Skip to main content
Key Specialties
Cardiology Diabetology Endocrinology Gastroenterology Geriatrics and Gerontology Gynecology and Obstetrics Hematology Infectious Disease Internal Medicine Nephrology Neurology Oncology Pediatrics Respiratory Medicine Rheumatology Surgery
Congress Coverage
2024 ACC Congress 2023 ESMO Congress 2023 EASD Congress 2023 ERS Congress 2023 ESC Congress 2023 EHA Congress 2023 ASCO Annual Meeting
Clinical Collections
Advances in Alzheimer’s

ACC 2024 Congress

Catch up on all the top stories and latest evidence in cardiology research with our ACC 2024 Congress hub page.
ADVANCED SEARCH
Log in
Top
Gut Pathogens
Published in: Gut Pathogens 1/2017

Open Access 01-12-2017 | Research

Phylogenomics of Colombian Helicobacter pylori isolates

Authors: Andrés Julián Gutiérrez-Escobar, Esperanza Trujillo, Orlando Acevedo, María Mercedes Bravo

Published in: Gut Pathogens | Issue 1/2017

Login to get access

Abstract

Background

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.

Results

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.

Conclusions

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.
Appendix
Available only for authorised users
Literature
1.
Perez-Perez GI, Rothenbacher D, Brenner H. Epidemiology of Helicobacter pylori infection. Helicobacter. 2004;9(Suppl 1):1–6.CrossRefPubMed
2.
3.
Amieva MR, El-Omar EM. Host-bacterial interactions in Helicobacter pylori infection. Gastroenterology. 2008;134:306–23.CrossRefPubMed
4.
5.
Fujimoto Y, Furusyo N, Toyoda K, Takeoka H, Sawayama Y, Hayashi J. Intrafamilial transmission of Helicobacter pylori among the population of endemic areas in Japan. Helicobacter. 2007;12:170–6.CrossRefPubMed
6.
7.
Linz B, Balloux F, Moodley Y, Manica A, Liu H, Roumagnac P, et al. An African origin for the intimate association between humans and Helicobacter pylori. Nature. 2007;445:915–8.CrossRefPubMedPubMedCentral
8.
Achtman M, Azuma T, Berg DE, Ito Y, Morelli G, Pan ZJ, et al. Recombination and clonal groupings within Helicobacter pylori from different geographical regions. Mol Microbiol. 1999;32:459–70.CrossRefPubMed
9.
Falush D, Wirth T, Linz B, Pritchard JK, Stephens M, Kidd M, et al. Traces of human migrations in Helicobacter pylori populations. Science. 2003;299:1582–5.CrossRefPubMed
10.
Moodley Y, Linz B, Yamaoka Y, Windsor HM, Breurec S, Wu JY, et al. The peopling of the Pacific from a bacterial perspective. Science. 2009;323:527–30.CrossRefPubMedPubMedCentral
11.
Devi SM, Ahmed I, Francalacci P, Hussain MA, Akhter Y, Alvi A, et al. Ancestral European roots of Helicobacter pylori in India. BMC Genom. 2007;8:184.CrossRef
12.
13.
Kersulyte D, Kalia A, Gilman RH, Mendez M, Herrera P, Cabrera L, et al. Helicobacter pylori from Peruvian amerindians: traces of human migrations in strains from remote Amazon, and genome sequence of an Amerind strain. PLoS ONE. 2010;5:e15076.CrossRefPubMedPubMedCentral
14.
Bianchine PJ, Russo TA. The role of epidemic infectious diseases in the discovery of America. Allergy Proc. 1992;13:225–32.CrossRefPubMed
15.
Parrish CR, Holmes EC, Morens DM, Park EC, Burke DS, Calisher CH, et al. Cross-species virus transmission and the emergence of new epidemic diseases. Microbiol Mol Biol Rev. 2008;72:457–70.CrossRefPubMedPubMedCentral
16.
de Sablet T, Piazuelo MB, Shaffer CL, Schneider BG, Asim M, Chaturvedi R, et al. Phylogeographic origin of Helicobacter pylori is a determinant of gastric cancer risk. Gut. 2011;60:1189–95.CrossRefPubMedPubMedCentral
17.
Shiota S, Suzuki R, Matsuo Y, Miftahussurur M, Tran TT, Binh TT, et al. Helicobacter pylori from gastric cancer and duodenal ulcer show same phylogeographic origin in the Andean region in Colombia. PLoS ONE. 2014;9:e105392.CrossRefPubMedPubMedCentral
18.
Munoz-Ramirez ZY, Mendez-Tenorio A, Kato I, Bravo MM, Rizzato C, Thorell K, et al. Whole genome sequence and phylogenetic analysis show Helicobacter pylori strains from latin America have followed a unique evolution pathway. Front Cell Infect Microbiol. 2017;7:50.CrossRefPubMedPubMedCentral
19.
Kodaman N, Pazos A, Schneider BG, Piazuelo MB, Mera R, Sobota RS, et al. Human and Helicobacter pylori coevolution shapes the risk of gastric disease. Proc Natl Acad Sci USA. 2014;111:1455–60.CrossRefPubMedPubMedCentral
20.
Dominguez-Bello MG, Perez ME, Bortolini MC, Salzano FM, Pericchi LR, Zambrano-Guzman O, et al. Amerindian Helicobacter pylori strains go extinct, as european strains expand their host range. PLoS ONE. 2008;3:e3307.CrossRefPubMedPubMedCentral
21.
Suzuki R, Shiota S, Yamaoka Y. Molecular epidemiology, population genetics, and pathogenic role of Helicobacter pylori. Infect Genet Evol. 2012;12:203–13.CrossRefPubMed
22.
Furuta Y, Konno M, Osaki T, Yonezawa H, Ishige T, Imai M, et al. Microevolution of virulence-related genes in Helicobacter pylori familial infection. PLoS ONE. 2015;10:e0127197.CrossRefPubMedPubMedCentral
23.
