Performance criteria of DNA fingerprinting methods for typing of Helicobacter pylori isolates: experimental results and meta-analysis

Recurrence Rate and Influencing Factors of Helicobacter Pylori Infection After Successful Eradication in Southern Coastal China

Purpose

Recurrence rate of Helicobacter pylori (H. pylori) infection after successful eradication have gained attention. This study was to assess the recurrence rate of H. pylori infection after successful eradication in the southern coastal provinces of China and to analyze its factors.

Patients and Methods

975 patients with upper gastrointestinal symptoms who were diagnosed with H. pylori infection using the 13C or 14C-urea breath test (UBT) underwent eradication treatment between August 2021 and December 2022. After eight to twelve weeks, repeat UBT was performed. Besides, 824 patients with successful eradication underwent a repeat UBT by completing questionnaires after a year. The 1-year recurrence rate was calculated, and the differences were analyzed based on baseline data, sociological characteristics, and lifestyle.

Results

A total of 734 patients completed the 1-year follow-up, out of which 26 (3.5%) patients experienced a recurrence of H. pylori infection. Exposure to other individuals infected with H. pylori (χ2=12.852, P<0.001), poor hygiene conditions at dining out places (χ2=6.839, P=0.009), frequent dining out (χ2=24.315, P<0.001), smoking (χ2=7.510, P=0.006), consumption of non-purified water (χ2=16.437, P<0.001), consumption of pickled foods (χ2=5.682, P=0.017), irregular meal patterns (χ2=16.877, P<0.001) and age (χ2=9.195, P=0.010) were significant factors for H. pylori infection recurrence. Exposure to other individuals infected with H. pylori, poor hygiene conditions at dining out places, consumption of non-purified water, frequent dining out and irregular meal patterns were independent risk factors (P=0.022, 0.016, 0.002, <0.001, <0.001; 95% CI 0.146-0.861, 0.121-0.806, 1.715-10.845, 0.085-0.521, 2.291-14.556).

Conclusion

The one-year recurrence rate of H. pylori infection post-eradication in the southern coastal provinces of China is 3.5%. Contacting with infected individuals, poor hygiene in dining places, consumption of non-purified water, frequent dining out, and irregular meal patterns were identified as significant independent factors influencing H. pylori recurrence.

Comparative Assessment of Different PCR-Based Typing Methods of Pseudomonas aeruginosa Isolates

Introduction

Pseudomonas aeruginosa is one of the important causes of nosocomial infections. Analyzing the diversity of these isolates is important to control the diseases caused by them. Studies of molecular epidemiology depend on the application of typing methods.

Purpose

This study aims to assess the performance of PCR- based typing techniques (RAPD, ribotyping, tDNA, and ERIC) in determining the genetic diversity of 44 P. aeruginosa urinary isolates.

Methods

Performance parameters were analyzed for each of the tested methods. The banding pattern was assessed by calculating polymorphism, genotypic gene diversity and the effective multiplex ratio. Moreover, strain diversity, typeability, and discriminatory power were used to measure the efficiency of typing methods. The congruence among typing methods was calculated by Rand’s and Wallace coefficients.

Results

P-640 among RAPD primers and Ribo-2 among ribotyping primers were more informative as they gave high strain diversity, the highest number of clusters, and highest discriminatory power (ISD=70.45%, 29 clusters at 70% cutoff, DI=0.97 and ISD=75%, 25 clusters at 70% cutoff DI=0.969, respectively). Comparison of typing methods showed that RAPD-PCR gave the highest mean percent polymorphism per assay (76.85%) followed by ERIC-PCR. ERIC-PCR outperformed in most marker parameters; highest mean number of alleles, number of monomorphic bands per assay unit, mean genotypic gene diversity, effective multiplex ratio, and assay efficiency index. Calculated congruence revealed that individual methods demonstrate moderate to poor predictive power. Interestingly, this power increased by combining data obtained from another method.

Conclusion

RAPD primer (P-640) had more discrimination power followed by ribo-2 and ERIC. The performance and predictive power of typing methods can be improved by combining data obtained from different methods as ERIC+OPA-02 and ERIC+P-640 combinations gave complete typeability and discrimination of isolates. ERIC, ERIC+OPA-02, and ERIC+P-640 combinations can provide finer discrimination and classification of P. aeruginosa strains than the other tested methods.

