Interferon gamma-signature transcript profiling and IL-23 upregulation in response to Helicobacter pylori infection.

Helicobacter pylori infection is the major cause of gastroduodenal pathologies including gastric cancer. The long persistence of bacteria and the type of immune and inflammatory response determine the clinical issue. In this study, the global gene expression profile after 6 and 12 months of H. pylori infection was investigated in the mouse stomach, using the Affymetrix GeneChip Mouse Expression Array A430. Genes related to the inflammatory and immune responses were focused. Levels of selected transcripts were confirmed by reverse transcription polymerase chain reaction. Twenty- five and nineteen percent of the differentially expressed genes observed at 6 and 12 months post-infection respectively, were related to immune response. They are characterized by an interferon (IFN)gamma-dependent expression associated to a T helper 1 (Th1) polarised response. In-depth analysis revealed that an up-regulation of IL-23p19, took place in the stomach of H. pylori infected-mice. Strong IL-23p19 levels were also confirmed in gastric biopsies from H. pylori-infected patients with chronic gastritis, as compared to healthy subjects. Our microarray analysis revealed also, a high decrease of H+K+-ATPase transcripts in the presence of the H. pylori infection. Association of gastric Th1 immune response with hypochlorhydria through the down-regulation of H+K+-ATPase contributes to the genesis of lesions upon the H. pylori infection. Our data highlight that the up-regulation of IL-23 and of many IFNgamma signature transcripts occur early on during the host response to H. pylori, and suggest that this type of immune response may promote the severity of the induced gastric lesions.

Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma(80) family of promoter signals.

Helicobacter pylori is adapted to life in a unique niche, the gastric epithelium of primates. Its promoters may therefore be different from those of other bacteria. Here, we determine motifs possibly involved in the recognition of such promoter sequences by the RNA polymerase using a new motif identification method. An important feature of this method is that the motifs are sought with the least possible assumptions about what they may look like. The method starts by considering the whole genome of H. pylori and attempts to infer directly from it a description for a family of promoters. Thus, this approach differs from searching for such promoters with a previously established description. The two algorithms are based on the idea of inferring motifs by flexibly comparing words in the sequences with an external object, instead of between themselves. The first algorithm infers single motifs, the second a combination of two motifs separated from one another by strictly defined, sterically constrained distances. Besides independently finding motifs known to be present in other bacteria, such as the Shine-Dalgarno sequence and the TATA-box, this approach suggests the existence in H. pylori of a new, combined motif, TTAAGC, followed optimally 21 bp downstream by TATAAT. Between these two motifs, there is in some cases another, TTTTAA or, less frequently, a repetition of TTAAGC separated optimally from the TATA-box by 12 bp. The combined motif TTAAGCx(21+/-2)TATAAT is present with no errors immediately upstream from the only two copies of the ribosomal 23 S-5 S RNA genes in H. pylori, and with one error upstream from the only two copies of the ribosomal 16 S RNA genes. The operons of both ribosomal RNA molecules are strongly expressed, representing an encouraging sign of the pertinence of the motifs found by the algorithms. In 25 cases out of a possible 30, the combined motif is found with no more than three substitutions immediately upstream from ribosomal proteins, or operons containing a ribosomal protein. This is roughly the same frequency of occurrence as for TTGACAx(15-19)TATAAT (with the same maximum number of substitutions allowed) described as being the sigma(70 )promoter sequence consensus in Bacillus subtilis and Escherichia coli. The frequency of occurrence of the new motif obtained, TTAAGCx(19-23)TATAAT, remains high when all protein genes in H. pylori are considered, as is the case for the TTGACAx(15-19)TATAAT motif in B. subtilis but not in E. coli.

Topoisomerase I of Helicobacter pylori: juxtaposition with a flagellin gene (flaB) and functional requirement of a fourth zinc finger motif.

