Abstract
Helicobacter pylori was the first bacterial species to have the genome of two independent strains completely sequenced. Infection with this pathogen, which may be the most frequent bacterial infection of humanity, causes peptic ulcer disease and gastric cancer. Other Helicobacter species are emerging as causes of infection, inflammation, and cancer in the intestine, liver, and biliary tract, although the true prevalence of these enterohepatic Helicobacter species in humans is not yet known. The murine pathogen Helicobacter hepaticus was the first enterohepatic Helicobacter species to have its genome completely sequenced. Here, we consider functional genomics of the genus Helicobacter, the comparative genomics of the genus Helicobacter, and the related genera Campylobacter and Wolinella.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Solnick, J. V. and Schauer, D. B. (2001) Emergence of diverse Helicobacter species in the pathogenesis of gastric and enterohepatic diseases. Clin. Microbiol. Rev. 14, 59–97.
Marshall, B. J. and Warren, J. R. (1984) Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration. Lancet 1, 1311–1315.
Goodwin, C. S., Armstrong, J. A., Chilvers, T., et al. (1989) Transfer of Campylobacter pylori and Campylobacter mustelae to Helicobacter gen. nov. as Helicobacter pylori comb. nov. and Helicobacter mustelae comb. nov., respectively. Int. J. Syst. Bacteriol. 39, 397–405.
Dunn, B. E., Cohen, H., and Blaser, M. J. (1997) Helicobacter pylori. Clin. Microbiol. Rev. 10, 720–741.
Suerbaum, S. and Michetti, P. (2002) Helicobacter pylori infection. N. Engl. J. Med. 347, 1175–1186.
Anonymous. (1994) NIH Consensus Conference. Helicobacter pylori in peptic ulcer disease. NIH Consensus Development Panel on Helicobacter pylori in Peptic Ulcer Disease. JAMA 272, 65-69.
Anonymous. (1994) Schistosomes, liver flukes and Helicobacter pylori. IARC Working Group on the Evaluation of Carcinogenic Risks to Humans. Lyon, 7-14 June 1994. IARC Monogr. Eval. Carcinog. Risks Hum. 61, 1-241.
Parsonnet, J., Hansen, S., Rodriguez, L., et al. (1994) Helicobacter pylori infection and gastric lymphoma. N. Engl. J. Med. 330, 1267–1271.
Paster, B. J., Lee, A., Fox, J. G., et al. (1991) Phylogeny of Helicobacter felis sp. nov., Helicobacter mustelae, and related bacteria. Int. J. Syst. Bacteriol. 41, 31–38.
Fox, J. G. and Lee, A. (1997) The role of Helicobacter species in newly recognized gastro-intestinal tract diseases of animals. Lab. Anim. Sci. 47, 222–255.
Rogers, A. B. and Fox, J. G. (2004) Inflammation and Cancer. I. Rodent models of infec-tious gastrointestinal and liver cancer. Am. J. Physiol. Gastrointest. Liver Physiol. 286, G361–G366.
Hanninen, M. L., Happonen, I., Saari, S., and Jalava, K. (1996) Culture and characteristics of Helicobacter bizzozeronii, a new canine gastric Helicobacter sp. Int. J. Syst. Bacteriol. 46, 160–166.
Jalava, K., Kaartinen, M., Utriainen, M., Happonen, I., and Hanninen, M. L. (1997) Helicobacter salomonis sp. nov., a canine gastric Helicobacter sp. related to Helicobacter felis and Helicobacter bizzozeronii. Int. J. Syst. Bacteriol. 47, 975–982.
Eaton, K. A., Dewhirst, F. E., Radin, M. J., et al. (1993) Helicobacter acinonyx sp. nov., isolated from cheetahs with gastritis. Int. J. Syst. Bacteriol. 43, 99–106.
