Differentiation of Helicobacter pylori strains directly from gastric biopsy specimens by PCR-based restriction fragment length polymorphism analysis without culture.

Recent studies have shown the usefulness of PCR-based restriction fragment length polymorphism (RFLP) analysis for differentiating Helicobacter pylori strains isolated by culture. For this study, a PCR-based RFLP assay was developed for directly typing H. pylori strains from gastric biopsy specimens. Nineteen gastric biopsy specimens obtained from patients undergoing endoscopy for gastrointestinal complaints were cultured for isolation of H. pylori. Genomic DNA preparations from these gastric biopsy specimens and the corresponding H. pylori isolates were tested by our PCR-based RFLP assay. The 1,179-bp H. pylori DNA fragments amplified by the PCR assay were digested with the restriction enzymes HhaI, MboI, and AluI and analyzed by agarose gel electrophoresis. HhaI, MboI, and AluI digestion produced 11, 10, and 6 distinguishable digestion patterns, respectively, from the 19 H. pylori isolates tested and generated 13, 11, and 6 different patterns, respectively, from the 19 gastric biopsy specimens. The patterns from 13 of the 19 gastric biopsy specimens matched those of the H. pylori isolates from the corresponding patients. The patterns from the remaining six biopsy specimens appeared to represent infection by two strains of H. pylori; the pattern of one strain was identical to that of the isolate from the corresponding patient. By combining all the restriction enzyme digestion patterns obtained by using HhaI, MboI, and AluI, we observed 19 distinct RFLP patterns from the 19 specimens. The results suggest that the PCR-based RFLP analysis method may be useful as a primary technique to identify and distinguish H. pylori strains directly from gastric biopsy specimens without culture of the organisms.     

Genome analysis of Helicobacter pylori by pulsed-field gel electrophoresis

The molecular epidemiology of total 121 isolates of Helicobacter pylori was analyzed by pulsed-field gel electrophoresis method with restriction enzyme Spe I. Seventy-seven isolates were separated from the clinical samples, 36 isolates from pyloric antrum and the body of stomach of 18 patients and 8 isolates from pyloric antrum of 4 patients that include one colony before and after sterilizing treatment to each patient. Seventy-five in 77 isolates showed different genomic types respectively, and the other 2 isolates had the same genomic type and were suspected to be caused by intersective infection of medical workers or the instruments that used in examination because they were from patients who were examined by gastric microscope in same time and same laboratory. In isolates from 4 patients who were treated by sterilizing method, 2 patients showed same genomic types with that observed before the treatment, and one patient showed an incomplete treatment because the genomic type of its colony was is similar, and another patient could be infected again because its isolates showed different genomic type. In 18 patients whose isolates were separated from pyloric antrum and body of the stomach respectively to each person, isolates of 3 patients showed different genomic types in the two different part of stomach indicating that they had two and more clones of H. pylori.     

Ribotyping of Helicobacter pylori from clinical specimens.

Ribotyping is a method used to type strains of bacteria by analyzing the restriction enzyme digestion patterns of the rRNA genes. This method was applied to 126 strains of Helicobacter pylori from 100 unrelated symptomatic patients who had endoscopies done and to 15 strains from 15 infected subjects from seven families. Analysis of the rRNA gene patterns revealed 77 distinct ribotypes from the 100 patients. From 15 of these subjects, isolates were recovered from antral mucosal biopsies at follow-up endoscopy. All follow-up isolates from the same patient, with one exception, yielded identical digest patterns. This patient had strains with two distinct digest patterns obtained from a set of three isolates cultured from biopsy specimens taken at different times. Five patients who had isolates recovered from different sites in the stomach (antrum, gastric body, duodenum, and pyloric channel) showed ribotyping patterns which were identical for each patient yet distinct between patients. In seven family groups studied, identical digest patterns were detected in members of two families, with variability in strains detected among members of the remaining families. This study demonstrates that ribotyping provides a useful, reliable, reproducible, and highly discriminatory typing scheme for the study of H. pylori infection.     

