Identification of a Latin American-specific BabA adhesin variant through whole genome sequencing of Helicobacter pylori patient isolates from Nicaragua
Abstract
In this study, Helicobacter pylori (H. pylori) is one of the most common bacterial infections in humans and this infection can lead to gastric ulcers and gastric cancer. H. pylori is one of the most genetically variable human pathogens and the ability of the bacterium to bind to the host epithelium as well as the presence of different virulence factors and genetic variants within these genes have been associated with disease severity. Nicaragua has particularly high gastric cancer incidence and we therefore studied Nicaraguan clinical H. pylori isolates for factors that could contribute to cancer risk. The complete genomes of fifty-two Nicaraguan H. pylorii isolates were sequenced and assembled de novo, and phylogenetic and virulence factor analyses were performed. The Nicaraguan isolates showed phylogenetic relationship with West African isolates in whole-genome sequence comparisons and with Western and urban South-and Central American isolates using MLSA (Multi-locus sequence analysis). A majority, 77 % of the isolates carried the cancer-associated virulence gene cagA and also the s1/i1/m1 vacuolating cytotoxin, vacA allele combination, which is linked to increased severity of disease. Specifically, we also found that Nicaraguan isolates have a blood group-binding adhesin (BabA) variant highly similar to previously reported BabA sequences from Latinmore »
- Authors:
-
- Univ. of Gothenburg, Gothenburg (Sweden); Univ. of Technology, Gothenburg (Sweden); Karolinska Institutet, Stockholm (Sweden)
- Chalmers Univ. of Technology, Gothenburg (Sweden)
- Hospital Salud Integral, Managua (Nicaragua)
- Univ. of Gothenburg, Gothenburg (Sweden)
- Baylor College of Medicine, Houston, TX (United States)
- Univ. of Toronto, Toronto (Canada)
- Chalmers Univ. of Technology, Gothenburg (Sweden); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Univ. of Gothenburg, Gothenburg (Sweden); Karolinska Institutet, Stockholm (Sweden)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1334458
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Evolutionary Biology (Online)
- Additional Journal Information:
- Journal Name: BMC Evolutionary Biology (Online); Journal Volume: 16; Journal Issue: 1; Journal ID: ISSN 1471-2148
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Helicobacter; whole-genome sequencing; phylogeny; virulence factors; BabA
Citation Formats
Thorell, Kaisa, Hosseini, Shaghayegh, Palacios Gonzales, Reyna Victoria Palacios, Chaotham, Chatchai, Graham, David Y., Paszat, Lawrence, Rabeneck, Linda, Lundin, Samuel B., Nookaew, Intawat, and Sjoling, Asa. Identification of a Latin American-specific BabA adhesin variant through whole genome sequencing of Helicobacter pylori patient isolates from Nicaragua. United States: N. p., 2016.
Web. doi:10.1186/s12862-016-0619-y.
Thorell, Kaisa, Hosseini, Shaghayegh, Palacios Gonzales, Reyna Victoria Palacios, Chaotham, Chatchai, Graham, David Y., Paszat, Lawrence, Rabeneck, Linda, Lundin, Samuel B., Nookaew, Intawat, & Sjoling, Asa. Identification of a Latin American-specific BabA adhesin variant through whole genome sequencing of Helicobacter pylori patient isolates from Nicaragua. United States. https://doi.org/10.1186/s12862-016-0619-y
Thorell, Kaisa, Hosseini, Shaghayegh, Palacios Gonzales, Reyna Victoria Palacios, Chaotham, Chatchai, Graham, David Y., Paszat, Lawrence, Rabeneck, Linda, Lundin, Samuel B., Nookaew, Intawat, and Sjoling, Asa. Mon .
"Identification of a Latin American-specific BabA adhesin variant through whole genome sequencing of Helicobacter pylori patient isolates from Nicaragua". United States. https://doi.org/10.1186/s12862-016-0619-y. https://www.osti.gov/servlets/purl/1334458.