Goto, K., Ohashi, H., Ebukuro, S., et al. (1998) Isolation and characterization of Helicobacter species from the stomach of the house musk shrew (Suncus murinus) with chronic gastritis. Curr. Microbiol. 37, 44–51.
Harper, C. G., Feng, Y., Xu, S., et al. (2002) Helicobacter cetorum sp. nov., a ureasepositive Helicobacter species isolated from dolphins and whales. J. Clin. Microbiol. 40, 4536–4543.
Murray, R. G. and Stackebrandt, E. (1995) Taxonomic note: implementation of the proviional status Candidatus for incompletely described procaryotes. Int. J. Syst. Bacteriol. 45, 186–187.
O’Rourke, J. L., Solnick, J. V., Neilan, B. A., et al. (2004) Description of ‘Candidatus Helicobacter heilmannii’ based on DNA sequence analysis of 16S rRNA and urease genes. Int. J. Syst. Evol. Microbiol. 54, 2203–2211.
De Groote, D., van Doorn, L. J., Ducatelle, R., et al. (1999) ‘Candidatus Helicobacter suis’, a gastric helicobacter from pigs, and its phylogenetic relatedness to other gastrospirilla. Int. J. Syst. Bacteriol. 49, 1769–1777.
De Groote, D., van Doorn, L. J., Ducatelle, R., et al. (1999) Phylogenetic characterization of ‘Candidatus Helicobacter bovis’, a new gastric helicobacter in cattle. Int. J. Syst. Bacteriol. 49, 1707–1715.
Fox, J. G. (2002) The non-H. pylori helicobacters: their expanding role in gastrointestinal and systemic diseases. Gut 50, 273–283.
Phillips, M. W. and Lee, A. (1983) Isolation and characterization of a spiral bacterium from the crypts of rodent gastrointestinal tracts. Appl. Environ. Microbiol. 45, 675–683.
Lee, A., Phillips, M. W., O’Rourke, J. L., et al. (1992) Helicobacter muridarum sp. nov., a microaerophilic helical bacterium with a novel ultrastructure isolated from the intestinal mucosa of rodents. Int. J. Syst. Bacteriol. 42, 27–36.
Lee, A., Chen, M., Coltro, N., et al. (1993) Long term infection of the gastric mucosa with Helicobacter species does induce atrophic gastritis in an animal model of Helicobacter pylori infection. Zentralbl. Bakteriol. 280, 38–50.
Jiang, H. Q., Kushnir, N., Thurnheer, M. C., Bos, N. A., and Cebra, J. J. (2002) Monoassociation of SCID mice with Helicobacter muridarum, but not four other enterics, provokes IBD upon receipt of T cells. Gastroenterology 122, 1346–1354.
Fox, J. G., Dewhirst, F. E., Tully, J. G., et al. (1994) Helicobacter hepaticus sp. nov., a microaerophilic bacterium isolated from livers and intestinal mucosal scrapings from mice. J. Clin. Microbiol. 32, 1238–1245.
Erdman, S. E., Poutahidis, T., Tomczak, M., et al. (2003) CD4+ CD25+ regulatory T lym-phocytes inhibit microbially induced colon cancer in Rag2-deficient mice. Am. J. Pathol. 162, 691–702.
Maurer, K. J., Ihrig, M. M., Rogers, A. B., et al. (2005) Identification of cholelithogenic enterohepatic helicobacter species and their role in murine cholesterol gallstone formation. Gastroenterology 128, 1023–1033.
Patterson, M. M., Schrenzel, M. D., Feng, Y., et al. (2000) Helicobacter aurati sp. nov., a urease-positive Helicobacter species cultured from gastrointestinal tissues of Syrian hamsters. J. Clin. Microbiol. 38, 3722–3728.
Shen, Z., Fox, J. G., Dewhirst, F. E., et al. (1997) Helicobacter rodentium sp. nov., a urease-negative Helicobacter species isolated from laboratory mice. Int. J. Syst. Bacteriol. 47, 627–634.
