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  • 1
    Electronic Resource
    Electronic Resource
    DNA Sequence Conservation and Diversity in Transposable Element IS605 of Helicobacter pylori (1998)
    Cambridge, MA, USA : Blackwell Science Inc, Boston, USA
    Helicobacter 3 (1998), S. 0 
    Details
    ISSN: 1523-5378
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: Background. IS605, a transposable element-like sequence identified in the virulence-associated cag region of Helicobacter pylori reference strain NCTC11638, is unusual in containing two oppositely-oriented open reading frames whose products are homologues of the single transposases of the unrelated elements, IS200 and IS1341. Methods. One hundred independent H. pylori isolates from different parts of the world were screened by PCR and dot blot hybridization to determine the presence of IS605. For some positive isolates, southern hybridizations and sequence analyses were done. Results. Of the 100 isolates, 31 were found to contain sequences related to each ORF with orientation and spacing matching those in canonical IS605-hybridizing sequences. No isolate containing just one ORF and not the other was found. The frequencies of IS605 carriage were independent of geographical origin (U.S. vs. non-U.S.), and of the probable virulence of the isolate (cag status, toxin production or vacA alleles, patient symptoms). Southern blot hybridization of six IS605-containing strains revealed one to nine IS605 copies per genome. Two types of DNA sequence diversity were found: first, a specific 100 bp deletion in two isolates; second, base substitution divergence of 0.4% to 7.5% in pairwise comparisons among the eight isolates characterized, a level of divergence similar to that seen in other H. pylori chromosomal genes. Conclusions. Based on these findings, we speculate that IS605 is a relatively ancient component of the H. pylori gene pool that has proliferated in this species by horizontal gene transfer, homologous recombination, and transposition.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1523-5378.1998.08011.x
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  • 2
    Electronic Resource
    Electronic Resource
    Distribution of Distinct vacA, cagA and iceA Alleles in Helicobacter pylori in Hong Kong (2001)
    Oxford, UK : Blackwell Science Ltd
    Helicobacter 6 (2001), S. 0 
    Details
    ISSN: 1523-5378
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: There is a substantial genetic heterogeneity among Helicobacter pylori strains, and certain genotypes have been suggested to be associated with the virulence of this pathogen. The aim of this study was to investigate the distribution of H. pylori vacA, cagA and iceA genotypes and their association with duodenal ulcer disease in Hong Kong.〈section xml:id="abs1-3"〉〈title type="main"〉Materials and Methods.Gastric biopsies of 72 H. pylori infected patients were analyzed by specific polymerase chain reactions.〈section xml:id="abs1-4"〉〈title type="main"〉Results.Of the 72 cases, 69 (95.8%) had vacA signal sequence s1c strains, and three (4.2%) had s1a strains. vacA middle region sequences, m1b and m2, were detected in 23 (31.9%) and 46 (63.9%), respectively. Six (8.3%) cases contained multiple vacA subtypes. vacA s2 allele was only observed in three (4.3%) cases, which were also infected with s1c subtype. cagA was present in 64 (88.9%) of 72 patients, and iceA1 subtype was detected in 46 (63.9%) cases. Neither cagA nor vacA and iceA were associated with duodenal ulcer disease.〈section xml:id="abs1-5"〉〈title type="main"〉Conclusion.The distribution of vacA, cagA and iceA alleles in H. pylori strains in Hong Kong is similar to that in east Asia. There is a difference in the distribution of genotypes between strains in Hong Kong and those in mainland China, although strains in the two regions exhibit a very close relation. The association of these virulence genes and duodenal ulcer disease needs reappraisal, particularly under geographic considerations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1523-5378.2001.00040.x
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  • 3
    Electronic Resource
    Electronic Resource
    Corrected Identity of Isolates of Helicobacter Pylori Reference Strain NCTC11637 (1997)
    Cambridge, MA, USA : Blackwell Science, Inc.