Cloning and nucleotide sequence analysis showed that in Helicobacter pylori the gene encoding topoisomerase I (topA) lies about 170 nucleotides upstream from flaB, a gene encoding one of the two flagellin proteins that is required for virulence. The topA and flaB genes are divergently transcribed. The orientation and spatial relationship between flaB and topA are remarkably conserved among strains of a bacterium in which genomic rearrangements are common. The deduced amino acid sequence of topoisomerase I revealed four zinc finger motifs, one more than has been reported previously for the Escherichia coli homologue. The additional motif, which is near the C-terminus of the protein, appears to be essential for function since mutations in that region are lethal. These data show that TopA proteins can be divided into several classes on the basis of zinc finger motifs and raise the interesting possibility that the H. pylori enzyme has local topological effects focussed on a flagellin gene.

Cloning of Campylobacter jejuni genes required for leucine biosynthesis, and construction of leu-negative mutant of C. jejuni by shuttle transposon mutagenesis.

Campylobacter jejuni is a Gram-negative pathogen responsible for diarrhoeal diseases in humans. To date, very little is known about the genetic organization and molecular biology of this microorganism. The cosmid vector pHC79 was used to construct a genomic library from the total genomic DNA of C. jejuni strain C31 in Escherichia coli and recombinant cosmids capable of complementing the auxotrophic defect in leucine biosynthesis of E. coli HB101 were identified. Three of 400 clones tested were found to be capable of complementing the nutritional defect of E. coli HB101 as well as those of independent leuB mutants of E. coli strains. These results indicated that the cloned genes responsible for leucine complementation encoded an enzyme analogous to the beta-isopropylmalate dehydrogenase specified by the leuB gene in E. coli strains. The sizes of the recombinant cosmids which became stabilized in E. coli cells ranged from 12.9 to 15.4 kb compared to the expected, originally packaged, 45- to 50-kb molecules, attesting to major rearrangements occurring in this background. The recombinant plasmid pILL547 was shown to carry genes that were analogous to the leuB gene and also to the leuC and leuD genes of E. coli. The gene required for leuB complementation was subcloned on a 1.6-kb restriction fragment and was mapped more precisely by insertional mutagenesis using as transposon a newly constructed (MiniTn3-Km) element engineered to mutagenize Campylobacter genes. The leuB gene of C. jejuni was shown to be expressed from its own promoter in E. coli cells. In E. coli minicells, the cloned insert encoded a polypeptide with an apparent molecular weight of 40 kDa. A leucine auxotrophic mutant of C. jejuni strain C31 was constructed in vitro by allelic exchange, replacing the original copy of the leucine gene by an allele mutated by the insertion of the kanamycin transposable element.

Identification of nonessential Helicobacter pylori genes using random mutagenesis and loop amplification.

Analysis of the published genome sequences of Helicobacter pylori revealed that approximately 40% of the predicted open reading frames (ORFs) were of unknown function. We have developed the random mutagenesis and loop amplification (RMLA) strategy, and used this approach both to characterize individual virulence factors and to collectively screen comparatively large numbers of H. pylori mutants to identify genes that are not essential for viability in vitro. The mini-Tn3-Km transposon was used to generate a random mutant library in H. pylori strain G27. By screening the library of mutants we were able to demonstrate that the transposon integrated randomly into the chromosome of H. pylori and that RMLA was able to identify mutants in known virulence genes (urease and catalase). To test whether this strategy could be used as a high-throughput approach for the simultaneous identification of a series of nonessential genes of H. pylori, the transposon-chromosomal junctions of a pool of mutants were amplified by inverse PCR using circular fragments of genomic DNA obtained after chromosomal DNA extracted from the pool of mutants had been digested with HindIII and self-ligated. The amplification products were radioactively labelled and hybridized to a high density macroarray membrane containing a duplicated target sequence for every gene of H. pylori strain 26695. For the positive ORFs the precise site of transposon insertion was confirmed by PCR mapping. In total 78 H. pylori genes were unambiguously identified as nonessential for viability in vitro, including 20 with orthologues of unknown function in other species and 21 which were H. pylori-specific.

Genotyping of Helicobacter pylori isolates by sequencing of PCR products and comparison with the RAPD technique.