Franklin, C. L., Gorelick, P. L., Riley, L. K., et al. (2001) Helicobacter typhlonius sp. nov., a novel murine urease-negative Helicobacter species. J. Clin. Microbiol. 39, 3920–3926.
Robertson, B. R., O’Rourke, J. L., Vandamme, P., On, S. L., and Lee, A. (2001) Helicobacter ganmani sp. nov., a urease-negative anaerobe isolated from the intestines of laboratory mice. Int. J. Syst. Evol. Microbiol. 51, 1881–1889.
Franklin, C. L., Beckwith, C. S., Livingston, R. S., et al. (1996) Isolation of a novel Helicobacter species, Helicobacter cholecystus sp. nov., from the gallbladders of Syrian hamsters with cholangiofibrosis and centrilobular pancreatitis. J. Clin. Microbiol. 34, 2952–2958.
Simmons, J. H., Riley, L. K., Besch-Williford, C. L., and Franklin, C. L. (2000) Helicobacter mesocricetorum sp. nov., A novel Helicobacter isolated from the feces of Syrian hamsters. J. Clin. Microbiol. 38, 1811–1817.
Dewhirst, F. E., Seymour, C., Fraser, G. J., Paster, B. J., and Fox, J. G. (1994) Phylogeny of Helicobacter isolates from bird and swine feces and description of Helicobacter pametensis sp. nov. Int. J. Syst. Bacteriol. 44, 553–560.
Dewhirst, F. E., Fox, J. G., Mendes, E. N., et al. (2000) ‘Flexispira rappini’ strains represent at least 10 Helicobacter taxa. Int. J. Syst. Evol. Microbiol. 50, 1781–1787.
Fox, J. G., Yan, L. L., Dewhirst, F. E., et al. (1995) Helicobacter bilis sp. nov., a novel Helicobacter species isolated from bile, livers, and intestines of aged, inbred mice. J. Clin. Microbiol. 33, 445–454.
Mendes, E. N., Queiroz, D. M., Dewhirst, F. E., Paster, B. J., Moura, S. B., and Fox, J. G. (1996) Helicobacter trogontum sp. nov., isolated from the rat intestine. Int. J. Syst. Bacteriol. 46, 916–921.
Hanninen, M. L., Utriainen, M., Happonen, I., and Dewhirst, F. E. (2003) Helicobacter sp. flexispira 16S rDNA taxa 1, 4 and 5 and Finnish porcine Helicobacter isolates are mem-bers of the species Helicobacter trogontum (taxon 6). Int. J. Syst. Evol. Microbiol. 53, 425–433.
Hanninen, M. L., Karenlampi, R. I., Koort, J. M., Mikkonen, T., and Bjorkroth, K. J. (2005) Extension of the species Helicobacter bilis to include the reference strains of Helicobacter sp. flexispira taxa 2, 3 and 8 and Finnish canine and feline flexispira strains. Int. J. Syst. Evol. Microbiol. 55, 891–898.
Romero, S., Archer, J. R., Hamacher, M. E., Bologna, S. M., and Schell, R. F. (1988) Case report of an unclassified microaerophilic bacterium associated with gastroenteritis. J. Clin. Microbiol. 26, 142–143.
Archer, J. R., Romero, S., Ritchie, A. E., et al. (1988) Characterization of an unclassified microaerophilic bacterium associated with gastroenteritis. J. Clin. Microbiol. 26, 101–105.
Gerrard, J., Alfredson, D., and Smith, I. (2001) Recurrent bacteremia and multifocal lower limb cellulitis due to Helicobacter-like organisms in a patient with X-linked hypogammaglobulinemia. Clin. Infect. Dis. 33, E116–E118.
Iten, A., Graf, S., Egger, M., Tauber, M., and Graf, J. (2001) Helicobacter sp. flexispira bacteremia in an immunocompetent young adult. J. Clin. Microbiol. 39, 1716–1720.