    Helicobacter 2 (1997), S. 0 
    Details
    ISSN: 1523-5378
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: The reference strains NCTC11637 and NCTC11638 were among the very first Helicobacters ever cultured and have been distributed through national reference culture collections to researchers throughout the world. Because H. pylori is an extremely diverse species, such reference strains are invaluable as universal standards, provided that they are identified correctly.〈section xml:id="abs1-2"〉〈title type="main"〉Materials and Methods. H. pylori strains (previously called “NCTC11637”) from three different sources and NCTC11638 were fingerprinted by the arbitrarily primed polymerase chain reaction (PCR) (also known as random amplified polymorphic DNA, or RAPD) method and further were characterized by NotI digestion and pulsed field gel electrophoresis of total genomic DNA (NotI-PFGE) and by restriction of PCR-amplified ureCD and flaA gene segments.〈section xml:id="abs1-3"〉〈title type="main"〉Results.RAPD tests of two “NCTC11637” strains from different sources (CCUG17874, UA1178) indicated that they were closely related or identical to NCTC11638. Given the diversity of H. pylori strains and the high sensitivity of the RAPD method, close matches in RAPD patterns from independent clinical isolates are not expected. In contrast, the version of “NCTC11637” from the American Type Culture Collection (ATCC 43504) did not match NCTC11638 in RAPD fingerprint. Concordant results were obtained by NotI-PFGE and by restriction of PCR amplified gene segments.〈section xml:id="abs1-4"〉〈title type="main"〉Conclusions.Two unrelated versions of the reference (type) H. pylori strain NCTC11637 are in general circulation and are distinguished easily by DNA fingerprinting. One matches another reference strain, NCTC11638, whereas the other is distinct from it, as expected of independent clinical isolates. Knowing which “NCTC11637” reference strain one has could be important, especially because H. pylori strains probably are diverse in phenotypic traits that are important for colonization or disease.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1523-5378.1997.tb00058.x
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  • 4
    Electronic Resource
    Electronic Resource
    Ordered cosmid library and high-resolution physical—genetic map of Helicobacter pylori strain NCTC11638 (1994)
    Oxford, UK : Blackwell Publishing Ltd
    Molecular microbiology 11 (1994), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Helicobacter pylori is a Gram-negative bacterium that infects the human gastric mucosa, causes gastritis and contributes to the development of peptic ulcers and gastric cancer. To facilitate molecular genetic analysis of this pathogen, we constructed a ∼20-fold redundant cosmid library and physical/genetic map of strain NCTC11638. Genomic DNA fragments were cloned into the cosmid vector Lorist6, and clones were ordered by hybridization with several types of probes: (i) ends of cloned DNAs; (ii) chromosomal Notl digest fragments; (iii) cosmids containing Notl sites; and (iv) specific genes. Seven hundred and fifty-one cosmids were mapped to one of thrM contigs covering 〉 90% of the chromosome, and are represented by a 68-cosmid miniset. The order of cosmids was confirmed and extents of overlap among them were estimated by restriction analysis.All currently known H. pylori genes were mapped, including those for a cytotoxin (vacA), cytotoxin-associated protein (cagA), urease and regulatory functions (ureAB, ureD and ureH), catalase (katA), major and minor flagellins (flaA and flaB), heat-shock (stress) and chaperone proteins (dnaK, htrA, hspB (groEL)), prokaryotic ferritin (pfr), an adhesin subunit (hpaA), a surface protein (26kDa), and 16S and 23S ribosomal RNAs (two genes each). The orientations of eight genes or clusters were determined, and two repetitive sequences were also found. The gene order and rRNA gene copy number determined here differed from that reported for an unrelated strain, which suggests considerable flexibility in H. pylori genome organization.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2958.1994.tb00332.x
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  • 5
    Electronic Resource
    Electronic Resource
    Helicobacter pylori with separate β- and β′-subunits of RNA polymerase is viable and can colonize conventional mice (1999)
    Oxford BSL : Blackwell Science Ltd