@article{osti_1334458,
title = {Identification of a Latin American-specific BabA adhesin variant through whole genome sequencing of Helicobacter pylori patient isolates from Nicaragua},
author = {Thorell, Kaisa and Hosseini, Shaghayegh and Palacios Gonzales, Reyna Victoria Palacios and Chaotham, Chatchai and Graham, David Y. and Paszat, Lawrence and Rabeneck, Linda and Lundin, Samuel B. and Nookaew, Intawat and Sjoling, Asa},
abstractNote = {In this study, Helicobacter pylori (H. pylori) is one of the most common bacterial infections in humans and this infection can lead to gastric ulcers and gastric cancer. H. pylori is one of the most genetically variable human pathogens and the ability of the bacterium to bind to the host epithelium as well as the presence of different virulence factors and genetic variants within these genes have been associated with disease severity. Nicaragua has particularly high gastric cancer incidence and we therefore studied Nicaraguan clinical H. pylori isolates for factors that could contribute to cancer risk. The complete genomes of fifty-two Nicaraguan H. pylorii isolates were sequenced and assembled de novo, and phylogenetic and virulence factor analyses were performed. The Nicaraguan isolates showed phylogenetic relationship with West African isolates in whole-genome sequence comparisons and with Western and urban South-and Central American isolates using MLSA (Multi-locus sequence analysis). A majority, 77 % of the isolates carried the cancer-associated virulence gene cagA and also the s1/i1/m1 vacuolating cytotoxin, vacA allele combination, which is linked to increased severity of disease. Specifically, we also found that Nicaraguan isolates have a blood group-binding adhesin (BabA) variant highly similar to previously reported BabA sequences from Latin America, including from isolates belonging to other phylogenetic groups. These BabA sequences were found to be under positive selection at several amino acid positions that differed from the global collection of isolates. In conclusion, the discovery of a Latin American BabA variant, independent of overall phylogenetic background, suggests hitherto unknown host or environmental factors within the Latin American population giving H. pylori isolates carrying this adhesin variant a selective advantage, which could affect pathogenesis and risk for sequelae through specific adherence properties.},
doi = {10.1186/s12862-016-0619-y},
journal = {BMC Evolutionary Biology (Online)},
number = 1,
volume = 16,
place = {United States},
year = {Mon Feb 29 00:00:00 EST 2016},
month = {Mon Feb 29 00:00:00 EST 2016}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 17 works
Citation information provided by
Web of Science
Web of Science
Figures / Tables:
Table 1: Strain information
All figures and tables
(10 total)
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
BayesHammer: Bayesian clustering for error correction in single-cell sequencing
journal, January 2013
- Nikolenko, Sergey I.; Korobeynikov, Anton I.; Alekseyev, Max A.
- BMC Genomics, Vol. 14, Issue Suppl 1
QUAST: quality assessment tool for genome assemblies
journal, February 2013
- Gurevich, Alexey; Saveliev, Vladislav; Vyahhi, Nikolay
- Bioinformatics, Vol. 29, Issue 8
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
journal, September 2010
- Cox, Murray P.; Peterson, Daniel A.; Biggs, Patrick J.
- BMC Bioinformatics, Vol. 11, Issue 1
Versatile and open software for comparing large genomes
journal, January 2004
- Kurtz, Stefan; Phillippy, Adam; Delcher, Arthur L.
- Genome Biology, Vol. 5, Issue 2, R12
THE PATHOGENESIS OF HELICOBACTER PYLORI –INDUCED GASTRO-DUODENAL DISEASES
journal, February 2006
- Atherton, John C.
- Annual Review of Pathology: Mechanisms of Disease, Vol. 1, Issue 1
Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative
journal, August 2006
- Anisimova, Maria; Gascuel, Olivier
- Systematic Biology, Vol. 55, Issue 4
Helicobacter pylori Sequences Reflect Past Human Migrations
book, January 2009
- Moodley, Y.; Linz, B.
- Microbial Pathogenomics
Functional Adaptation of BabA, the H. pylori ABO Blood Group Antigen Binding Adhesin
journal, July 2004
- Aspholm-Hurtig, M.
- Science, Vol. 305, Issue 5683
Helicobacter pylori genome evolution during human infection
journal, March 2011
- Kennemann, L.; Didelot, X.; Aebischer, T.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 12
Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution
journal, December 2014
- Kumar, Narender; Mariappan, Vanitha; Baddam, Ramani
- Nucleic Acids Research, Vol. 43, Issue 1
Dynamics of Lewis b Binding and Sequence Variation of the babA Adhesin Gene during Chronic Helicobacter pylori Infection in Humans
journal, December 2014
- Nell, Sandra; Kennemann, Lynn; Schwarz, Sandra
- mBio, Vol. 5, Issue 6
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
journal, November 2014
- Croucher, Nicholas J.; Page, Andrew J.; Connor, Thomas R.