Cuccherini, B., Chua, K., Gill, V., et al. (2000) Bacteremia and skin/bone infections in two patients with X-linked agammaglobulinemia caused by an unusual organism related to Flexispira/Helicobacter species. Clin. Immunol. 97, 121–129.
Weir, S., Cuccherini, B., Whitney, A. M., et al. (1999) Recurrent bacteremia caused by a “Flexispira”-like organism in a patient with X-linked (Bruton’s) agammaglobulinemia. J. Clin. Microbiol. 37, 2439–2445.
Tee, W., Leder, K., Karroum, E., and Dyall-Smith, M. (1998) “Flexispira rappini” bactere-mia in a child with pneumonia. J. Clin. Microbiol. 36, 1679–1682.
Sorlin, P., Vandamme, P., Nortier, J., et al. (1999) Recurrent “Flexispira rappini” bacteremia in an adult patient undergoing hemodialysis: case report. J. Clin. Microbiol. 37, 1319–1323.
Fox, J. G., Dewhirst, F. E., Shen, Z., et al. (1998) Hepatic Helicobacter species identified in bile and gallbladder tissue from Chileans with chronic cholecystitis. Gastroenterology 114, 755–763.
Matsukura, N., Yokomuro, S., Yamada, S., et al. (2002) Association between Helicobacter bilis in bile and biliary tract malignancies: H. bilis in bile from Japanese and Thai patients with benign and malignant diseases in the biliary tract. Jpn. J. Cancer Res. 93, 842–847.
Murata, H., Tsuji, S., Tsujii, M., et al. (2004) Helicobacter bilis infection in biliary tract cancer. Aliment. Pharmacol. Ther. 20, 90–94.
Kobayashi, T., Harada, K., Miwa, K., and Nakanuma, Y. (2005) Helicobacter genus DNA fragments are commonly detectable in bile from patients with extrahepatic biliary diseases and associated with their pathogenesis. Dig. Dis. Sci. 50, 862–867.
Vandamme, P., Falsen, E., Rossau, R., et al. (1991) Revision of Campylobacter, Helicobacter, and Wolinella taxonomy: emendation of generic descriptions and proposal of Arcobacter gen. nov. Int. J. Syst. Bacteriol. 41, 88–103.
Totten, P. A., Fennell, C. L., Tenover, F. C., et al. (1985) Campylobacter cinaedi (sp. nov.) and Campylobacter fennelliae (sp. nov.): two new Campylobacter species associated with enteric disease in homosexual men. J. Infect. Dis. 151, 131–139.
Stanley, J., Linton, D., Burnens, A. P., et al. (1993) Helicobacter canis sp. nov., a new species from dogs: an integrated study of phenotype and genotype. J. Gen. Microbiol. 139, 2495–2504.
Stanley, J., Linton, D., Burnens, A. P., et al. (1994) Helicobacter pullorum sp. nov.-geno-type and phenotype of a new species isolated from poultry and from human patients with gastroenteritis. Microbiology 140, 3441–3449.
Fox, J. G., Chien, C. C., Dewhirst, F. E., et al. (2000) Helicobacter canadensis sp. nov. iso-lated from humans with diarrhea as an example of an emerging pathogen. J. Clin. Microbiol. 38, 2546–2549.
Tomb, J. F., White, O., Kerlavage, A. R., et al. (1997) The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388, 539–547.
Alm, R. A., Ling, L. S., Moir, D. T., et al. (1999) Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397, 176–180.
Ge, Z. and Taylor, D. E. (1999) Contributions of genome sequencing to understanding the biology of Helicobacter pylori. Annu. Rev. Microbiol. 53, 353–387.
Alm, R. A. and Trust, T. J. (1999) Analysis of the genetic diversity of Helicobacter pylori: the tale of two genomes. J. Mol. Med. 77, 834–846.
