Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • Archive
    • Minireviews
    • JB Special Collection
    • JB Classic Spotlights
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About JB
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Journal of Bacteriology
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • Archive
    • Minireviews
    • JB Special Collection
    • JB Classic Spotlights
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About JB
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
GENOME ANNOUNCEMENT

Genome Sequence of the Emerging Pathogen Helicobacter canadensis

N. J. Loman, L. A. S. Snyder, J. D. Linton, R. Langdon, A. J. Lawson, G. M. Weinstock, B. W. Wren, M. J. Pallen
N. J. Loman
1Centre for Systems Biology, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
L. A. S. Snyder
1Centre for Systems Biology, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
J. D. Linton
2Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
R. Langdon
3Pathogen Molecular Biology Unit, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
A. J. Lawson
4Gastrointestinal Infections Reference Unit, Laboratory of Gastrointestinal Pathogens, Health Protection Agency Centre for Infections, 61 Colindale Avenue, London NW9 5EQ, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
G. M. Weinstock
5Baylor College of Medicine, One Baylor Plaza, Houston, Texas
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
B. W. Wren
3Pathogen Molecular Biology Unit, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
M. J. Pallen
1Centre for Systems Biology, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: m.pallen@bham.ac.uk
DOI: 10.1128/JB.00729-09
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

We determined the genome sequence of the type strain of Helicobacter canadensis, an emerging human pathogen with diverse animal reservoirs. Potential virulence determinants carried by the genome include systems for N-linked glycosylation and capsular export. A protein-based phylogenetic analysis places H. canadensis close to Wolinella succinogenes.

Helicobacter canadensis is an emerging pathogen that has been isolated from four Canadian patients with diarrhea and an Australian patient with bacteremia (3, 10). Wild geese have been identified as a reservoir in Europe (12, 13), while in China, the organism has been isolated from the feces of wild rodents (5). H. canadensis has also been isolated from laboratory rabbits (11) and from Guinea fowl in France (8). Atypical isolates have been obtained from swine feces from The Netherlands and Denmark (6). To shed light on the virulence and colonization factors of H. canadensis and to reassess its phylogenetic status, we performed whole-genome sequencing of the type strain, H. canadensis strain MIT 98-5491/NCTC 13241.

Single- and paired-end whole-genome shotgun sequencing was performed using 454 pyrosequencing technology, supplemented by Solexa sequencing. An initial assembly of the 454 single-end and paired-end data was created using a Newbler assembler (Roche), generating four scaffolds with an average size of 402 kb. The genome sequence was completed using a combination of BLASTX searches and analysis of the Solexa data, followed by confirmatory PCRs, PCR-assisted contig extension (1), and combinatorial PCR, with conventional and long-PCR protocols. Annotation was performed using GenDB (7).

The genome of H. canadensis NCTC 13241 consists of a single circular chromosome 1,623,845 bp in length, with a G+C content of 34%. There are 1,535 protein-coding sequences (CDSs), 40 transfer RNAs, and three rRNA loci.

Although phylogenetic analyses based on 16S rRNA gene sequences place H. canadensis in the genus Helicobacter (3), analysis of 23S rRNA sequences supports a clade containing H. canadensis and Wolinella succinogenes (2). Our own phylogenetic analysis using a concatenation of 482 conserved CDSs from the H. canadensis genome and related genomes provides strong support for a W. succinogenes/H. canadensis clade (data not shown), suggesting that the current taxonomy should be reevaluated.

One hundred seventeen CDSs from H. canadensis have no detectable ortholog in eight other genome-sequenced epsilonproteobacteria. We found only one contiguous region of difference longer than 10 genes (ROD1; HCAN_0630-HCAN_0663). Most CDSs in ROD1 are of unknown function, although, curiously, the region carries three versions of asparagine synthetase and contains six homopolymeric tracts. A second region of difference (ROD2; HCAN_0479-HCAN_0496) shows homology to HHGI1, a pathogenicity island from Helicobacter hepaticus strain ATCC 51449 that contributes to virulence in H. hepaticus (4).

The H. canadensis NCTC 13241 genome contains 29 potentially phase-variable genes with homopolymeric tracts, including several genes that, by homology, might be implicated in virulence, e.g., an immunoglobulin A protease (HCAN_0234) and two homologues of the vacuolating cytotoxin from H elicobacter pylori (HCAN_0457 and HCAN_714). The genome contains a capsular polysaccharide export locus similar to that in Campylobacter jejuni (9). Also, like C. jejuni, H. canadensis possesses genes encoding an N-linked glycosylation pathway, including two copies of PglB (HCAN_0729 and HCAN_0930).

Nucleotide sequence accession numbers.

The completed chromosome of H. canadensis has been deposited in GenBank under accession number CM000776 and project identification number 30719.

ACKNOWLEDGMENTS

Nick Loman and Lori Snyder were supported by BBSRC grant BBE111791.