- Nucleic Acids Research, Vol. 43, Issue 3
Helicobacter pylori from Peruvian Amerindians: Traces of Human Migrations in Strains from Remote Amazon, and Genome Sequence of an Amerind Strain
journal, November 2010
- Kersulyte, Dangeruta; Kalia, Awdhesh; Gilman, Robert H.
- PLoS ONE, Vol. 5, Issue 11
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
Comparative Analysis of the Full Genome of Helicobacter pylori Isolate Sahul64 Identifies Genes of High Divergence
journal, December 2013
- Lu, W.; Wise, M. J.; Tay, C. Y.
- Journal of Bacteriology, Vol. 196, Issue 5
Helicobacter pylori: gastric cancer and beyond
journal, June 2010
- Polk, D. Brent; Peek, Richard M.
- Nature Reviews Cancer, Vol. 10, Issue 6
Achieving self-sufficiency of red blood cells based on universal voluntary blood donation in Latin America. The case of Nicaragua
journal, December 2013
- Berrios, René; Gonzalez, Alcides; Cruz, José Ramiro
- Transfusion and Apheresis Science, Vol. 49, Issue 3
Clinical relevance of cagA and vacA gene polymorphisms in Helicobacter pylori isolates from Senegalese patients
journal, February 2012
- Breurec, S.; Michel, R.; Seck, A.
- Clinical Microbiology and Infection, Vol. 18, Issue 2
Gastric carcinogenesis
journal, May 2011
- Bornschein, Jan; Malfertheiner, Peter
- Langenbeck's Archives of Surgery, Vol. 396, Issue 6
Phylogeographic origin of Helicobacter pylori is a determinant of gastric cancer risk
journal, February 2011
- de Sablet, T.; Piazuelo, M. B.; Shaffer, C. L.
- Gut, Vol. 60, Issue 9
Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data
journal, March 2006
- Pérez-Losada, Marcos; Browne, Emily B.; Madsen, Aaron
- Infection, Genetics and Evolution, Vol. 6, Issue 2
SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building
journal, October 2009
- Gouy, M.; Guindon, S.; Gascuel, O.
- Molecular Biology and Evolution, Vol. 27, Issue 2
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
journal, January 2013
- Katoh, K.; Standley, D. M.
- Molecular Biology and Evolution, Vol. 30, Issue 4
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008
- Zerbino, D. R.; Birney, E.
- Genome Research, Vol. 18, Issue 5
Traces of Human Migrations in Helicobacter pylori Populations
journal, March 2003
- Falush, D.
- Science, Vol. 299, Issue 5612
An African origin for the intimate association between humans and Helicobacter pylori
journal, February 2007
- Linz, Bodo; Balloux, François; Moodley, Yoshan
- Nature, Vol. 445, Issue 7130
Helicobacter pylori Genotyping from American Indigenous Groups Shows Novel Amerindian vacA and cagA Alleles and Asian, African and European Admixture
journal, November 2011
- Camorlinga-Ponce, Margarita; Perez-Perez, Guillermo; Gonzalez-Valencia, Gerardo
- PLoS ONE, Vol. 6, Issue 11
A Global Overview of the Genetic and Functional Diversity in the Helicobacter pylori cag Pathogenicity Island
journal, August 2010
- Olbermann, Patrick; Josenhans, Christine; Moodley, Yoshan
- PLoS Genetics, Vol. 6, Issue 8
Biological activity of the Helicobacter pylori virulence factor CagA is determined by variation in the tyrosine phosphorylation sites
journal, October 2002
- Higashi, H.; Tsutsumi, R.; Fujita, A.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 22
Mosaicism in Vacuolating Cytotoxin Alleles of Helicobacter pylori : ASSOCIATION OF SPECIFIC
journal, July 1995
- Atherton, John C.; Cao, Ping; Peek, Richard M.
- Journal of Biological Chemistry, Vol. 270, Issue 30
Prokka: rapid prokaryotic genome annotation
journal, March 2014
- Seemann, T.