Characterization and presumptive identification of Helicobacter pylori isolates from rhesus monkeys.

We characterized 38 Helicobacter isolates, including 22 from gastric biopsy samples obtained from 14 rhesus monkeys and single isolates from 16 monkeys in a different colony. Biochemical profiles of these isolates were nearly identical to that of Helicobacter pylori ATCC 43504. Restriction fragment length polymorphism (RFLP) analysis indicated that each infected monkey harbored one to four strains. The 17 RFLP types found among these 22 isolates differed from all seven RFLPs found among the other 16 isolates. Thus, monkeys within a given colony are more likely to be infected by Helicobacter isolates with the same or a similar RFLP than are monkeys from different colonies. A 16S rRNA gene was amplified by PCR and cloned from the Helicobacter isolate from rhesus monkey 85D08. Ribotyping with this probe demonstrated less diversity among isolates from rhesus monkeys than was reported among isolates of H. pylori from humans, as did RFLP analysis of a PCR fragment of the ureA-ureB gene cluster. The DNA sequence of the cloned 16S rRNA gene was determined and compared with sequences reported for H. pylori and other Helicobacter species. Our analysis of 127 nucleotides (corresponding with residues 1240 to 1366 of the Escherichia coli 16S rRNA gene) indicated that the Helicobacter isolate from monkey 85D08 was 99.2 to 100% homologous to isolates of H. pylori from humans but only 83.5 to 96.9% homologous with other Helicobacter species in this region of the 16S rRNA gene. These data provide strong support for the presumptive identification of these isolates as H. pylori.     

Molecular typing of Helicobacter pylori isolates from a multicenter U.S. clinical trial by ureC restriction fragment length polymorphism.

The molecular typing of 81 pretreatment Helicobacter pylori isolates and the comparison of 18 pretreatment-posttreatment pairs is described by restriction fragment length polymorphism (RFLP) of the ureC gene. The results of our study show the extreme genomic diversity of H. pylori and indicate that infection by H. pylori in the United States does not appear to be limited to a small number of RFLP types.     

Use of a pilin gene probe to study molecular epidemiology of Pseudomonas aeruginosa.

Strains of Pseudomonas aeruginosa from patients with cystic fibrosis (CF) are unusual. The majority have a rough lipopolysaccharide (LPS) which renders them nontypeable by conventional typing systems based on a serological reaction with the O polysaccharide of smooth LPS. We developed a new typing scheme using a pilin gene probe as a marker for hybridization with endonuclease-digested genomic DNA from P. aeruginosa. Twenty-one different restriction fragment length polymorphism (RFLP) types were found among 249 isolates. RFLP type 7 was recovered only from patients with thermal burns (9 of 14 isolates) in both Vancouver, British Columbia, and Edmonton, Alberta, Canada. None of the other RFLP types showed a clear predilection for disease state or environmental niche. Multiple morphologically different isolates from individual patients with CF were studied; each isolate in 33 of 40 sputum samples had an identical RFLP type, despite considerable LPS serotype heterogeneity. Sequential isolates from 23 patients were studied; in 10 isolates there was a clear change in both the RFLP and the LPS serotype. We conclude that patients with CF usually harbor a single P. aeruginosa RFLP type in their sputa, but that one strain can replace another as the predominant colonizing type.     

Typing of Campylobacter pylori by bacterial DNA restriction endonuclease analysis and determination of plasmid profile.

