Helicobacter pylori from Peruvian Amerindians: Traces of Human Migrations in Strains from Remote Amazon, and Genome Sequence of an Amerind Strain

Abstract

BackgroundThe gastric pathogen Helicobacter pylori is extraordinary in its genetic diversity, the differences between strains from well-separated human populations, and the range of diseases that infection promotes.Principal FindingsHousekeeping gene sequences from H. pylori from residents of an Amerindian village in the Peruvian Amazon, Shimaa, were related to, but not intermingled with, those from Asia. This suggests descent of Shimaa strains from H. pylori that had infected the people who migrated from Asia into The Americas some 15,000+ years ago. In contrast, European type sequences predominated in strains from Amerindian Lima shantytown residents, but with some 12% Amerindian or East Asian-like admixture, which indicates displacement of ancestral purely Amerindian strains by those of hybrid or European ancestry. The genome of one Shimaa village strain, Shi470, was sequenced completely. Its SNP pattern was more Asian- than European-like genome-wide, indicating a purely Amerind ancestry. Among its unusual features were two cagA virulence genes, each distinct from those known from elsewhere; and a novel allele of gene hp0519, whose encoded protein is postulated to interact with host tissue. More generally, however, the Shi470 genome is similar in gene content and organization to those of strains from industrialized countries.ConclusionsOur data indicate that Shimaa village H. pylori descend from Asian strains brought to The Americas many millennia ago; and that Amerind strains are less fit than, and were substantially displaced by, hybrid or European strains in less isolated communities. Genome comparisons of H. pylori from Amerindian and other communities should help elucidate evolutionary forces that have shaped pathogen populations in The Americas and worldwide.

J-Western Forms of Helicobacter pylori cagA Constitute a Distinct Phylogenetic Group with a Widespread Geographic Distribution

“…As previously reported, the EPIYA motifs in CagA sequences of group 4 (classified as hspAmerind) are quite different from EPIYA-C or EPIYA-D motifs (34,36,53). These Amerindian EPIYA motifs contain a 5-amino-acid segment (DDLGG) found in EPIYA-C motifs, as well as a 12-amino-acid segment (GVGXFSGXGXXD) that is not present in EPIYA-C motifs (Fig.…”

“…4). Group 4 corresponds to Amerindian cagA sequences (34,36,53), and these are from strains classified as hspAmerind (Fig. 4).…”

“…These studies have detected striking geographic differences in cagA sequences (26,36,53,60,63). For example, cagA sequences in H. pylori strains from East Asia or H. pylori strains from Amerindian persons within the Amazon are phylogenetically distinct from the cagA sequences that are commonly found in H. pylori strains from Western countries (26,34,36,53). Interestingly, two different subtypes of cagA have been detected in Japan.…”

Next-Generation Sequencing and De Novo Assembly, Genome Organization, and Comparative Genomic Analyses of the Genomes of Two Helicobacter pylori Isolates from Duodenal Ulcer Patients in India

“…H elicobacter pylori's coevolution with its host (10,11,16) and its tight compartmentalization (13,16,18,19) into several different populations and subpopulations have delivered an excellent premise to pursue the idea of geographic evolution/spread of humans and their pathogens from Africa and to gain insights into pathogen adaptation mechanisms (1,3). Based partly on these conventions, Indian H. pylori isolates have shown to have European origins (9) and are widely held as mostly innocuous or only mildly pathogenic.…”

Genomes of Two Chronological Isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori Strain 908 Obtained from a Single Patient

“…DNA profiling reveals minor differences in clinical or related strains, suggestive of microevolution (5,18,19,22,25,28), although such methods do not explain the underlying rearrangements. Multiple genome sequences of H. pylori better explain its lifestyle and evolution (7,11,15,21,24,27). However, chronological isolates, especially those obtained from single patients (18,19,25) or single families (28), have not been sequenced.…”