- Bioinformatics, Vol. 30, Issue 14
Genome Sequences of Three hpAfrica2 Strains of Helicobacter pylori
journal, August 2013
- Duncan, S. S.; Bertoli, M. T.; Kersulyte, D.
- Genome Announcements, Vol. 1, Issue 5
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
journal, July 2002
- Katoh, K.
- Nucleic Acids Research, Vol. 30, Issue 14
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
journal, May 2012
- Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry
- Journal of Computational Biology, Vol. 19, Issue 5
Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island
journal, July 2006
- Devi, S. Manjulata; Ahmed, Irshad; Khan, Aleem A.
- BMC Genomics, Vol. 7, Issue 1
Genome-Wide Survey of Mutual Homologous Recombination in a Highly Sexual Bacterial Species
journal, January 2012
- Yahara, Koji; Kawai, Mikihiko; Furuta, Yoshikazu
- Genome Biology and Evolution, Vol. 4, Issue 5
Helicobacter pylori SabA Adhesin in Persistent Infection and Chronic Inflammation
journal, July 2002
- Mahdavi, J.
- Science, Vol. 297, Issue 5581
cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors
journal, December 1996
- Censini, S.; Lange, C.; Xiang, Z.
- Proceedings of the National Academy of Sciences, Vol. 93, Issue 25
Recombination and clonal groupings within Helicobacter pylori from different geographical regions
journal, May 1999
- Achtman, Mark; Azuma, Takeshi; Berg, Douglas E.
- Molecular Microbiology, Vol. 32, Issue 3
A New Helicobacter pylori Vacuolating Cytotoxin Determinant, the Intermediate Region, Is Associated With Gastric Cancer
journal, September 2007
- Rhead, Joanne L.; Letley, Darren P.; Mohammadi, Marjan
- Gastroenterology, Vol. 133, Issue 3
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach
journal, May 2007
- Stern, A.; Doron-Faigenboim, A.; Erez, E.
- Nucleic Acids Research, Vol. 35, Issue Web Server
Pathology of Gastric Cancer and Its Precursor Lesions
journal, June 2013
- Yakirevich, Evgeny; Resnick, Murray B.
- Gastroenterology Clinics of North America, Vol. 42, Issue 2
Failure To Detect Helicobacter pylori DNA in Drinking and Environmental Water in Dhaka, Bangladesh, Using Highly Sensitive Real-Time PCR Assays
journal, March 2009
- Janzon, A.; Sjoling, A.; Lothigius, A.
- Applied and Environmental Microbiology, Vol. 75, Issue 10
Pathogenesis of Helicobacter pylori Infection: H. pylori Pathogenesis
journal, September 2011
- Backert, Steffen; Clyne, Marguerite
- Helicobacter, Vol. 16
Basic local alignment search tool
journal, October 1990
- Altschul, Stephen F.; Gish, Warren; Miller, Webb
- Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
Molecular epidemiology, population genetics, and pathogenic role of Helicobacter pylori
journal, March 2012
- Suzuki, Rumiko; Shiota, Seiji; Yamaoka, Yoshio
- Infection, Genetics and Evolution, Vol. 12, Issue 2
Tyrosine phosphorylation of the Helicobacter pylori CagA antigen after cag-driven host cell translocation
journal, February 2000
- Stein, M.; Rappuoli, R.; Covacci, A.
- Proceedings of the National Academy of Sciences, Vol. 97, Issue 3
Human Gastric Mucins Differently Regulate Helicobacter pylori Proliferation, Gene Expression and Interactions with Host Cells
journal, May 2012
- Skoog, Emma C.; Sjöling, Åsa; Navabi, Nazanin
- PLoS ONE, Vol. 7, Issue 5
Helicobacter pylori Adhesin Binding Fucosylated Histo-Blood Group Antigens Revealed by Retagging
journal, January 1998
- Ilver, D.
- Science, Vol. 279, Issue 5349
The Three-dimensional Structure of the Extracellular Adhesion Domain of the Sialic Acid-binding Adhesin SabA from Helicobacter pylori
journal, December 2013
- Pang, Siew Siew; Nguyen, Stanley Thai Son; Perry, Andrew J.