Two genotyping methods were performed on bacterial suspensions of the human pathogen Helicobacter pylori. A total of 29 clinical isolates were analysed by sequencing of a 294-bp PCR-derived internal segment of the essential ureC/glmM gene of H. pylori, and by random amplified polymorphic DNA (RAPD) using a single 11-bp oligonucleotide made up of an arbitrary nucleotide sequence. Each isolate exhibited a distinct sequence over a 210-bp stretch of the ureC/glmM gene. Similarly, the isolates bore different profiles when tested by RAPD fingerprinting. Successive strains arising from patients who relapsed following antibiotic treatment and strains isolated from two patients institutionalized in the same care centre had identical ureC/glmM gene sequences and RAPD profiles. Both methods were found to be discriminatory. However, PCR sequencing of the ureC/glmM gene appeared to be more reproducible and more reliable for distinguishing between strains than the RAPD technique.

Heat shock proteins of Helicobacter pylori.

As in any other bacterium, Helicobacter pylori synthesizes two heat shock proteins, the HspA (GroES or Hsp 10 homologue) and the HspB (GroEL or Hsp60 homologue). This article summarizes the present knowledge of genetics, function and the antigenic, immunogenic and protective properties of these two abundant proteins. H. pylori HspA and HspB antigens have vital functions for the bacterium; they share most of the bacterial chaperonin characteristics. However, the unique structure of HspA and its unique capacity to specifically bind nickel ions, strongly suggest an essential role of HspA with regard to the urease metallo-enzyme. The putative role of the H. pylori Hsp antigens in autoimmunity is also addressed.

Second-line treatment for failure to eradicate Helicobacter pylori: a randomized trial comparing four treatment strategies.

AIM: To compare the efficacy of different regimens in patients in whom previous Helicobacter pylori eradication therapy has failed. METHODS: In this study named StratHegy patients (n=287) were randomized to receive one of three empirical triple therapy regimens or a strategy based on antibiotic susceptibility. The empirical regimens were omeprazole, 20 mg b.d., plus amoxicillin, 1000 mg b.d., and clarithromycin, 500 mg b.d., for 7 days (OAC7), clarithromycin, 500 mg b.d., for 14 days (OAC14) or metronidazole, 500 mg b.d., for 14 days (OAM14). In the susceptibility-based strategy, patients with clarithromycin-susceptible strains received OAC14, whilst the others received OAM14. The 13C-urea breath test was performed before randomization and 4-5 weeks after eradication therapy. RESULTS: In the intention-to-treat analysis, the eradication rates for empirical therapies were as follows: OAC7, 47.4% (27/57); OAC14, 34.5% (20/58); OAM14, 63.2% (36/57); it was 74.3% (84/113) for the susceptibility-based treatment (P<0.01 when compared with OAC7 and OAC14). In patients receiving clarithromycin, the eradication rates were 80% for clarithromycin-susceptible strains and 16% for clarithromycin-resistant strains; in patients receiving OAM14, the eradication rates were 81% for metronidazole-susceptible strains and 59% for metronidazole-resistant strains. CONCLUSIONS: Eradication rates of approximately 75% can be achieved with second-line triple therapy based on antibiotic susceptibility testing. If susceptibility testing is not available, OAM14 is an appropriate alternative.

Occurrence of pap-, sfa-, and afa-related sequences among F165-positive Escherichia coli from diseased animals.

A total of 160 Escherichia coli positive for F165 fimbrial antigen and isolated from diarrheic and septicemic animals, were examined for the presence of the pap, afa, and sfa/foc operons or related nucleotide sequences using colony hybridization. Most isolates shared DNA sequences with the pap operon sequences alone or in association with afa or sfa. Thus, our results indicate that F165-positive E. coli from diseased animals share DNA sequences with operons coding for adhesins important in human extra-intestinal disease and that multiple adhesin systems are often found in single isolates. However, 20% of the F165-positive isolates did not show any homology with the probes representing the three adhesin systems, suggesting that one of the operons responsible for F165 production could be different from the pap, sfa/foc, and afa operons.

PCR-DNA Sequence Typing.