Campylobacter pylori isolates from 37 symptomatic patients and 3 asymptomatic volunteers were examined by chromosomal DNA restriction endonuclease analysis and determination of plasmid profile. Restriction digests with HindIII, HaeIII, PvuII, and BglII produced clear and reproducible results that permitted discrimination between different strains. Only 35% of C. pylori isolates were found to have plasmid DNA. Isolates from different patients, including those from two pairs of siblings, had unique restriction patterns and plasmid profiles. Consecutive isolates obtained 1 year apart from each of two asymptomatic volunteers had identical restriction patterns and plasmid profiles, suggesting persistence of the same strain. A pair of isolates obtained one year apart from the third volunteer differed in plasmid DNA content but had similar chromosomal DNA restriction patterns. Plasmid profile determination and bacterial DNA restriction endonuclease analysis provide a reliable means of discriminating between different strains of C. pylori and may be useful for typing these organisms in epidemiologic studies.     

Isolation of Helicobacter pylori from saliva.

Helicobacter pylori was grown in low numbers from the saliva of one of nine patients who were positive for gastric H. pylori. The saliva-derived isolate from this patient was identical to the antral biopsy-derived isolate from the same patient and differed from isolates cultured from the antral biopsies of all other patients by soluble-protein electrophoresis, restriction endonuclease DNA analysis, and Southern blot hybridization. This is the first observation, to our knowledge, of the recovery of viable H. pylori from saliva.     

Helicobacter pylori-induced gastritis in the domestic cat.

Helicobacter pylori has been cultured from the inflamed gastric mucosae of naturally infected cats; the lesions in H. pylori-infected cat stomachs mimic many of the features seen in H. pylori-infected human stomachs. To determine whether H. pylori-negative specific-pathogen-free cats with normal gastric mucosae were susceptible to colonization by this bacterium and whether gastritis developed after infections, four H. pylori-negative cats treated with cimetidine were orally dosed three times with 3 ml (1.5 x 10(8) CFU/ml) of H. pylori every 4 days. All four cats became persistently colonized as determined by gastric cultures and PCRs from serial gastric biopsy samples and necropsy samples at 7 months postinfection. H. pylori was not isolated from the two control cats, nor were their gastric tissues positive by PCR; one of the two cats had a few focal lymphocytic aggregates in the body submucosa, whereas the second cat had a normal gastric mucosa. All four H. pylori-infected cats had multifocal gastritis consisting of lymphoid aggregates plus multiple large lymphoid nodules, which were most noticeable in the antral mucosa. In addition, one H. pylori-infected cat had a moderate diffuse infiltration of polymorphonuclear leukocytes in the subglandular region of the antrum. H. pylori-like organisms were focally distributed in glandular crypts of the antrum. Two of the H. pylori-infected cats had significant (eightfold) increases over baseline in levels of immunoglobulin G H. pylori serum antibody. The H. pylori isolates from the four experimentally infected cats had restriction fragment length polymorphism patterns specific for the flaA gene that were identical to those of the inoculating strain. H. pylori readily colonizes the cat stomach and produces persistent gastritis.     

Restriction enzyme analysis of plasmid DNA and bacteriophage typing of paired Staphylococcus aureus blood culture isolates

We compared restriction enzyme analysis of plasmid (REAP) DNA profiling with bacteriophage typing for determination of similarities and differences among 50 pairs of Staphylococcus aureus blood isolates from patients with multiple positive blood cultures. Isolates from 17 pairs did not have detectable plasmids. Isolates from 33 pairs had plasmids classified into 17 distinct REAP DNA profiles. Paired isolates from 31 of these episodes were identical to one another. By phage typing, 35 pairs had strong lytic reactions to a phage(s), 9 pairs lacked strong reactions, and 6 pairs consisted of a strongly reactive isolate and an isolate with no strong reaction to a phage. When consolidated into 11 general phage groups, pairs from 44 of the 50 episodes were in the same general group. REAP DNA profiles were highly reproducible (99%), whereas phage typing was not. REAP DNA profiling is superior to phage typing as a technique for determining similarities and differences among S. aureus blood isolates.     

Failure to detect Helicobacter pylori in nasal mucus in H pylori positive dyspeptic patients.