- Journal of Biological Chemistry, Vol. 289, Issue 10
A Role for the Vacuolating Cytotoxin, VacA, in Colonization and Helicobacter pylori–Induced Metaplasia in the Stomach
journal, March 2014
- Winter, Jody A.; Letley, Darren P.; Cook, Katherine W.
- The Journal of Infectious Diseases, Vol. 210, Issue 6
The Peopling of the Pacific from a Bacterial Perspective
journal, January 2009
- Moodley, Y.; Linz, B.; Yamaoka, Y.
- Science, Vol. 323, Issue 5913
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
journal, April 2009
- Price, M. N.; Dehal, P. S.; Arkin, A. P.
- Molecular Biology and Evolution, Vol. 26, Issue 7
Protein database searches using compositionally adjusted substitution matrices
journal, October 2005
- Altschul, Stephen F.; Wootton, John C.; Gertz, E. Michael
- FEBS Journal, Vol. 272, Issue 20
Epidemiology of Helicobacter pylori infection in six Latin American countries (SWOG Trial S0701)
journal, December 2012
- Porras, Carolina; Nodora, Jesse; Sexton, Rachael
- Cancer Causes & Control, Vol. 24, Issue 2
Attachment of Helicobacter pylori to human gastric epithelium mediated by blood group antigens
journal, December 1993
- Boren, T.; Falk, P.; Roth, K.
- Science, Vol. 262, Issue 5141
Socioeconomic and Nutritional Factors Account for the Association of Gastric Cancer with Amerindian Ancestry in a Latin American Admixed Population
journal, August 2012
- Pereira, Latife; Zamudio, Roxana; Soares-Souza, Giordano
- PLoS ONE, Vol. 7, Issue 8
Re-annotation of the genome sequence of Helicobacter pylori 26695
journal, December 2013
- Resende, Tiago; Correia, Daniela M.; Rocha, Miguel
- Journal of Integrative Bioinformatics, Vol. 10, Issue 3
Pathogenesis of Helicobacter pylori infection
journal, October 2003
- Lamarque, Dominique; M. Peek, Richard
- Helicobacter, Vol. 8, Issue s1
Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins
journal, March 2021
- Carim, Sean; Azadeh, Ashley L.; Kazakov, Alexey E.
- The ISME Journal, Vol. 15, Issue 8
Mutations in virus-derived small RNAs
journal, June 2020
- Nigam, Deepti; LaTourrette, Katherine; Garcia-Ruiz, Hernan
- Scientific Reports, Vol. 10, Issue 1
Pathogenesis of Helicobacter pylori Infection
journal, October 2006
- Hatakeyama, Masanori; Brzozowski, Tomasz
- Helicobacter, Vol. 11, Issue s1
Draft Genome Sequence of Comamonas aquatilis Strain LK (= CSUR P6418 = CECT 9772), Isolated from the Planarian Schmidtea mediterranea
journal, February 2021
- Kangale, Luis Johnson; Levasseur, Anthony; Raoult, Didier
- Microbiology Resource Announcements, Vol. 10, Issue 5
Draft Genome Sequence of Medusavirus Stheno, Isolated from the Tatakai River of Uji, Japan
journal, January 2021
- Yoshida, Koki; Zhang, Ruixuan; Garcia, Kimberly G.
- Microbiology Resource Announcements, Vol. 10, Issue 1
Attachment of Helicobacter pylori to human gastric epithelium mediated by blood group antigens: Borén T, Falk P, Roth KA, et al. Science 262:1892–1895, 1993
journal, January 1995
- ,
- Transfusion Medicine Reviews, Vol. 9, Issue 1, p. 82
Pathogenesis of Helicobacter pylori infection
journal, January 2000
- McGee, David J.; Mobley, Harry L. T.
- Current Opinion in Gastroenterology, Vol. 16, Issue 1
Re-annotation of the genome sequence of Helicobacter pylori 26695
text, January 2013
- Resende, Tiago; Correia, Daniela M.; Rocha, Miguel
- Journal of Integrative Bioinformatics
Pathogenesis of Helicobacter pylori infection
journal, January 1998
- Kelly, Ciar??n P.; Michetti, Pierre
- Current Opinion in Gastroenterology, Vol. 14, Issue 1
Pathogenesis of Helicobacter pylori Infection
journal, October 2007
- Maeda, Shin; Mentis, Andreas F.