Israel, D. A., Salama, N., Krishna, U., et al. (2001) Helicobacter pylori genetic diversity within the gastric niche of a single human host. Proc. Natl. Acad. Sci. USA 98, 14,625–14,630.
Falush, D., Kraft, C., Taylor, N. S., et al. (2001) Recombination and mutation during longterm gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age. Proc. Natl. Acad. Sci. USA 98, 15,056–15,061.
Falush, D., Wirth, T., Linz, B., et al. (2003) Traces of human migrations in Helicobacter pylori populations. Science 299, 1582–1585.
Taylor, D. E., Chang, N., Taylor, N. S., and Fox, J. G. (1994) Genome conservation in Helicobacter mustelae as determined by pulsed-field gel electrophoresis. FEMS Microbiol. Lett. 118, 31–36.
Saunders, K. E., McGovern, K. J., and Fox, J. G. (1997) Use of pulsed-field gel electro phoresis to determine genomic diversity in strains of Helicobacter hepaticus from geographically distant locations. J. Clin. Microbiol. 35, 2859–2863.
Suerbaum, S., Josenhans, C., Sterzenbach, T., et al. (2003) The complete genome sequence of the carcinogenic bacterium Helicobacter hepaticus. Proc. Natl. Acad. Sci. USA 100, 7901–7906.
Colland, F., Rain, J. C., Gounon, P., Labigne, A., Legrain, P., and De Reuse, H. (2001) Identification of the Helicobacter pylori anti-σ28 factor. Mol. Microbiol. 41, 477–487.
Josenhans, C., Niehus, E., Amersbach, S., et al. (2002) Functional characterization of the antagonistic flagellar late regulators FliA and FlgM of Helicobacter pylori and their effects on the H. pylori transcriptome. Mol. Microbiol. 43, 307–322.
Schilling, C. H., Covert, M. W., Famili, I., Church, G. M., Edwards, J. S., and Palsson, B. O. (2002) Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 184, 4582–4593.
Salama, N. R., Shepherd, B., and Falkow, S. (2004) Global transposon mutagenesis and essential gene analysis of Helicobacter pylori. J. Bacteriol. 186, 7926–7935.
Censini, S., Lange, C., Xiang, Z., et al. (1996) cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors. Proc. Natl. Acad. Sci. USA 93, 14,648–14,653.
Akopyants, N. S., Clifton, S. W., Kersulyte, D., et al. (1998) Analyses of the cag pathogenicity island of Helicobacter pylori. Mol. Microbiol. 28, 37–53.
Christie, P. J. (2001) Type IV secretion: intercellular transfer of macromolecules by systems ancestrally related to conjugation machines. Mol. Microbiol. 40, 294–305.
Nagai, H. and Roy, C. R. (2003) Show me the substrates: modulation of host cell function by type IV secretion systems. Cell Microbiol. 5, 373–383.
Fischer, W., Puls, J., Buhrdorf, R., Gebert, B., Odenbreit, S., and Haas, R. (2001) Systematic mutagenesis of the Helicobacter pylori cag pathogenicity island: essential genes for CagA translocation in host cells and induction of interleukin-8. Mol. Microbiol. 42, 1337–1348.
Bourzac, K. M. and Guillemin, K. (2005) Helicobacter pylori-host cell interactions mediated by type IV secretion. Cell Microbiol. 7, 911–919.
Selbach, M., Moese, S., Meyer, T. F., and Backert, S. (2002) Functional analysis of the Helicobacter pylori cag pathogenicity island reveals both VirD4-CagA-dependent and VirD4-CagA-independent mechanisms. Infect. Immun. 70, 665–671.
Peek, R. M. Jr. (2001) IV. Helicobacter pylori strain-specific activation of signal transduc-tion cascades related to gastric inflammation. Am. J. Physiol. Gastrointest. Liver Physiol. 280, G525–G530.