Heterogeneity of Helicobacter pylori Strains Isolated from Patients with Gastric Disorders in Guiyang, China

Purpose

Chronic Helicobacter pylori infection causes peptic ulcers in a subpopulation of individuals and is a risk factor for the development of gastric cancer. Multiple infections and heteroresistant H. pylori contribute to poor treatment efficacy. Here, we investigated the extent of genetic diversity among H. pylori strains within a given host and its influence on the results of antibiotic (metronidazole, levofloxacin, clarithromycin, amoxicillin, and tetracycline) susceptibility testing.

Materials and Methods

Gastric mucosa biopsy samples were obtained from patients with gastric disorders, including 48 H. pylori positive patients, who were never previously treated for H. pylori infection. Five potential H. pylori colonies isolated from each sample were subcultured for enrichment. Enriched H. pylori colonies were identified through Gram staining and assays for urease, oxidase, and catalase. For each H. pylori monoclonal colony, the antibiotic susceptibility was assessed, genomic DNA was sequenced, and the cytotoxin-associated gene A (cagA) genotype was verified. Co-infection with multiple H. pylori strains was determined using random amplified polymorphic DNA (RAPD)-polymerase chain reaction (PCR).

Results

Thirteen gastric mucosa biopsy samples were positive for H. pylori. Five monoclonal strains isolated from each of these 13 patients were identified as H. pylori. RAPD-PCR indicated that intra-patient monoclonal strains of H. pylori in 10 of the 13 samples exhibited heterogeneity. Among the 13 patients, intra-patient monoclonal strains isolated from 4 patients had identical cagA genotype, whereas intra-patient monoclonal strains isolated from the other 9 patients harbored more than one cagA genotype. The antibiotic susceptibility of five intra-patient monoclonal strains from seven patients was inconsistent.

Conclusion

The existence of heterogeneous H. pylori strains with resistance to different drugs and virulence were common within the gastric mucosa of an individual patient.

Where to Biopsy to Detect Helicobacter pylori and How Many Biopsies Are Needed to Detect Antibiotic Resistance in a Human Stomach

This study aims to determine the gastric distribution, density, and diversity of Helicobacter pylori infection. Subtotal resection of the stomachs of three H. pylori-infected and asymptomatic obese patients were collected after a sleeve gastrectomy. Distribution and density of H. pylori were determined using culture and RT-PCR on multiple gastric sites (88, 176, and 101 biopsies per patient). Diversity of H. pylori strains was studied using antibiotic susceptibility testing, random amplified polymorphism DNA (RAPD) typing and cagA gene detection on single-colony isolates (44, 96, and 49 isolates per patient). H. pylori was detected in nearly all analyzed sites (354/365 biopsies, 97%). Antral density was higher in one patient only. The three stomachs were almost exclusively infected by an antibiotic-susceptible strain. One clarithromycin-resistant isolate in one biopsy was detected in two stomachs (1/44 and 1/49 isolates), while in the third one, eight (8/96 isolates) metronidazole-resistant isolates were detected. DNA typing showed infection with cagA-negative strains for one patient, cagA-positive strains for a second patient and the third patient was infected with two different strains of distinct cagA genotypes. Infection with H. pylori is shown to spread to the whole surface of the stomach, but a possibility of minor sub-population of antibiotic-resistant clones, undetectable in routine practice.

Comparison of virulence gene profiles and genomic fingerprints of Vibrio cholerae O1 and non-O1/non-O139 isolates from diarrheal patients in southern Thailand

BACKGROUND

Vibrio cholerae is associated with severe watery diarrheal disease among people in many parts of the world, including the coastal provinces of Southern Thailand. There are relatively few studies focusing on the genetic characterization among V. cholerae isolates in this region. Therefore, this study aimed at exploring the presence of virulence genes and DNA fingerprints among V. cholerae O1 and non-O1/non-O139 isolates obtained from clinical samples in four southern coastal provinces during the period of 2001-2009 (n = 21).