There is a great need to develop molecular techniques for the typing of Helicobacter pylori isolates since classical bacteriological assays, such as serotyping or lysotyping, are lacking. Such techniques would provide the microbiologist with the tools necessary to differentiate one strain from another one (essential for epidemiological studies), to determine whether individuals might be colonized by several isolates, and to elucidate whether ulcer relapse following treatment is associated with the colonization of the gastric mucosa by the same isolate or is caused by reinfection.

Random Mutagenesis of the H. pylori Genome.

Transposable elements are well-known genetic tools that enable the geneticist to generate mutations by disrupting the linear continuity of a specific gene and, consequently, affect its expression. This approach, in addition to providing an efficient way to create mutants, which are easily detectable because of the acquisition of drug resistance phenotype (when a drug-resistance transposable element is used), also provides an easy way to recover and identify the mutated gene. Several genetic systems have been developed in the past for many bacterial species and have permitted random and generalized mutagenesis to be performed on given genomes by introducing, via conjugation, suicide plasmids harboring transposable elements. Unfortunately, such transposon delivery systems have not yet been found to be functional in Helicobacter pylori.

Gastric helicobacters in cats.

The types of helicobacter which are found in the stomachs of carnivorous pets, especially cats, have been traditionally referred to as 'gastric helicobacter-like organisms' (GHLOs). These are microaerophilic, Gram-negative, spiral bacteria with multiple terminal flagellae and are endowed with high-level urease activity which allows them to survive in an acidic environment. Certain species have one or more periplasmic fibrils. The two GHLOs most commonly found in cats are Helicobacter felis and a species related to H heilmannii which was recently cultured from dogs. All phenotypic and genotypic (16S RNA gene sequences) evidence suggests that both of these bacteria belong in the genus Helicobacter. Whether or not helicobacters can be transmitted to humans from carnivorous pets is controversial but the recent discovery of H pylori -infected cats may be evidence of an animal reservoir for this pathogen. Although the role of H pylori in inducing antral gastritis and perpetuating pyloric ulcers in humans is well established, whether or not Helicobacter spp are causally involved in any feline gastric inflammatory conditions is unknown.

[UreI: a Helicobacter pylori protein essential for resistance to acidity and for the early steps of murine gastric mucosa infection]. / UreI: une protéine de Helicobacter pylori essentielle à la résistance à l'acidité et aux étapes précoces de l'infection de la muqueuse gastrique murine.

UNLABELLED: Helicobacter pylori (H. pylori) is a Gram negative microaerophilic bacteria whose only known niche is the human gastric mucosa. The presence of H. pylori is associated with various pathologies ranging from peptic ulcer disease to gastric carcinoma. H. pylori virulence is dependent on its exceptional ability to resist to the stomach acidity by hydrolyzing urea into ammonia. Survival of H. pylori to acidity in the presence of urea relies on the activity of a membrane protein, UreI. AIMS: We decided to better characterize the role of UreI (i) in vitro in ammonia production through the action of urease, and (ii) in vivo in the colonization of the gastric mucosa. METHODS: Ammonia production by a wild type strain of H. pylori or by a UreI-deficient strain was measured as a function of extracellular pH. In addition, the kinetics of elimination of a UreI-deficient mutant in vivo were realized in the mouse model for colonization. RESULTS: UreI was associated with an increase of ammonia production in acidic conditions in vitro and was necessary for the initial steps of the mouse stomach colonization. CONCLUSION: UreI thus behaves as a sensor of extracellular pH. This protein activates urease at acidic pH; thereby, it probably allows H. pylori to resist to acidity in vivo during the first steps of infection.

[Development of genetic and molecular approaches for the diagnosis and study of the pathogenicity of Helicobacter pylori, agent of gastric inflammatory diseases]. / Développement d'approches génétiques et moléculaires pour le diagnostic et l'étude du pouvoir pathogène de Helicobacter pylori, agent des maladies inflammatoires gastriques.