Stomach biopsies and samples of nasal mucus were cultured in patients with dyspeptic symptoms who underwent endoscopy to evaluate the possible route of transmission of Helicobacter pylori (H pylori). 42 patients were examined. For each patient two biopsies from the stomach corpus and antrum were taken and, before endoscopy, one nasal swab was obtained. Biopsy samples were tested for urease test, microbiological culture, and histological examination. The nasal swab was processed for microbiological examination. H pylori was not found in the nasal mucus of any of the patients, including the 36 who had H pylori in gastric biopsies.     

Mycobacterial interspersed repetitive unit typing of Mycobacterium tuberculosis compared to IS6110-based restriction fragment length polymorphism analysis for investigation of apparently clustered cases of tuberculosis

An evaluation of the utility of IS6110-based restriction fragment length polymorphism (RFLP) typing compared to a combination of variable number tandem repeat (VNTR) typing and mycobacterial interspersed repetitive unit (MIRU) typing was undertaken. A total of 53 patient isolates of Mycobacterium tuberculosis from four presumed episodes of cross-infection were examined. Genomic DNA was extracted from the isolates by a cetyl trimethylammonium bromide method. The number of copies of tandem repeats of the five loci ETR(A) to ETR(E) and 12 MIRU loci was determined by PCR amplification and agarose gel electrophoresis of the amplicons. VNTR typing identified the major clusters of strains in the three investigations in which they occurred (each representing a different evolutionary clade: 32333, 42235, and 32433). The majority of unrelated isolates (by epidemiology and RFLP typing) were also identified by VNTR typing. The concordance between the RFLP and MIRU typing was complete, with the exception of two isolates with RFLP patterns that differed by one band each from the rest of the major epidemiologically linked groups of isolates in investigation A. All of these isolates had identical MIRU and VNTR types. A further pair of isolates differed in the number of tandem repeat copies at two MIRU alleles but had identical RFLP patterns. The speed of the combined VNTR and MIRU typing approach enabled results for some of the investigations to be supplied in "real time," influencing choices in contact tracing. The ease of comparison of results of MIRU and VNTR typing, which are recorded as single multidigit numbers, was also found to greatly facilitate investigation management and the communication of results to health care professionals.     

Characterization of IS6110 insertions in the dnaA–dnaN intergenic region of Mycobacterium tuberculosis clinical isolates

Mycobacterium tuberculosis isolates with identical IS 6110 restriction fragment length polymorphism (RFLP) patterns are considered to be clonally related. The presence of IS 6110 in the dnaA–dnaN intergenic region, one preferential locus for the integration of IS 6110 , was evaluated in 125 M. tuberculosis isolates. Five isolates had IS 6110 inserted in this region, and two consisted of a mix of isogenic strains that putatively have evolved during a single infection. Strains from the same isolate had identical spoligo and mycobacterial interspersed repetitive unit–variable-number tandem repeat profiles, but had slight variations in IS 6110 RFLP patterns, due to the presence of IS 6110 in the dnaA–dnaN intergenic region. Duplication of the dnaA–dnaN intergenic region was found in one isogenic strain.     

Differentiation between reinfection and recrudescence of helicobacter pylori strains using PCR-based restriction fragment length polymorphism analysis

The aim of this study was to evaluate whether PCR-based restriction fragment length polymorphism (RFLP) analysis was effective in differentiating between reinfection and recrudescence of H. pylori strains. Following a 1-2 week regimen of omeprazole 20 mg, amoxicillin 1.0 g, and clarithromycin 500 mg twice daily, twenty patients with duodenal ulcer were enrolled in the study. Ten patients (group 1, control) were not successfully treated, and another 10 patients (group 2) exhibited recurrence of infection 6-24 months following the therapy. Follow-up diagnosis was performed by Giemsa stain and CLO test. RFLP profiles of antral and midbody biopsy specimens were compared before and after therapy. PCR products using the ureC gene were digested with restriction enzymes Hha I, Mbo I, and Hind III, and the fragments generated were analyzed by agarose gel electrophoresis. Hha I, Mbo I, and Hind III digestion produced 13, 7, and 2 distinguishable digestion patterns, respectively. There was no difference in RFLP profiles seen before and after the therapy in 17 duodenal ulcer patients, while different RFLP profiles were discovered in 3 patients. Following treatment, one (group 2) patient differed in Mbo I, and two (one each from both groups) patients differed in Hha I and Mbo I RFLP patterns. Eight of group 2 patients showed recrudescence of previous infection and two patients had reinfection by another strain. This study supports the hypothesis that PCR-based RFLP analysis can be effective for differentiating reinfection and recrudescence of H. pylori strains following triple therapy.     