Amieva, M. R., Vogelmann, R., Covacci, A., Tompkins, L. S., Nelson, W. J., and Falkow, S. (2003) Disruption of the epithelial apical-junctional complex by Helicobacter pylori CagA. Science 300, 1430–1434.
Higashi, H., Tsutsumi, R., Muto, S., et al. (2002) SHP-2 tyrosine phosphatase as an intra-cellular target of Helicobacter pylori CagA protein. Science 295, 683–686.
Higashi, H., Nakaya, A., Tsutsumi, R., et al. (2004) Helicobacter pylori CagA induces Ras-independent morphogenetic response through SHP-2 recruitment and activation. J. Biol. Chem. 279, 17,205–17,216.
Fleischmann, R. D., Adams, M. D., White, O., et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512.
Eppinger, M., Baar, C., Raddatz, G., Huson, D. H., and Schuster, S. C. (2004) Comparative analysis of four Campylobacterales. Nat. Rev. Microbiol. 2, 872–885.
Fouts, D. E., Mongodin, E. F., Mandrell, R. E., et al. (2005) Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biol. 3, e15.
Bacon, D. J., Alm, R. A., Hu, L., et al. (2002) DNA sequence and mutational analyses of the pVir plasmid of Campylobacter jejuni 81-176. Infect. Immun. 70, 6242–6250.
Jiang, Q., Hiratsuka, K., and Taylor, D. E. (1996) Variability of gene order in different Helicobacter pylori strains contributes to genome diversity. Mol. Microbiol. 20, 833–842.
Covacci, A., Falkow, S., Berg, D. E., and Rappuoli, R. (1997) Did the inheritance of a patho-genicity island modify the virulence of Helicobacter pylori? Trends Microbiol. 5, 205–208.
Suerbaum, S., Smith, J. M., Bapumia, K., et al. (1998) Free recombination within Helicobacter pylori. Proc. Natl. Acad. Sci. USA 95, 12,619–12,624.
Ge, Z., Feng, Y., Whary, M. T., et al. (2005) Cytolethal distending toxin is essential for Helicobacter hepaticus colonization in outbred Swiss Webster mice. Infect. Immun. 73, 3559–3567.
Fox, J. G., Rogers, A. B., Whary, M. T., et al. (2004) Gastroenteritis in NF-KB-deficient mice is produced with wild-type Camplyobacter jejuni but not with C. jejuni lacking cytolethal distending toxin despite persistent colonization with both strains. Infect. Immun. 72, 1116–1125.
Chien, C. C., Taylor, N. S., Ge, Z., Schauer, D. B., Young, V. B., and Fox, J. G. (2000) Identification of cdtB homologues and cytolethal distending toxin activity in enterohepatic Helicobacter spp. J. Med. Microbiol. 49, 525–534.
Taylor, N. S., Ge, Z., Shen, Z., Dewhirst, F. E., and Fox, J. G. (2003) Cytolethal distending toxin: a potential virulence factor for Helicobacter cinaedi. J. Infect. Dis. 188, 1892–1897.
Young, V. B., Knox, K. A., and Schauer, D. B. (2000) Cytolethal distending toxin sequence and activity in the enterohepatic pathogen Helicobacter hepaticus. Infect. Immun. 68, 184–191.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Humana Press Inc., Totowa, NJ
About this chapter
Cite this chapter
Ge, Z., Schauer, D.B. (2006). Genomics of Helicobacter Species. In: Chan, V.L., Sherman, P.M., Bourke, B. (eds) Bacterial Genomes and Infectious Diseases. Humana Press. https://doi.org/10.1007/978-1-59745-152-9_6
Download citation
DOI: https://doi.org/10.1007/978-1-59745-152-9_6
Publisher Name: Humana Press
Print ISBN: 978-1-58829-496-8
Online ISBN: 978-1-59745-152-9
eBook Packages: MedicineMedicine (R0)