title: Whole Genome Sequence and Phylogenetic Analysis ShowHelicobacter pyloriStrains 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 ofcagPAIvirulence 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. WithcagPAIsequence 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. pylorihas 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.
authors.affiliation: Laboratorio de Biotecnología y Bioinformática Genómica, ENCB, Instituto Politécnico Nacional Ciudad de México, Mexico.
authors.forename: Zilia Y
authors.initials: ZY
authors.lastname: Muñoz-Ramírez
authors.affiliation: Laboratorio de Biotecnología y Bioinformática Genómica, ENCB, Instituto Politécnico Nacional Ciudad de México, Mexico.
authors.forename: Alfonso
authors.initials: A
authors.lastname: Mendez-Tenorio
authors.affiliation: Department of Oncology and of Pathology, Wayne State University School of Medicine Detroit, MI, USA.
authors.forename: Ikuko
authors.initials: I
authors.lastname: Kato
authors.affiliation: Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerologia Bogota, Colombia.
authors.forename: Maria M
authors.initials: MM
authors.lastname: Bravo
authors.affiliation: Dipartmento di Ricerca Traslazionale e Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa Pisa, Italy.
authors.forename: Cosmeri
authors.initials: C
authors.lastname: Rizzato
authors.affiliation: Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Stockholm, Sweden.
authors.forename: Kaisa
authors.initials: K
authors.lastname: Thorell
authors.affiliation: Laboratorio de Biotecnología y Bioinformática Genómica, ENCB, Instituto Politécnico Nacional Ciudad de México, Mexico.
authors.forename: Roberto
authors.initials: R
authors.lastname: Torres
authors.affiliation: Unidad de Investigacion en Enfermedades Infecciosas, IMSS Ciudad de México, Mexico.
authors.forename: Francisco
authors.initials: F
authors.lastname: Aviles-Jimenez
authors.affiliation: Unidad de Investigacion en Enfermedades Infecciosas, IMSS Ciudad de México, Mexico.
authors.forename: Margarita
authors.initials: M
authors.lastname: Camorlinga
authors.affiliation: Genomic Epidemiology Group, German Cancer Research Center (DKFZ) Heidelberg, Germany.
authors.forename: Federico
authors.initials: F
authors.lastname: Canzian
authors.affiliation: Unidad de Investigacion en Enfermedades Infecciosas, IMSS Ciudad de México, Mexico.
authors.forename: Javier
authors.initials: J
authors.lastname: Torres
mesh_terms: D000349:Africa; D000569:Americas; D001208:Asia; D001426:Bacterial Proteins / Q000235:genetics; D016000:Cluster Analysis; D016172:DNA Fingerprinting; D015342:DNA Probes; D030561:Databases, Nucleic Acid; D005060:Europe; D019143:Evolution, Molecular; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics*; D005838:Genotype; D016480:Helicobacter pylori / Q000235:genetics* / Q000472:pathogenicity*; D006801:Humans; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D058974:Phylogeography; D012689:Sequence Homology, Nucleic Acid; D014774:Virulence / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D015342:DNA Probes
keywords: H. pylori; Latin America; phylogenetic analysis; whole genome sequence