Cao Q, Didelot X, Wu Z, Li Z, He L, Li Y, et al. Progressive genomic convergence of two Helicobacter pylori strains during mixed infection of a patient with chronic gastritis. Gut. 2015;64:554–61.CrossRefPubMed
24.
Thorell K, Yahara K, Berthenet E, Lawson DJ, Mikhail J, Kato I, et al. Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas. PLoS Genet. 2017;13:e1006546.CrossRefPubMedPubMedCentral
25.
26.
Snelling WJ, Moran AP, Ryan KA, Scully P, McGourty K, Cooney JC, et al. HorB (HP0127) is a gastric epithelial cell adhesin. Helicobacter. 2007;12:200–9.CrossRefPubMed
27.
Jones KR, Whitmire JM, Merrell DS. A tale of two toxins: Helicobacter pylori CagA and VacA modulate host pathways that impact disease. Front Microbiol. 2010;1:115.CrossRefPubMedPubMedCentral
28.
29.
Peng Y, Leung HC, Yiu SM, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28:1420–8.CrossRefPubMed
30.
Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 2011;27:578–9.CrossRefPubMed
31.
Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics. 2015;31:587–9.CrossRefPubMed
32.
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res. 2014;42:D206–14.CrossRefPubMed
33.
34.
35.
Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44:W242–5.CrossRefPubMedPubMedCentral
36.
Agren J, Sundstrom A, Hafstrom T, Segerman B. Gegenees: fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups. PLoS ONE. 2012;7:e39107.CrossRefPubMedPubMedCentral
37.
Kumar N, Mukhopadhyay AK, Patra R, De R, Baddam R, Shaik S, et al. Next-generation sequencing and de novo assembly, genome organization, and comparative genomic analyses of the genomes of two Helicobacter pylori isolates from duodenal ulcer patients in India. J Bacteriol. 2012;194:5963–4.CrossRefPubMedPubMedCentral
38.
Huson DH. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics. 1998;14:68–73.CrossRefPubMed
39.
Gardner SN, Slezak T, Hall BG. kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics. 2015;31:2877–8.CrossRefPubMed
40.
van Vliet AH, Kusters JG. Use of alignment-free phylogenetics for rapid genome sequence-based typing of Helicobacter pylori virulence markers and antibiotic susceptibility. J Clin Microbiol. 2015;53:2877–88.CrossRefPubMedPubMedCentral
41.
Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol. 2013;79:7696–701.CrossRefPubMedPubMedCentral
42.
Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.PubMed
43.
Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123:585–95.PubMedPubMedCentral
44.
Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007;56:564–77.CrossRefPubMed
45.
Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25:1451–2.CrossRefPubMed
46.
Ruiz-Linares A, Adhikari K, Acuna-Alonzo V, Quinto-Sanchez M, Jaramillo C, Arias W, et al. Admixture in Latin America: geographic structure, phenotypic diversity and self-perception of ancestry based on 7342 individuals. PLoS Genet. 2014;10:e1004572.CrossRefPubMedPubMedCentral
47.
Linz B, Vololonantenainab CR, Seck A, Carod JF, Dia D, Garin B, et al. Population genetic structure and isolation by distance of Helicobacter pylori in Senegal and Madagascar. PLoS ONE. 2014;9:e87355.CrossRefPubMedPubMedCentral
48.
49.
Camorlinga-Ponce M, Perez-Perez G, Gonzalez-Valencia G, Mendoza I, Penaloza-Espinosa R, Ramos I, et al. Helicobacter pylori genotyping from American indigenous groups shows novel Amerindian vacA and cagA alleles and Asian, African and European admixture. PLoS ONE. 2011;6:e27212.CrossRefPubMedPubMedCentral
50.
Sicinschi LA, Correa P, Peek RM, Camargo MC, Piazuelo MB, Romero-Gallo J, et al. CagA C-terminal variations in Helicobacter pylori strains from Colombian patients with gastric precancerous lesions. Clin Microbiol Infect. 2010;16:369–78.CrossRefPubMed
51.
Thorell K, Hosseini S, Palacios Gonzales RV, Chaotham C, Graham DY, Paszat L, et al. Identification of a Latin American-specific BabA adhesin variant through whole genome sequencing of Helicobacter pylori patient isolates from Nicaragua. BMC Evol Biol. 2016;16:53.CrossRefPubMedPubMedCentral
52.
Yamaoka Y, Orito E, Mizokami M, Gutierrez O, Saitou N, Kodama T, et al. Helicobacter pylori in North and South America before Columbus. FEBS Lett. 2002;517:180–4.CrossRefPubMed
53.
54.
Suzuki M, Kiga K, Kersulyte D, Cok J, Hooper CC, Mimuro H, et al. Attenuated CagA oncoprotein in Helicobacter pylori from Amerindians in Peruvian Amazon. J Biol Chem. 2011;286:29964–72.CrossRefPubMedPubMedCentral
55.
Kumar N, Mariappan V, Baddam R, Lankapalli AK, Shaik S, Goh KL, et al. Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution. Nucleic Acids Res. 2015;43:324–35.CrossRefPubMed
56.
Kumar N, Albert MJ, Al AH, Siddique I, Ahmed N. What constitutes an Arabian Helicobacter pylori? Lessons from comparative genomics. Helicobacter. 2016;22:1–11.
Metadata
Title
Phylogenomics of Colombian Helicobacter pylori isolates
Authors
Andrés Julián Gutiérrez-Escobar
Esperanza Trujillo
Orlando Acevedo
María Mercedes Bravo
Publication date
01-12-2017
Publisher
BioMed Central
Published in
Gut Pathogens / Issue 1/2017
Electronic ISSN: 1757-4749
DOI
https://doi.org/10.1186/s13099-017-0201-1