RESULTS

All V. cholerae O1 isolates possessed ctxA, tcpA, zot, ace, hlyA, and vasH genes. However, only hlyA, vcsV2, and vasH genes were detected in the majority of the non-O1/non-O139 isolates. All O1 isolates showed indistinguishable PCR fingerprints by arbitrarily primed (AP)-PCR and enterobacterial repetitive intergenic consensus (ERIC)-PCR regardless of the geographical area and period of isolation. However, the multi-locus variable-number of tandem-repeat analysis (MLVA) could differentiate these O1 isolates (n = 11) into eight profiles. Isolates exhibiting an undistinguished MLVA profile also showed identical pulsed-field gel electrophoresis (PFGE). In addition, the O1 isolates were grouped into the same cluster by all methods used in this study.

CONCLUSIONS

This study demonstrated the presence of virulence genes and genetic diversity among different serogroups of V. cholerae isolates from clinical samples in southern Thailand. V. cholerae O1 isolated over a period of multiple years were genetically related, suggesting that they had a clonal origin, whereas non-O1/non-O139 isolates could have evolved independently.

CRISPR-like sequences in Helicobacter pylori and application in genotyping

Background

Many bacteria and archaea possess a defense system called clustered regularly interspaced short palindromic repeats (CRISPR) associated proteins (CRISPR-Cas system) against invaders such as phages or plasmids. This system has not been demonstrated in Helicobacter pylori. The numbers of spacer in CRISPR array differ among bacterial strains and can be used as a genetic marker for bacterial typing.

Results

A total of 36 H. pylori isolates were collected from patients in three hospitals located in the central (PBH) and southern (SKH) regions of Thailand. It is of interest that CRISPR-like sequences of this bacterium were detected in vlpC encoded for VacA-like protein C. Virulence genes were investigated and the most pathogenic genotype (cagA vacA s1m1) was detected in 17 out of 29 (58.6%) isolates from PBH and 5 out of 7 (71.4%) from SKH. vapD gene was identified in each one isolate from PBH and SKH. CRISPR-like sequences and virulence genes of 20 isolates of H. pylori obtained in this study were analyzed and CRISPR-virulence typing was constructed and compared to profiles obtained by the random amplification of polymorphic DNA (RAPD) technique. The discriminatory power (DI) of CRISPR-virulence typing was not different from RAPD typing.

Conclusion

CRISPR-virulence typing in H. pylori is easy and reliable for epidemiology and can be used for inter-laboratory interpretation.

Electronic supplementary material

The online version of this article (10.1186/s13099-017-0215-8) contains supplementary material, which is available to authorized users.

Application of the Random Amplified Polymorphic DNA (RAPD) Fingerprinting to Analyze Genetic Variation in Community Associated-Methicillin Resistant Staphylococcus Aureus (CA-MRSA) Isolates in Iran

The aim of this study was to apply RAPD technique to analyze the genetic variability among the Iranian CA-MRSA isolates.

The RAPD amplification was implemented on 25 strains isolated from the anterior nares of 410 healthy children using four randomly selected oligonucleotide primers from the stocks available in our laboratory, including the primers 1254, GE6, OLP6 and OLP13 from our stock. The amplified PCR products were detected on a 1.5% agarose gel and subjected to further analysis to establish the band profiles and genetic relationships using the Gel Compar® program.

The Iranian CA-MRSA isolates produced distinct RAPD patterns which varied based on the primer used, however, the primer 1254 revealed highly polymorphic patterns consisting 5 discernable RAPD types (RT), “RT1” (12, 48%), “RT2” (8, 32%), “RT3” (3, 12%), and “RT4 and RT5”, (a single RAPD type each, 4%). Phylogenetic analysis based on RAPD profiles divided most of the CA-MRSA isolates into 2 distinct but related RAPD clusters, a small group and two single unrelated RAPD types.

This study shows that the simple and cost-effective but rather difficult to optimize RAPD fingerprinting could be used to evaluate genetic and epidemiological relationships of CA-MRSA isolates on condition that the patterns are obtained from carefully optimized laboratory tests.

Molecular Identification of Clinical Isolates of Mycobacterium fortuitum by Random Amplified Polymorphic DNA (RAPD) Polymerase Chain Reaction and ERIC PCR

BACKGROUNDS

Non tuberculous mycobacteria (NTM) are of importance now-a-days due to their increasing virulence outbreaks and emerging antibiotic resistance. Since the most common NTM in Iran is reportedly Mycobacterium fortuitum, the present study was designed with the aim of molecular identification of clinical isolates of M. foruitum to analyse their heterogeneity.