- Helicobacter, Vol. 12, Issue s1
BayesHammer: Bayesian clustering for error correction in single-cell sequencing
text, January 2012
- Nikolenko, Sergey I.; Korobeynikov, Anton I.; Alekseyev, Max A.
- arXiv
Sequential eradication of Helicobacter pylori as a treatment for immune thrombocytopenia in patients with moderate thrombocytopenia: a multicenter prospective randomized phase 3 study
journal, May 2022
- Han, Boram; Kim, Hyo Jung; Yhim, Ho-Young
- Annals of Hematology, Vol. 101, Issue 7
Gastric carcinogenesis
journal, May 2011
- Bornschein, Jan; Malfertheiner, Peter
- Langenbeck's Archives of Surgery, Vol. 396, Issue 6
Is Helicobacter pylori infection associated with osteoporosis? a systematic review and meta-analysis
journal, November 2022
- Xiong, Chuang; Zhao, Runhan; Xu, Jingtao
- Journal of Bone and Mineral Metabolism, Vol. 41, Issue 1
Pathology of Gastric Cancer and Its Precursor Lesions
journal, June 2013
- Yakirevich, Evgeny; Resnick, Murray B.
- Gastroenterology Clinics of North America, Vol. 42, Issue 2
Molecular epidemiology, population genetics, and pathogenic role of Helicobacter pylori
journal, March 2012
- Suzuki, Rumiko; Shiota, Seiji; Yamaoka, Yoshio
- Infection, Genetics and Evolution, Vol. 12, Issue 2
Achieving self-sufficiency of red blood cells based on universal voluntary blood donation in Latin America. The case of Nicaragua
journal, December 2013
- Berrios, René; Gonzalez, Alcides; Cruz, José Ramiro
- Transfusion and Apheresis Science, Vol. 49, Issue 3
Helicobacter pylori: gastric cancer and beyond
journal, June 2010
- Polk, D. Brent; Peek, Richard M.
- Nature Reviews Cancer, Vol. 10, Issue 6
Commensal Pseudomonas protect Arabidopsis thaliana from a coexisting pathogen via multiple lineage-dependent mechanisms
journal, December 2021
- Shalev, Or; Ashkenazy, Haim; Neumann, Manuela
- The ISME Journal, Vol. 16, Issue 5
Full-length transcriptome analysis of multiple organs and identification of adaptive genes and pathways in Mikania micrantha
journal, February 2022
- Ruan, Xiaoxian; Wang, Zhen; Su, Yingjuan
- Scientific Reports, Vol. 12, Issue 1
Recombination and clonal groupings within Helicobacter pylori from different geographical regions
journal, May 1999
- Achtman, Mark; Azuma, Takeshi; Berg, Douglas E.
- Molecular Microbiology, Vol. 32, Issue 3
A New Helicobacter pylori Vacuolating Cytotoxin Determinant, the Intermediate Region, Is Associated With Gastric Cancer
journal, September 2007
- Rhead, Joanne L.; Letley, Darren P.; Mohammadi, Marjan
- Gastroenterology, Vol. 133, Issue 3
Helicobacter pylori genome evolution during human infection
journal, March 2011
- Kennemann, L.; Didelot, X.; Aebischer, T.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 12
Biological activity of the Helicobacter pylori virulence factor CagA is determined by variation in the tyrosine phosphorylation sites
journal, October 2002
- Higashi, H.; Tsutsumi, R.; Fujita, A.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 22
cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors
journal, December 1996
- Censini, S.; Lange, C.; Xiang, Z.
- Proceedings of the National Academy of Sciences, Vol. 93, Issue 25
Tyrosine phosphorylation of the Helicobacter pylori CagA antigen after cag-driven host cell translocation
journal, February 2000
- Stein, M.; Rappuoli, R.; Covacci, A.