Helicobacter pylori (H. pylori) is a small gram-negative bacillus, recently discovered, found in the stomach of patients with active chronic gastritis and duodenal ulcers. Production of a potent urease has been described as a trait common to all H. pylori so far isolated. To clarify the role of urease in the pathogenic process, as well as to engineer genetic tools useful for the diagnosis of H. pylori, we cloned the genes responsible for urease activity. A genomic library was constructed in Escherichia coli (E. coli) from the chromosomal DNA of the H. pylori strain 85P using a shuttle cosmind vector that we constructed in vitro capable of replicating both in E. coli and Campylobacter jejuni (C. jejuni). The genes responsible for the urease biosynthesis were cloned into E. coli host, then mobilized into C. jejuni where they were expressed. At least six different genes were shown to be required for the expression of the synthesis of an active enzyme; these genes belong to the same cluster and are regulated at the transcriptional level. The two genes encoding the two subunits of the urease enzyme were identified and sequenced; the products of these genes were compared to the other bacterial ureases. The genetic approach allowed to determine the amino-acid sequence of the most immunogenic antigens of H. pylori. In addition, it provides us with genetic tools: a 294-base pairs (bp) DNA fragment internal to one of the urease genes, was shown to be specific of H. pylori strains. This fragment was selectively amplified by polymerase chain reaction (P.C.R.) using two primers designed to target the urease region of all H. pylori isolates present in biological specimen. In addition, P.C.R. followed by direct DNA sequencing of the 294-bp amplified product was shown to be useful to identify and to distinguish between different H. pylori isolates.

[Helicobacter infections of man and of domestic carnivores: comparative data]. / Hélicobactérioses de l'homme et des carnivores domestiques: quelques données comparatives.

The role of Helicobacter pylori in generating of the chronic gastritis and in the maintaining of the gastroduodenal ulcerous disease, has been a major medical discovery of these past years in human gastroenterology. More recently in Man, studies have showed that the gastric tumours (adenocarcinoma, lymphoma) are epidemiologically associated with the H. pylori infection. Although the H. pylori infection is the one of the most frequent in the word, the epidemiologic and ecologic aspects of this infections are still not very well known. Thanks to phylogenic studies using the new molecular biology techniques and to fundamental experimental studies, we know more about helicobacteria in domestic carnivores as well as their morphologic characteristic, their taxonomia and more importantly details concerning their ecological niche. Few clinical studies have been made to this day, but the ones that have been undertaken are interesting in confirming the extensive prevalence of Helicobacter infections in domestic carnivores and in underlining their role in the genesis of the inflammatory gastropathies observed in these species. Recent observations have demonstrated the ubiquitous character of these helicobacteria by showing their presence in the stomach of man, dogs and cats. This ubiquitous character has led some scientists to consider the potential zoonotic risk of the human infection by Helicobacter heilmannii, felis or pylori. Finally, the Helicobacter infection of animals seems to be an interesting model not only in the study of the affections caused by these bacteria, but also in the elaboration of a future vaccine against the H. pylori infection in man.

[Bacteriology and pathogenicity of Helicobacter pylori]. / Bactériologie et pathogénicité d'Helicobacter pylori.

Helicobacter pylori is the prototype of bacteria belonging to a new genus, the Helicobacter genus. It is a gram-negative, highly motile and microaerophilic bacterium, with a spiral shape, that colonizes the human gastric mucosa and causes several gastroduodenal diseases. Pathogenicity of H. pylori relies upon its capacity to adapt to a hostile environment and to escape the host response. Resistance to acidity, motility, adhesion, molecular mimicry, resistance to phagocytosis, synthesis of a cytotoxin, induction of an inflammatory response are the major strategies developed by H. pylori to colonize persistently and damage gastric tissue.

Evidence for specific secretion rather than autolysis in the release of some Helicobacter pylori proteins.

