island (cagPAI) from these strains was
analyzed using PCR and the geographic type of cagA phosphorylation motif EPIYA was determined
by gene sequencing. We observed that while European genotype (hp-Europe) predominates in
native Peruvian strains, approximately 20% of these strains represent a sub-population with an
Amerindian ancestry (hsp-Amerind). All of these strains however, irrespective of their ancestral
affiliation harbored a complete, 'western' type cagPAI and the motifs surrounding it. This indicates
a possible acquisition of cagPAI by the hsp-Amerind strains from the European strains, during
decades of co-colonization.Conclusion: Our observations suggest presence of ancestralH. pylori(hsp-Amerind) in Peruvian
Amerindians which possibly managed to survive and compete against the Spanish strains that
arrived to the New World about 500 years ago. We suggest that this might have happened after
native PeruvianH. pyloristrains acquired cagPAI sequences, either by new acquisition in cagnegative
strains or by recombination in cag positive Amerindian strains.