FOOTNOTES

    • Received 4 June 2009.
    • Accepted 11 June 2009.
  • Copyright © 2009 American Society for Microbiology

REFERENCES

  1. 1.↵
    Carraro, D. M., A. A. Camargo, A. C. Salim, M. Grivet, A. T. Vasconcelos, and A. J. Simpson. 2003. PCR-assisted contig extension: stepwise strategy for bacterial genome closure. BioTechniques 34 : 626-628, 630-632.
    OpenUrlCrossRefPubMed
  2. 2.↵
    Dewhirst, F. E., Z. Shen, M. S. Scimeca, L. N. Stokes, T. Boumenna, T. Chen, B. J. Paster, and J. G. Fox. 2005. Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: implications for phylogenetic inference and systematics. J. Bacteriol. 187 : 6106-6118.
    OpenUrlAbstract/FREE Full Text
  3. 3.↵
    Fox, J. G., C. C. Chien, F. E. Dewhirst, B. J. Paster, Z. Shen, P. L. Melito, D. L. Woodward, and F. G. Rodgers. 2000. Helicobacter canadensis sp. nov. isolated from humans with diarrhea as an example of an emerging pathogen. J. Clin. Microbiol. 38 : 2546-2549.
    OpenUrlAbstract/FREE Full Text
  4. 4.↵
    Ge, Z., T. Sterzenbach, M. T. Whary, B. H. Rickman, A. B. Rogers, Z. Shen, N. S. Taylor, D. B. Schauer, C. Josenhans, S. Suerbaum, and J. G. Fox. 2008. Helicobacter hepaticus HHGI1 is a pathogenicity island associated with typhlocolitis in B6.129-IL10 tm1Cgn mice. Microbes Infect. 10 : 726-733.
    OpenUrlCrossRefPubMed
  5. 5.↵
    Goto, K., W. Jiang, Q. Zheng, Y. Oku, H. Kamiya, T. Itoh, and M. Ito. 2004. Epidemiology of Helicobacter infection in wild rodents in the Xinjiang-Uygur autonomous region of China. Curr. Microbiol. 49 : 221-223.
    OpenUrlCrossRefPubMed
  6. 6.↵
    Inglis, G. D., M. McConville, and A. de Jong. 2006. Atypical Helicobacter canadensis strains associated with swine. Appl. Environ. Microbiol. 72 : 4464-4471.
    OpenUrlAbstract/FREE Full Text
  7. 7.↵
    Meyer, F., A. Goesmann, A. C. McHardy, D. Bartels, T. Bekel, J. Clausen, J. Kalinowski, B. Linke, O. Rupp, R. Giegerich, and A. Puhler. 2003. GenDB—an open-source genome annotation system for prokaryote genomes. Nucleic Acids Res. 31 : 2187-2195.
    OpenUrlCrossRefPubMedWeb of Science
  8. 8.↵
    Nebbia, P., C. Tramuta, M. Ortoffi, E. Bert, S. Cerruti Sola, and P. Robino. 2007. Identification of enteric Helicobacter in avian species. Schweiz. Arch. Tierheilkd. 149 : 403-407.
    OpenUrlCrossRefPubMed
  9. 9.↵
    Parkhill, J., B. W. Wren, K. Mungall, J. M. Ketley, C. Churcher, D. Basham, T. Chillingworth, R. M. Davies, T. Feltwell, S. Holroyd, K. Jagels, A. V. Karlyshev, S. Moule, M. J. Pallen, C. W. Penn, M. A. Quail, M. A. Rajandream, K. M. Rutherford, A. H. van Vliet, S. Whitehead, and B. G. Barrell. 2000. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403 : 665-668.
    OpenUrlCrossRefPubMedWeb of Science
  10. 10.↵
    Tee, W., J. Montgomery, and M. Dyall-Smith. 2001. Bacteremia caused by a Helicobacter pullorum-like organism. Clin. Infect. Dis. 33 : 1789-1791.
    OpenUrlCrossRefPubMedWeb of Science
  11. 11.↵
    Van den Bulck, K., A. Decostere, M. Baele, M. Marechal, R. Ducatelle, and F. Haesebrouck. 2006. Low frequency of Helicobacter species in the stomachs of experimental rabbits. Lab. Anim. 40 : 282-287.
    OpenUrlCrossRefPubMed
  12. 12.↵
    Waldenström, J., S. L. On, R. Ottvall, D. Hasselquist, C. S. Harrington, and B. Olsen. 2003. Avian reservoirs and zoonotic potential of the emerging human pathogen Helicobacter canadensis. Appl. Environ. Microbiol. 69 : 7523-7526.
    OpenUrlAbstract/FREE Full Text
  13. 13.↵
    Waldenstrom, J., S. L. On, R. Ottvall, D. Hasselquist, and B. Olsen. 2007. Species diversity of campylobacteria in a wild bird community in Sweden. J. Appl. Microbiol. 102 : 424-432.
    OpenUrlCrossRefPubMedWeb of Science
PreviousNext
Back to top
Download PDF
Citation Tools
Genome Sequence of the Emerging Pathogen Helicobacter canadensis
N. J. Loman, L. A. S. Snyder, J. D. Linton, R. Langdon, A. J. Lawson, G. M. Weinstock, B. W. Wren, M. J. Pallen
Journal of Bacteriology Aug 2009, 191 (17) 5566-5567; DOI: 10.1128/JB.00729-09

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print

Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Journal of Bacteriology article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Genome Sequence of the Emerging Pathogen Helicobacter canadensis
(Your Name) has forwarded a page to you from Journal of Bacteriology
(Your Name) thought you would be interested in this article in Journal of Bacteriology.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Genome Sequence of the Emerging Pathogen Helicobacter canadensis
N. J. Loman, L. A. S. Snyder, J. D. Linton, R. Langdon, A. J. Lawson, G. M. Weinstock, B. W. Wren, M. J. Pallen
Journal of Bacteriology Aug 2009, 191 (17) 5566-5567; DOI: 10.1128/JB.00729-09
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • Nucleotide sequence accession numbers.
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Info & Metrics
  • PDF

KEYWORDS

DNA, Bacterial
Genome, Bacterial
Helicobacter
Sequence Analysis, DNA

Related Articles

Cited By...

About

  • About JB
  • Editor in Chief
  • Editorial Board
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • ASM Author Center
  • Submit a Manuscript
  • Article Types
  • Ethics
  • Contact Us

Follow #Jbacteriology

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Print ISSN: 0021-9193; Online ISSN: 1098-5530