MATERIALS AND METHODS

A total of 81 isolates of NTM isolated from various samples were collected. The clinical isolates were assigned to species M. fortuitum by using conventional and molecular methods. The DNA banding patterns of ERIC- PCR and RAPD- PCR were analysed by using Bionumeric 7.5 software.

RESULTS

Out of 81 tested NTM, 36 strains of M. fortuitum were identified. 33 isolates were selected for molecular typing in this study. Based on RAPD and ERIC analysis, M. fortuitum isolates were divided into 3 and 6 clusters, respectively. Most of the isolates were distributed into types of II RAPD (20 members/ 60.6 %) and V (14 members/ 42.4% with sub cluster I & II) of ERIC. In RAPD analysis, the major fragments were 300 bp, followed by fragment 1000. In ERIC analysis, the major fragments were 280 bp followed by fragment 1200 bp.

CONCLUSION

In conclusion, though the results from this study represented higher discriminatory power of ERIC, however the combination of RAPD and ERIC analysis were able to sufficiently discriminate the genotypic diversity, infection control, and gain useful epidemiological information regarding M. fortuitum isolates.

Microevolution of Virulence-Related Genes in Helicobacter pylori Familial Infection

Helicobacter pylori, a bacterial pathogen that can infect human stomach causing gastritis, ulcers and cancer, is known to have a high degree of genome/epigenome diversity as the result of mutation and recombination. The bacteria often infect in childhood and persist for the life of the host. One of the reasons of the rapid evolution of H. pylori is that it changes its genome drastically for adaptation to a new host. To investigate microevolution and adaptation of the H. pylori genome, we undertook whole genome sequencing of the same or very similar sequence type in multi-locus sequence typing (MLST) with seven genes in members of the same family consisting of parents and children in Japan. Detection of nucleotide substitutions revealed likely transmission pathways involving children. Nonsynonymous (amino acid changing) mutations were found in virulence-related genes (cag genes, vacA, hcpDX, tnfα, ggt, htrA and the collagenase gene), outer membrane protein (OMP) genes and other cell surface-related protein genes, signal transduction genes and restriction-modification genes. We reconstructed various pathways by which H. pylori can adapt to a new human host, and our results raised the possibility that the mutational changes in virulence-related genes have a role in adaptation to a child host. Changes in restriction-modification genes might remodel the methylome and transcriptome to help adaptation. This study has provided insights into H. pylori transmission and virulence and has implications for basic research as well as clinical practice.

The frequency of Helicobacter pylori in dental plaque is possibly underestimated

OBJECTIVE

The commonest bacteria, causing infection across the world is Helicobacter pylori, which colonizes the human stomach. This bacteria has also been detected in some extra-gastric ecological niches such as the oral cavity and water. However, the results of H. pylori detection in extra-gastric ecological niche are controversial. The improvement of the sensitivity and the specificity of the detection methods appear to be some of the main bottleneck issues in providing compelling evidence. The aim of this study was to detect the presence of this organism in dental plaque samples using an analytically sensitive and specific Polymerase Chain Reaction (PCR) as well as a new nucleic acid detection method termed the Loop-mediated Isothermal Amplification (LAMP).

DESIGN

In a descriptive cross-sectional study 45 participants enrolled and dental plaque samples were collected from at least two teeth surfaces (one anterior and one posterior tooth) using a sterile periodontal curette. The DNA content was extracted from the samples and the presence of H. pylori was determined by PCR and LAMP reactions.

RESULTS

The frequency of detection of H. pylori in the dental plaque samples were 44% (20/45), 66.67% (30/45) and 77.78% (35/45) using PCR, LAMP and positivity for both tests, respectively.

CONCLUSION

The high frequency of H. pylori was detected in the dental plaque samples of the participants, which concurs with the high prevalence of this bacteria in the population. This is one of the highest reported rates around the world. The results reveal that dental plaque can be one of the main causes of re-infection and also be the cause of oral-oral transmission.