- Proceedings of the National Academy of Sciences, Vol. 97, Issue 3
BabA-mediated Adherence Is a Potentiator of the Helicobacter pylori Type IV Secretion System Activity
journal, May 2011
- Ishijima, Nozomi; Suzuki, Masato; Ashida, Hiroshi
- Journal of Biological Chemistry, Vol. 286, Issue 28
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
journal, May 2012
- Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry
- Journal of Computational Biology, Vol. 19, Issue 5
QUAST: quality assessment tool for genome assemblies
journal, February 2013
- Gurevich, Alexey; Saveliev, Vladislav; Vyahhi, Nikolay
- Bioinformatics, Vol. 29, Issue 8
Genome-Wide Survey of Mutual Homologous Recombination in a Highly Sexual Bacterial Species
journal, January 2012
- Yahara, Koji; Kawai, Mikihiko; Furuta, Yoshikazu
- Genome Biology and Evolution, Vol. 4, Issue 5
A Role for the Vacuolating Cytotoxin, VacA, in Colonization and Helicobacter pylori–Induced Metaplasia in the Stomach
journal, March 2014
- Winter, Jody A.; Letley, Darren P.; Cook, Katherine W.
- The Journal of Infectious Diseases, Vol. 210, Issue 6
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
journal, April 2009
- Price, M. N.; Dehal, P. S.; Arkin, A. P.
- Molecular Biology and Evolution, Vol. 26, Issue 7
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
journal, July 2002
- Katoh, K.
- Nucleic Acids Research, Vol. 30, Issue 14
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach
journal, May 2007
- Stern, A.; Doron-Faigenboim, A.; Erez, E.
- Nucleic Acids Research, Vol. 35, Issue Web Server
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
journal, November 2014
- Croucher, Nicholas J.; Page, Andrew J.; Connor, Thomas R.
- Nucleic Acids Research, Vol. 43, Issue 3
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008
- Zerbino, D. R.; Birney, E.
- Genome Research, Vol. 18, Issue 5
Expression, purification and X-ray crystallographic analysis of the Helicobacter pylori blood group antigen-binding adhesin BabA
journal, November 2014
- Subedi, Suresh; Moonens, Kristof; Romão, Ema
- Acta Crystallographica Section F Structural Biology Communications, Vol. 70, Issue 12
Clinical relevance of cagA and vacA gene polymorphisms in Helicobacter pylori isolates from Senegalese patients
journal, February 2012
- Breurec, S.; Michel, R.; Seck, A.
- Clinical Microbiology and Infection, Vol. 18, Issue 2
Pathogenesis of Helicobacter pylori Infection: H. pylori Pathogenesis
journal, September 2011
- Backert, Steffen; Clyne, Marguerite
- Helicobacter, Vol. 16
Protein database searches using compositionally adjusted substitution matrices
journal, October 2005
- Altschul, Stephen F.; Wootton, John C.; Gertz, E. Michael
- FEBS Journal, Vol. 272, Issue 20
Helicobacter pylori SabA Adhesin in Persistent Infection and Chronic Inflammation
journal, July 2002
- Mahdavi, J.
- Science, Vol. 297, Issue 5581
Traces of Human Migrations in Helicobacter pylori Populations
journal, March 2003
- Falush, D.
- Science, Vol. 299, Issue 5612
Functional Adaptation of BabA, the H. pylori ABO Blood Group Antigen Binding Adhesin
journal, July 2004
- Aspholm-Hurtig, M.
- Science, Vol. 305, Issue 5683
Helicobacter pylori Adhesin Binding Fucosylated Histo-Blood Group Antigens Revealed by Retagging
journal, January 1998
- Ilver, D.
- Science, Vol. 279, Issue 5349
Attachment of Helicobacter pylori to human gastric epithelium mediated by blood group antigens
journal, December 1993
- Boren, T.; Falk, P.; Roth, K.
- Science, Vol. 262, Issue 5141
Comparative Genomics of Helicobacter pylori: Analysis of the Outer Membrane Protein Families
journal, July 2000
- Alm, R. A.; Bina, J.; Andrews, B. M.
- Infection and Immunity, Vol. 68, Issue 7
Allelic Variation within Helicobacter pylori babA and babB
journal, February 2001
- Pride, D. T.; Meinersmann, R. J.; Blaser, M. J.
- Infection and Immunity, Vol. 69, Issue 2
THE PATHOGENESIS OF HELICOBACTER PYLORI –INDUCED GASTRO-DUODENAL DISEASES
journal, February 2006
- Atherton, John C.
- Annual Review of Pathology: Mechanisms of Disease, Vol. 1, Issue 1
Helicobacter pylori Sequences Reflect Past Human Migrations
book, January 2009
- Moodley, Y.; Linz, B.