Helicobacter pylori intrafamilial infections: change in source of infection of a child from father to mother after eradication therapy.

Biopsy specimens of the antrum and corpus were obtained from four Helicobacter pylori-infected members of a family and from the same boy (son 1) in whom the infection reappeared after simultaneous successful eradication treatment of three family members, excluding the mother. A total of 18 to 60 H. pylori isolates were obtained from each specimen and subjected to rRNA gene restriction pattern analysis. The father's isolates and the initial isolates from son 1 showed the same HindIII type, which was divided into three HaeIII subtypes. Isolates from the mother and a brother (son 2) and posttreatment isolates from son 1 showed a distinct HindIII type (with one minor subtype), which was divided into six HaeIII subtypes. All subtypes of the initial isolates from son 1 were present in the father's isolates, and all subtypes of the posttreatment isolates from son 1 were present in the mother's isolates but not in son 2's. Electron microscopic analysis of the biopsy specimens demonstrated extremely high levels of H. pylori colonization in the father's gastric mucosa. H. pylori adherence with a ruffle formation was also demonstrated. The findings suggest that son 1 was infected initially with the H. pylori strain of the father and son 2 was infected with the H. pylori strain of the mother and that after eradication therapy son 1 was reinfected with the H. pylori strain of the mother, who did not undergo eradication therapy.     

Characterization of feline Helicobacter pylori strains and associated gastritis in a colony of domestic cats.

Twenty-four young adult domestic cats from a commercial vendor were found to be infected with Helicobacter pylori. Histopathologic analyses, selected electron microscopy, and urease mapping were performed on mucosal samples collected from the cardias and fundi, bodies, and antra of these cats' stomachs. H. pylori organisms were abundant in all areas of the stomach on the basis of histologic evaluation and urease mapping. H. pylori infection was associated with a moderate to severe lymphofollicular gastritis in 21 of 24 cats (88%). The gastritis was most pronounced in the antral region and consisted mainly of multifocal lymphoplasmacytic follicular infiltrates in the deep mucosa. The severity of gastritis in the antrum corresponded to high numbers of H. pylori there on the basis of the use of the urease assay as an indicator of H. pylori colonization. Ten of 24 cats (42%) also had small to moderate numbers of eosinophils in the gastric mucosa. All 24 cats had gastric lymphoid follicles, with follicles being most prevalent in the antrum. Electron microscopy of gastric tissue revealed numerous H. pylori organisms, some of which were closely adhered to the mucosal epithelium. Human H. pylori gene-specific primers to ureA and ureB amplified products of similar sizes from H. pylori cat isolates. Digestion of the products with restriction enzymes resulted in fragments characteristic of the restriction fragment length polymorphism patterns of H. pylori isolates from humans.(ABSTRACT TRUNCATED AT 250 WORDS)     

Molecular epidemiology of a fast-food restaurant-associated outbreak of Escherichia coli O157:H7 in Washington State.