Other articles of this Issue 1/2017

Gut Pathogens 1/2017 Go to the issue

Genome Report

Complete genome sequence of the Vibrio vulnificus strain VV2014DJH, a human-pathogenic bacterium isolated from a death case in China

Genome Report

Complete genome sequence of Vibrio campbellii strain 20130629003S01 isolated from shrimp with acute hepatopancreatic necrosis disease

Research

Assessment of antibiotic susceptibility in Lactobacillus isolates from chickens

Case report

Carbuncle due to Salmonella Enteritidis: a novel presentation

Research

The in vitro and ex vivo effect of Auranta 3001 in preventing Cryptosporidium hominis and Cryptosporidium parvum infection

Genome report

Complete genome sequence of Clostridium perfringens CBA7123 isolated from a faecal sample from Korea

ACC 2024 Congress Coverage

Cardiology Video

Highlights from the ACC 2024 Congress

Watch now

Watch official videos from the ACC congress summarizing key highlights from the last year in heart failure, cardiomyopathies, valvular disease, pulmonary vascular disease, and pediatric cardiology.

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

16-04-2024 Type 2 Diabetes News

Incentivised to exercise

11-04-2024 Lifestyle Modifications News

New intervention for STEMI-related cardiogenic shock

10-04-2024 Myocardial Infarction News

» View more highlights on the ACC 2024 congress hub page

Image Credits