- Microbial Pathogenomics
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
snpTree - a web-server to identify and construct SNP trees from whole genome sequence data
journal, January 2012
- Leekitcharoenphon, Pimlapas; Kaas, Rolf S.; Thomsen, Martin Christen
- BMC Genomics, Vol. 13, Issue Suppl 7
Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island
journal, July 2006
- Devi, S. Manjulata; Ahmed, Irshad; Khan, Aleem A.
- BMC Genomics, Vol. 7, Issue 1
A Global Overview of the Genetic and Functional Diversity in the Helicobacter pylori cag Pathogenicity Island
journal, August 2010
- Olbermann, Patrick; Josenhans, Christine; Moodley, Yoshan
- PLoS Genetics, Vol. 6, Issue 8
Helicobacter pylori from Peruvian Amerindians: Traces of Human Migrations in Strains from Remote Amazon, and Genome Sequence of an Amerind Strain
journal, November 2010
- Kersulyte, Dangeruta; Kalia, Awdhesh; Gilman, Robert H.
- PLoS ONE, Vol. 5, Issue 11
Socioeconomic and Nutritional Factors Account for the Association of Gastric Cancer with Amerindian Ancestry in a Latin American Admixed Population
journal, August 2012
- Pereira, Latife; Zamudio, Roxana; Soares-Souza, Giordano
- PLoS ONE, Vol. 7, Issue 8
Re-annotation of the genome sequence of Helicobacter pylori 26695
journal, December 2013
- Resende, Tiago; Correia, Daniela M.; Rocha, Miguel
- Journal of Integrative Bioinformatics, Vol. 10, Issue 3
BayesHammer: Bayesian clustering for error correction in single-cell sequencing
text, January 2012
- Nikolenko, Sergey I.; Korobeynikov, Anton I.; Alekseyev, Max A.
- arXiv
Works referencing / citing this record:
In Vivo Analysis of the Viable Microbiota and Helicobacter pylori Transcriptome in Gastric Infection and Early Stages of Carcinogenesis
journal, July 2017
- Thorell, Kaisa; Bengtsson-Palme, Johan; Liu, Oscar Hsin-Fu
- Infection and Immunity, Vol. 85, Issue 10
A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk
journal, August 2018
- Berthenet, Elvire; Yahara, Koji; Thorell, Kaisa
- BMC Biology, Vol. 16, Issue 1
Phylogenomics of Colombian Helicobacter pylori isolates
journal, September 2017
- Gutiérrez-Escobar, Andrés Julián; Trujillo, Esperanza; Acevedo, Orlando
- Gut Pathogens, Vol. 9, Issue 1
Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas
journal, February 2017
- Thorell, Kaisa; Yahara, Koji; Berthenet, Elvire
- PLOS Genetics, Vol. 13, Issue 2
Whole Genome Sequence and Phylogenetic Analysis Show Helicobacter pylori Strains from Latin America Have Followed a Unique Evolution Pathway
journal, February 2017
- Muñoz-Ramírez, Zilia Y.; Mendez-Tenorio, Alfonso; Kato, Ikuko
- Frontiers in Cellular and Infection Microbiology, Vol. 7
Comparative Analysis of Two Helicobacter pylori Strains using Genomics and Mass Spectrometry-Based Proteomics
journal, November 2016
- Karlsson, Roger; Thorell, Kaisa; Hosseini, Shaghayegh
- Frontiers in Microbiology, Vol. 7
Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas
journal, August 2016
- Thorell, Kaisa; Yahara, Koji; Berthenet, Elvire
- bioRxiv
Comparative Analysis of Two Helicobacter pylori Strains using Genomics and Mass Spectrometry-Based Proteomics
journal, November 2016
- Karlsson, Roger; Thorell, Kaisa; Hosseini, Shaghayegh
- Frontiers in Microbiology, Vol. 7
Rapid evolution of theHelicobacter pyloriAlpA adhesin in a high gastric cancer risk region from Colombia
journal, May 2018
- Gutiérrez-Escobar, Andrés Julián; Méndez-Callejas, Gina; Acevedo, Orlando
- PeerJ, Vol. 6
Review of current diagnostic methods and advances in Helicobacter pylori diagnostics in the era of next generation sequencing.
text, January 2019
- Pohl, Daniel; Keller, Peter M.; Bordier, Valentine
- WJG Press
Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.