We studied the molecular epidemiology of the recent fast-food restaurant chain-associated Escherichia coli O157:H7 outbreak in Washington State. Genomic DNAs prepared from strains isolated from 433 patients were probed with radiolabelled Shiga-like toxin (SLT) I and SLT II genes and bacteriophage lambda DNA and were subsequently analyzed for their restriction fragment length polymorphism (RFLP) patterns. The SLT RFLP and lambda RFLP profiles of an E. coli O157:H7 strain isolated from the incriminated beef and prototype patient were compared with those of the patient isolates for determination of the concordance between patterns. Of the 377 patients with primary and secondary cases of infection epidemiologically linked to the outbreak, isolates from 367 (97.3%) of the patients displayed SLT RFLP and lambda RFLP profiles identical to those of the outbreak strains. Isolates from 10 of the 377 (2.6%) patients possessed SLT RFLP and lambda RFLP profiles different from those of the outbreak strains, and the patients from whom those isolates were obtained were subsequently characterized as having non-outbreak-related infections. The E. coli O157:H7 strains isolated from 31 of 44 (70.4%) patients who were epidemiologically excluded from the outbreak were linked to the outbreak by RFLP typing. Our results indicate that SLT RFLP and lambda RFLP analyses are stable and sensitive methods, and when they are used in conjunction with an epidemiological investigation they could result in an earlier recognition of outbreaks and their sources, hence prompting measures to prevent the continued transmission of E. coli O157:H7.     

Ribotyping patterns and emergence of metronidazole resistance in paired clinical samples of Helicobacter pylori.

Metronidazole-susceptible pretreatment isolates and metronidazole-resistant posttreatment isolates of Helicobacter pylori from 11 patients before and after unsuccessful triple therapy consisting of metronidazole, amoxicillin, and colloidal bismuth subcitrate were studied. Ribotyping (rRNA gene restriction pattern analysis) of the isolates demonstrated that all patients except one had identical digest patterns for pre- and posttreatment isolates.     

The IS6110 Restriction Fragment Length Polymorphism in Particular Multidrug-Resistant Mycobacterium tuberculosis Strains May Evolve Too Fast for Reliable Use in Outbreak Investigation

To study possible nosocomial transmission of multidrug-resistant (MDR) Mycobacterium tuberculosis, strain types and other information on 24, mostly human immunodeficiency virus-positive patients, were collected. Isolates from 11 patients had identical IS6110 restriction fragment length polymorphism (RFLP) patterns as well as spoligotype patterns and resistance profiles. Noticeably, nine other isolates from related cases also exhibited identical spoligotypes but slightly different RFLP patterns. These results indicate that for some MDR strains, the evolutionary clock of IS6110 RFLP may run too fast for reliable interpretation of strain typing results over a period of a few years.     

Mixed infections of Helicobacter pylori: tissue tropism and histological significance

Mixed infections with Helicobacter pylori facilitate interstrain gene transfer and the maintenance of genetic diversity for adaptation to the gastric environment, but whether mixed infections with histological significance and tissue tropism occur in the human stomach is still unclear. Helicobacter pylori was isolated from the antrum and the corpus of 30 dyspeptic patients. Four to eight colonies were randomly collected from each site. The genetic diversity of each isolate was evaluated by comparing random amplified polymorphic DNA banding patterns. The prevalence of mixed infections was 23.3% (7/30), and different dominant strains were isolated from the antrum and the corpus specimens. In the 23 patients infected with a single strain, the acute inflammation (AI) score, chronic inflammation (CI) score, atrophy (AT) score and lymphoid follicle (LF) score of the antrum were usually higher than those of the corpus (p ≤0.002). However, in the seven patients with mixed infections, the CI, H. pylori density (HPD), AT and LF scores of the antrum and the corpus were similar (p >0.05). Moreover, the patients with mixed infections had marginally higher CI and HPD scores than those with single-strain infection (p 0.062 and p 0.095, respectively) in the corpus and had a significantly higher rate of appearance of intestinal metaplasia (IM) in the antrum (p 0.005). These data show that H. pylori tissue tropism was found in the human stomach, and suggest that mixed infections could change the histological features in the antrum and in the corpus, and that they could be associated with the appearance of IM in the antrum.