    Molecular microbiology 32 (1999), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The genes encoding the β- and β′-subunits of RNA polymerase (rpoB and rpoC respectively) are fused as one continuous open reading frame in Helicobacter pylori and in other members of this genus, but are separate in other bacterial taxonomic groups, including the closely related genus Campylobacter. To test whether this β–β′ tethering is essential, we used polymerase chain reaction-based cloning to separate the rpoB and rpoC moieties of the H. pylori rpoB–rpoC fusion gene with a non-polar chloramphenicol resistance cassette containing a new translational start, and introduced this construct into H. pylori by electrotransformation. H. pylori containing these separated rpoB and rpoC genes in place of the native fusion gene produced non-tethered β and β′ RNAP subunits, grew well in culture and colonized and proliferated well in conventional C57BL/6 mice. Thus, the extraordinary β–β′ tethering is not essential for H. pylori viability and gastric colonization.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.1999.01336.x
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  • 6
    Electronic Resource
    Electronic Resource
    Emergence of recombinant strains of Helicobacter pylori during human infection (1999)
    Oxford BSL : Blackwell Science Ltd
    Molecular microbiology 31 (1999), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Genetic recombination can be important evolutionarily in speeding the adaptation of organisms to new environments and in purging deleterious mutations. Here, we describe polymerase chain reaction (PCR), hybridization and DNA sequence-based evidence of six such exchanges between two strains of Helicobacter pylori during natural mixed infection of a patient in Lithuania. One parent strain contained the 37 kb long, virulence-associated cag pathogenicity island (PAI), and the other strain lacked this PAI. Most H. pylori from the patient had descended from the cag+ parent, but had become cag− during infection. This had resulted from transfer of DNA containing the ‘empty site’ allele from the cag− strain and homologous recombination, not from excision of the cag PAI without DNA transfer. Other cases of recombination involved genes for an outer membrane protein (omp5 and omp29; also called HP0227 and HP1342) and a putative phosphoenolpyruvate synthase (ppsA ; HP0121). Replacement of a short patch of DNA sequence (36–124 bp) was also seen. As the chance of forming any given recombinant is small, the abundance of recombinants in this patient suggests selection for particular recombinant genotypes during years of chronic infection. We suggest that genetic exchange among unrelated H. pylori strains, as documented here, is important because of the diversity of this gastric pathogen and its human hosts. Certain H. pylori recombinants may grow better in a given host than either parent. The vigour of growth, in turn, could impact on the severity of disease that infection can elicit.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.1999.01140.x
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  • 7
    Electronic Resource
    Electronic Resource
    Recombination and clonal groupings within Helicobacter pylori from different geographical regions[Authors' n] (1999)
    Oxford BSL : Blackwell Science Ltd
    Molecular microbiology 32 (1999), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: A collection of 20 strains of Helicobacter pylori from several regions of the world was studied to better understand the population genetic structure and diversity of this species. Sequences of fragments from seven housekeeping genes (atpA, efp, mutY, ppa, trpC, ureI, yphC ) and two virulence-associated genes (cagA, vacA) showed high levels of synonymous sequence variation (mean percentage Ks of 10–27%) and lower levels of non-synonymous variation (mean percentage Ka of 0.2–5.6%). Cluster analysis of pairwise differences between alleles revealed the existence of two weakly clonal groupings, which included half of the strains investigated. All six strains isolated from Japanese and coastal Chinese were assigned to the ‘Asian’ clonal grouping, probably reflecting descent from a distinct common ancestor. The clonal groupings were not totally uniform; recombination, as measured by the homoplasy test and compatibility matrices, was extremely common within all genes tested, except cagA. The fact that clonal descent could still be discerned despite such frequent recombination possibly reflects founder effects and geographical separation and/or selection for particular alleles of these genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.1999.01382.x
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  • 8
    Electronic Resource
    Electronic Resource
    Metronidazole resistance in Helicobacter pylori is due to null mutations in a gene (rdxA) that encodes an oxygen-insensitive NADPH nitroreductase (1998)
    Oxford BSL : Blackwell Science Ltd, UK
