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

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.

Keywords: H. pylori; Latin America; phylogenetic analysis; whole genome sequence.

Figure 1

Phylogenetic analyses of 113 Latin American and 54 worldwide H. pylori strains using the Multi Locus Sequence Typing method with seven housekeeping genes (Falush et al., 2003).

Figure 2

Phylogenetic analyses of 113 Latin American and 54 worldwide H. pylori strains using whole genome sequences analyzed with a virtual hybridization technique (VGF). The genome of the related H. acinonychis Sheeba strain was used to root the tree.

Figure 3

Phylogenetic analyses of 96 Latin American and 43 worldwide H. pylori strains using the sequences of the genes of the cagPAI virulence island. Phylogenetic analyses were done with MEGA 5.02, and distance-based phylogenetic trees were calculated using the T92+G+I model. Phylogenetic trees were edited and annotated with iTol v3.

Figure 4

Phylogenetic analyses of 94 Latin American and 43 worldwide H. pylori strains using the sequence of the cagA gene. Phylogenetic analyses were done with MEGA 5.02, and distance-based phylogenetic trees were calculated using the T92+G+I model. Phylogenetic trees were edited and annotated with iTol v3.

Figure 5

Phylogenetic network analyses of 113 Latin American and 54 worldwide H. pylori strains using whole genome sequences. To the right is an amplified view of the central part of the figure to better observe the reticulation events among strains.