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Gut Pathog. 2017 Sep 11;9:52. doi: 10.1186/s13099-017-0201-1. eCollection 2017.

Phylogenomics of Colombian Helicobacter pylori isolates.

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Grupo de Investigaciones Biomédicas y Genética Humana Aplicada, Programa de Medicina, Universidad de Ciencias Aplicadas y Ambientales, Calle 222 55-37, Bogotá, Colombia.
Programa de Doctorado en Ciencias Biológicas, Universidad Javeriana, Carrera 7 40-62, Bogotá, Colombia.
Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Calle 1 9-85, Bogotá, Colombia.
Grupo de Biofísica y Bioquímica Estructural, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7 40-62, Bogotá, Colombia.



During the Spanish colonisation of South America, African slaves and Europeans arrived in the continent with their corresponding load of pathogens, including Helicobacter pylori. Colombian strains have been clustered with the hpEurope population and with the hspWestAfrica subpopulation in multilocus sequence typing (MLST) studies. However, ancestry studies have revealed the presence of population components specific to H. pylori in Colombia. The aim of this study was to perform a thorough phylogenomic analysis to describe the evolution of the Colombian urban H. pylori isolates.


A total of 115 genomes of H. pylori were sequenced with Illumina technology from H. pylori isolates obtained in Colombia in a region of high risk for gastric cancer. The genomes were assembled, annotated and underwent phylogenomic analysis with 36 reference strains. Additionally, population differentiation analyses were performed for two bacterial genes. The phylogenetic tree revealed clustering of the Colombian strains with hspWestAfrica and hpEurope, along with three clades formed exclusively by Colombian strains, suggesting the presence of independent evolutionary lines for Colombia. Additionally, the nucleotide diversity of horB and vacA genes from Colombian isolates was lower than in the reference strains and showed a significant genetic differentiation supporting the hypothesis of independent clades with recent evolution.


The presence of specific lineages suggest the existence of an hspColombia subtype that emerged from a small and relatively isolated ancestral population that accompanied crossbreeding of human population in Colombia.


Helicobacter pylori; Phylogenomic analysis; Whole genome sequence

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