We investigated whether Helicobacter pylori cells actively secrete proteins such as the urease subunits UreA and UreB and the GroES and GroEL homologs HspA and HspB or whether these proteins were present in the extracellular compartment as a consequence of autolysis. Using a subcellular fractionation approach associated with quantitative Western blot analyses, we showed that the supernatant protein profiles were very different from those of the cell pellets, even for bacteria harvested in the late growth phase; this suggests that the release process is selective. A typical cytoplasmic protein, a beta-galactosidase homolog, was found exclusively associated with the pellet of whole-cell extracts, and no traces were found in the supernatant. In contrast, UreA, UreB, HspA, and HspB were mostly found in the pellet but significant amounts were also present in the supernatant. HspA and UreB were released into the supernatant at the same rate throughout the growth phase (3%), whereas large portions of HspB and UreA were released during the stationary phase (over 30 and 20%, respectively) rather than during the early growth phase (20% and 6, respectively). The profiles of protein obtained after water extraction of the bacteria with those of the proteins naturally released within the liquid culture supernatants demonstrated that water extraction led to the release of a large amount of protein due to artifactual lysis. Our data support the conclusion that a specific and selective mechanism(s) is involved in the secretion of some H. pylori antigens. A programmed autolysis process does not seem to make a major contribution.

Shuttle cloning and nucleotide sequences of Helicobacter pylori genes responsible for urease activity.

Production of a potent urease has been described as a trait common to all Helicobacter pylori so far isolated from humans with gastritis as well as peptic ulceration. The detection of urease activity from genes cloned from H. pylori was made possible by use of a shuttle cosmid vector, allowing replication and movement of cloned DNA sequences in either Escherichia coli or Campylobacter jejuni. With this approach, we cloned a 44-kb portion of H. pylori chromosomal DNA which did not lead to urease activity when introduced into E. coli but permitted, although temporarily, biosynthesis of the urease when transferred by conjugation to C. jejuni. The recombinant cosmid (pILL585) expressing the urease phenotype was mapped and used to subclone an 8.1-kb fragment (pILL590) able to confer the same property to C. jejuni recipient strains. By a series of deletions and subclonings, the urease genes were localized to a 4.2-kb region of DNA and were sequenced by the dideoxy method. Four open reading frames were found, encoding polypeptides with predicted molecular weights of 26,500 (ureA), 61,600 (ureB), 49,200 (ureC), and 15,000 (ureD). The predicted UreA and UreB polypeptides correspond to the two structural subunits of the urease enzyme; they exhibit a high degree of homology with the three structural subunits of Proteus mirabilis (56% exact matches) as well as with the unique structural subunit of jack bean urease (55.5% exact matches). Although the UreD-predicted polypeptide has domains relevant to transmembrane proteins, no precise role could be attributed to this polypeptide or to the UreC polypeptide, which both mapped to a DNA sequence shown to be required to confer urease activity to a C. jejuni recipient strain.

[Development of genetic and molecular approaches for the diagnosis and the study of the pathogenic power of Helicobacter pylori, agent of inflammatory gastric diseases]. / Développement d'approches génétiques et moléculaires pour le diagnostic et l'étude du pouvoir pathogène de Helicobacter pylori, agent des maladies inflammatoires gastriques.

Helicobacter pylori (H. pylori) is a small Gram negative bacillus, recently discovered, found in the stomach of patients with active chronic gastritis and duodenal ulcers. Production of a potent urease has been described as a trait common to all H. pylori so far isolated. To clarify the role of urease in the pathogenic process, as well as to engineer genetic tools useful for the diagnosis of H. pylori, we cloned the genes responsible for urease activity. A genomic library was constructed in Escherichia coli (E. coli) from the chromosomal DNA of the H. pylori stain 85P using a shuttle cosmid vector that we constructed in vitro capable of replicating both in E. coli and Campylobacter jejuni (C. jejuni). The genes responsible for the urease biosynthesis were cloned into E. coli host, then mobilized into C. jejuni where they were expressed. At least six different genes were shown to be required for the expression of the synthesis of an active enzyme: these genes belong to the same cluster and are regulated at the transcriptional level. The two genes encoding the two subunits of the urease enzyme were identified and sequenced; the products of these genes were compared to be other bacterial ureases. The genetic approach allowed to determine the amino-acid sequence of the most immunogenic antigens of H. pylori. In addition, it provides us with genetic tools: a 294-base pairs (bp) DNA fragment internal to one of the urease genes, was shown to be specific of H. pylori strains.(ABSTRACT TRUNCATED AT 250 WORDS)