Whole Genome Sequence and Phylogenetic Analysis Show Helicobacter pylori Strains from Latin America Have Followed a Unique Evolution Pathway.

Zilia Y Muñoz-Ramírez,Javier Torres,Margarita Camorlinga,Francisco Aviles-Jimenez,Cosmeri Rizzato,Federico Canzian,Kaisa Thorell,Alfonso Mendez-Tenorio,Roberto Torres,Maria M Bravo,Ikuko Kato

doi:10.3389/fcimb.2017.00050

Abstract

Helicobacter pylori (HP) genetics may determine its clinical outcomes. Despite high prevalence of HP infection in Latin America (LA), there have been no phylogenetic studies in the region. We aimed to understand the structure of HP populations in LA mestizo individuals, where gastric cancer incidence remains high. The genome of 107 HP strains from Mexico, Nicaragua and Colombia were analyzed with 59 publicly available worldwide genomes. To study bacterial relationship on whole genome level we propose a virtual hybridization technique using thousands of high-entropy 13 bp DNA probes to generate fingerprints. Phylogenetic virtual genome fingerprint (VGF) was compared with Multi Locus Sequence Analysis (MLST) and with phylogenetic analyses of cagPAI virulence island sequences. With MLST some Nicaraguan and Mexican strains clustered close to Africa isolates, whereas European isolates were spread without clustering and intermingled with LA isolates. VGF analysis resulted in increased resolution of populations, separating European from LA strains. Furthermore, clusters with exclusively Colombian, Mexican, or Nicaraguan strains were observed, where the Colombian cluster separated from Europe, Asia, and Africa, while Nicaraguan and Mexican clades grouped close to Africa. In addition, a mixed large LA cluster including Mexican, Colombian, Nicaraguan, Peruvian, and Salvadorian strains was observed; all LA clusters separated from the Amerind clade. With cagPAI sequence analyses LA clades clearly separated from Europe, Asia and Amerind, and Colombian strains formed a single cluster. A NeighborNet analyses suggested frequent and recent recombination events particularly among LA strains. Results suggests that in the new world, H. pylori has evolved to fit mestizo LA populations, already 500 years after the Spanish colonization. This co-adaption may account for regional variability in gastric cancer risk.

Highlights

Helicobacter pylori is a Gram negative bacterium that colonizes the human gastric mucosa of approximately 50% of the human population and induces a chronic inflammatory process
We tested the hypothesis that phylogenetic analyses using whole-genome sequences instead of Multi Locus Sequence Typing (MLST) may lead to the discovery of a distinct population structure, for populations in Latin America (LA)
In our initial analysis with MLST the hpEurope group was rather spread in a number of different clusters and mixed with some of the LA strains, as previously reported (Falush et al, 2003; Thorell et al, 2016)

Summary

Introduction

Helicobacter pylori is a Gram negative bacterium that colonizes the human gastric mucosa of approximately 50% of the human population and induces a chronic inflammatory process. The H. pylori pathogenic mechanisms are complex, but one of the best recognized virulence factors involved in carcinogenesis is the CagA protein and the presence of the type four secretion system (T4SS) encoded in the cag pathogenicity island (cagPAI) (Blaser et al, 1995; Odenbreit et al, 2000; Ohnishi et al, 2008). Several other genes might be associated with disease development and analysis at whole genome level is necessary to better understand the mechanisms involved in cancer pathogenesis. A comprehensive study of the genome of 39 H. pylori strains estimated a total of 59,958 genes for the pangenome, and a core or central genome comprised of approximately 1,193 core gene-families (Ali et al, 2015)

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