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Whole Genome Sequence and Phylogenetic Analysis Show Helicobacter pylori Strains from Latin America Have Followed a Unique Evolution Pathway
- Source :
- Frontiers in Cellular and Infection Microbiology
- Publication Year :
- 2017
- Publisher :
- Frontiers Media S.A., 2017.
-
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.
- Subjects :
- 0301 basic medicine
Microbiology (medical)
Asia
Genotype
Sequence analysis
Immunology
Locus (genetics)
Biology
Genome
Microbiology
Evolution, Molecular
03 medical and health sciences
Bacterial Proteins
Sequence Homology, Nucleic Acid
Cluster Analysis
Humans
Colonization
Clade
Phylogeny
Original Research
Genetics
Whole genome sequencing
Phylogenetic tree
Helicobacter pylori
Virulence
phylogenetic analysis
whole genome sequence
Genetic Variation
DNA Fingerprinting
Europe
Phylogeography
030104 developmental biology
Infectious Diseases
Latin America
Africa
Multilocus sequence typing
Americas
DNA Probes
Databases, Nucleic Acid
H. pylori
Genome, Bacterial
Multilocus Sequence Typing
Subjects
Details
- Language :
- English
- ISSN :
- 22352988
- Volume :
- 7
- Database :
- OpenAIRE
- Journal :
- Frontiers in Cellular and Infection Microbiology
- Accession number :
- edsair.doi.dedup.....489ef60197ec6354693702156ed24911