Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori

Alm, Richard A.; Ling, Lo-See L.; Moir, Donald T.; King, Benjamin L.; Brown, Eric D.; Doig, Peter C.; Smith, Douglas R.; Noonan, Brian; Guild, Braydon C.; deJonge, Boudewijn L.; Carmel, Gilles; Tummino, Peter J.; Caruso, Anthony; Uria-Nickelsen, Maria; Mills, Debra M.; Ives, Cameron; Gibson, Rene; Merberg, David; Mills, Scott D.; Jiang, Qin; Taylor, Diane E.; Vovis, Gerald F.; Trust, Trevor J.

doi:10.1038/16495

Cited by 1,893Helicobacter pylori-related gastroenterology studiesGenomics and Phylogenetic StudiesMicrobial infections and disease research

Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori

Alm, Richard A., Ling, Lo-See L., Moir, Donald T., King, Benjamin L., Brown, Eric D., Doig, Peter C., Smith, Douglas R., Noonan, Brian +15 more·1999·Nature

DOI 10.1038/16495

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Abstract

Helicobacter pylori, one of the most common bacterial pathogens of humans, colonizes the gastric mucosa, where it appears to persist throughout the host's life unless the patient is treated. Colonization induces chronic gastric inflammation which can progress to a variety of diseases, ranging in severity from superficial gastritis and peptic ulcer to gastric cancer and mucosal-associated lymphoma. Strain-specific genetic diversity has been proposed to be involved in the organism's ability to cause different diseases or even be beneficial to the infected host and to participate in the lifelong chronicity of infection. Here we compare the complete genomic sequences of two unrelated H. pylori isolates. This is, to our knowledge, the first such genomic comparison. H. pylori was believed to exhibit a large degree of genomic and allelic diversity, but we find that the overall genomic organization, gene order and predicted proteomes (sets of proteins encoded by the genomes) of the two strains are quite similar. Between 6 to 7% of the genes are specific to each strain, with almost half of these genes being clustered in a single hypervariable region.

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The complete genome sequences of H. pylori strains 26695 and J99 demonstrate that this organism contains only two rRNA operons.
“The complete genome sequences of two H. pylori strains, 26695 and J99 (1, 34), have been published elsewhere and demonstrate that this organism contains only two rRNA operons, increasing the likelihood that rRNA mutations could arise.”
From Mutations in the 16S rRNA Genes ofHelicobacter pyloriMediate Resistance to Tetracycline (2002) · cites this paper as [1]
Analysis of H. pylori genome sequences indicates that the smallest distances between rdxA and one of the 16S rRNA genes are 193 kb in strain 26695 and 205 kb in strain J99.
“Analysis of the H. pylori genome sequences (1, 34) indicates that the smallest distances between rdxA and one of the 16S rRNA genes are 193 kb in strain 26695 and 205 kb in strain J99.”
From Mutations in the 16S rRNA Genes ofHelicobacter pyloriMediate Resistance to Tetracycline (2002) · cites this paper as [1]

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Identification of strain-specific genes located outside the plasticity zone in nine clinical isolates of Helicobacter pylori b bThe GenBank accession numbers for the H. pylori sequences reported in this paper are AF326599–AF326607 for region A, AF326608–AF326616 for region B, AF326617–AF326625 for region C, AF326626–AF326634 for region D, AF327212–AF327220 for region E, AF328909–AF328916 and AF328924 for region F, and AF32917–AF32923 for region G.
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Comparative genomics of Helicobacter pylori
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Authors: Alm, R. A., Ling, L.-S. L., Moir, D. T., King, B. L., Brown, E. D., Doig, P. C., Smith, D. R., Noonan, B., Guild, B. C., deJonge, B. L., Carmel, G., Tummino, P. J., Caruso, A., Uria-Nickelsen, M., Mills, D. M., Ives, C., Gibson, R., Merberg, D., Mills, S. D., Jiang, Q., Taylor, D. E., Vovis, G. F., & Trust, T. J.
Affiliations: University of Alberta (CA)
Corresponding author: Alm, Richard A.
ORCID: Alm, Richard A.
Moir, Donald T.
King, Benjamin L.
Brown, Eric D.
Smith, Douglas R.
deJonge, Boudewijn L.
Tummino, Peter J.
Merberg, David
Jiang, Qin
Taylor, Diane E.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 1999-01-14
Volume: 397
Issue: 6715
Pages: 176-180
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/16495
OpenAlex: W2016299826
Cited by: 1,893
References: 21
Citations by year: 2026: 9 · 2025: 18 · 2024: 21 · 2023: 18 · 2022: 16 · 2021: 25 · 2020: 21 · 2019: 24 · 2018: 33 · 2017: 30 · 2016: 46 · 2015: 53 · 2014: 94 · 2013: 49 · 2012: 56
FWCI: 171.93
Type: journal article
Language: en
Update notices: erratum (1999-02-25)
Open access: closed
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Topics: Health Sciences › Medicine › Surgery › Helicobacter pylori-related gastroenterology studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Immunology and Microbiology › Microbiology › Microbial infections and disease research
Keywords: Helicobacter pylori, comparative genomics, hypervariable region, gene order, proteome, gastric colonization, chronic gastritis, peptic ulcer, gastric cancer, bacterial genomics
MeSH terms: Duodenal Ulcer, Humans, Molecular Sequence Data, Species Specificity, Gene Expression Regulation, Bacterial, Sequence Alignment, Helicobacter pylori, Helicobacter Infections, Genome, Bacterial, Sequence Analysis, DNA

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Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori

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