    Molecular microbiology 28 (1998), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Metronidazole (Mtz) is a critical component of combination therapies that are used against Helicobacter pylori, the major cause of peptic ulcer disease. Many H. pylori strains are Mtz resistant (MtzR), however, and here we show that MtzR results from loss of oxygen-insensitive NADPH nitroreductase activity. The underlying gene (called ‘rdxA’) was identified in several steps: transformation of Mtz-susceptible (MtzS) H. pylori with cosmids from a MtzR strain, subcloning, polymerase chain reaction (PCR) and DNA sequencing. We also found that (i) E. coli (normally MtzR) was rendered MtzS by a functional H. pylori rdxA gene; (ii) introduction of rdxA on a shuttle vector plasmid into formerly MtzRH. pylori rendered it MtzS; and (iii) replacement of rdxA in MtzSH. pylori with an rdxA::camR null insertion allele resulted in a MtzR phenotype. The 630 bp rdxA genes of five pairs of H. pylori isolates from infections that were mixed (MtzR/MtzS), but uniform in overall genotype, were sequenced. In each case, the paired rdxA genes differed from one another by one to three base substitutions. Typical rdxA genes from unrelated isolates differ by ≈ 5% in DNA sequence. Therefore, the near identity of rdxA genes from paired MtzR and MtzS isolates implicates de novo mutation, rather than horizontal gene transfer in the development of MtzR. Horizontal gene transfer could readily be demonstrated under laboratory conditions with mutant rdxA alleles. RdxA is a homologue of the classical nitroreductases (CNRs) of the enteric bacteria, but differs in cysteine content (6 vs. 1 or 2 in CNRs) and isoelectric point (pI = 7.99 vs. 5.4–5.6), which might account for its reduction of low redox drugs such as Mtz. We suggest that many rdxA (MtzR) mutations may have been selected by prior use of Mtz against other infections. H. pylori itself is an early risk factor for gastric cancer; the possibility that its carcinogenic effects are exacerbated by Mtz use, which is frequent in many societies, or the reduction of nitroaromatic compounds to toxic, mutagenic and carcinogenic products, may be of significant concern in public health.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.1998.00806.x
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  • 9
    Electronic Resource
    Electronic Resource
    Analyses of the cag pathogenicity island of Helicobacter pylori (1998)
    Oxford BSL : Blackwell Science Ltd, UK
    Molecular microbiology 28 (1998), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Most strains of Helicobacter pylori from patients with peptic ulcer disease or intestinal-type gastric cancer carry cagA, a gene that encodes an immunodominant protein of unknown function, whereas many of the strains from asymptomatically infected persons lack this gene. Recent studies showed that the cagA gene lies near the right end of a ≈37 kb DNA segment (a pathogenicity island, or PAI) that is unique to cagA+ strains and that the cag PAI was split in half by a transposable element insertion in the reference strain NCTC11638. In complementary experiments reported here, we also found the same cag PAI, and sequenced a 39 kb cosmid clone containing the left ‘cagII’ half of this PAI. Encoded in cagII were four proteins each with homology to four components of multiprotein complexes of Bordetella pertussis (‘Ptl’), Agrobacterium tumefaciens (‘Vir’), and conjugative plasmids (‘Tra’) that help deliver pertussis toxin and T (tumour inducing) and plasmid DNA, respectively, to target eukaryotic or prokaryotic cells, and also homologues of eukaryotic proteins that are involved in cytoskeletal structure. To the left of cagII in this cosmid were genes for homologues of HslU (heat-shock protein) and Era (essential GTPase); to the right of cagII were homologues of genes for a type I restriction endonuclease and ion transport functions. Deletion of the cag PAI had no effect on synthesis of the vacuolating cytotoxin, but this deletion and several cag insertion mutations blocked induction of synthesis of proinflammatory cytokine IL-8 in gastric epithelial cells. Comparisons among H. pylori strains indicated that cag PAI gene content and arrangement are rather well conserved. We also identified two genome rearrangements with end-points in the cag PAI. One, in reference strain NCTC11638, involved IS605, a recently described transposable element (as also found by others). Another rearrangement, in 3 of 10 strains tested (including type strain NCTC11637), separated the normally adjacent cagA and picA genes and did not involve IS605. Our results are discussed in terms of how cag-encoded proteins might help trigger the damaging inflammatory responses in the gastric epithelium and possible contributions of DNA rearrangements to genome evolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.1998.00770.x
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  • 10
    Electronic Resource
    Electronic Resource
    The complete genome sequence of the gastric pathogen Helicobacter pylori (1997)
    [s.l.] : Macmillan Magazines Ltd.
    Nature 388 (1997), S. 539-547 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/388539a0
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