Clinical Application of the DiversiLab Microbial Typing System Using Repetitive Sequence-Based PCR for Characterization of Helicobacter pylori in Japan

We evaluated the DiversiLab (DL) system with universal primers, a semiautomated repetitive extragenic palindromic sequence-based polymerase chain reaction (PCR) (rep-PCR) system, for the characterization of Helicobacter pylori in Japan. All 135 isolates from Japanese patients with gastric cancer (GC, n = 55) or non-GC (n = 80) were used and subjected to the drug susceptibility examinations (amoxicillin, AMPC; metronidazole, MNZ; and clarithromycin, CAM) by E-test. There were 28 MNZ-resistant (20.7%), 35 CAM-resistant (25.9%), and 16 MNZ/CAM-resistant (11.9%) isolates. DL rep-PCR fingerprinting analysis at the level of 95% similarity revealed five major groups (A-E) and the other including 45 isolates. The occupation rates of GC-derived isolates in groups B (54.2%) and E (58.8%) were higher than in the other groups: A (26.7%), C (28.6%), D (30.0%), and the other (40.0%). Relative higher occupation rates of drug resistants, such as MNZ-, CAM- and double MNZ/CAM-resistant isolates, were observed in groups B (45.8%), C (42.6%), and D (40%). Five of eight GC-derived isolates with MNZ/CAM resistance were significantly assigned to group B (P = 0.0312, χ(2) -test). These results suggest that the isolates classified in group B have a potential to contribute to the development of severe gastric disorders. The DL system, rapid and high sensitive technology, would be widely available in clinical laboratory for pathological and epidemiological analyses even in H. pylori.

Multiple infection and microdiversity among Helicobacter pylori isolates in a single host in India

Helicobacter pylori is one of the most diverse bacterial species that chronically infects more than 70% of Indian population. Interestingly, data showing microdiversity of the H. pylori strains within a particular gastric niche remained scarce. To understand the extent of genetic diversity among H. pylori strains within a given host, 30 patients with gastro-duodenal problems were subjected to endoscopy and from each patient 10 single colonies were isolated. Characterization of each of these 10 single colonies by DNA fingerprinting as well as genotyping of several important genetic markers viz. cagA, vacA, iceA, vapD, cag PAI empty site, IS605, RFLP and two other genetic segments within cag PAI revealed that all of the 30 patients were infected with more than one strain and sometimes strains with 5 to 6 types of genetic variants. Analyses of certain genetic loci showed the microdiversity among the colonies from single patient, which may be due to the recombination events during long-term carriage of the pathogen. These results suggest that most of the patients have acquired H. pylori due to repeated exposure to this pathogen with different genetic make-up, which may increase the possibility of super infections. Genetic exchanges between these unrelated H. pylori strains may support certain H. pylori variant to grow better in a given host than the parental strain and thereby increasing the possibility for the severity of the infection.

Molecular epidemiologic analysis and antimicrobial resistance of Helicobacter cinaedi isolated from seven hospitals in Japan

Helicobacter cinaedi colonizes the colons of human and animals and can cause colitis, cellulitis, and sepsis in humans, with infections in immunocompromised patients being increasingly recognized. However, methods for analyzing the molecular epidemiology of H. cinaedi are not yet established. A genotyping method involving multilocus sequence typing (MLST) was developed and used to analyze 50 H. cinaedi isolates from Japanese hospitals in addition to 6 reference strains. Pulsed-field gel electrophoresis (PFGE) results were also compared with the MLST results. Based on the genomic information from strain CCUG18818, 21 housekeeping genes were selected as candidates for MLST and were observed to have high homology (96.5 to 100%) between isolates. Following a comparison of the 21 housekeeping genes from 8 H. cinaedi isolates, 7 genes were chosen for MLST, revealing 14 sequence types (STs). The isolates from 3 hospitals belonged to the same STs, but the isolates from the other 4 hospitals belonged to different STs. Isolates belonging to ST6 were analyzed by PFGE and showed similar, but not identical, patterns between isolates. Isolates belonging to ST9, ST10, and ST11, which belonged to the same clonal complex, had the same pattern. All isolates were found to contain mutations in GyrA and the 23S rRNA gene that confer ciprofloxacin and clarithromycin resistance, respectively, in H. cinaedi. These results raise concerns about the increase in H. cinaedi isolates resistant to clarithromycin and ciprofloxacin in Japan.

Phenotypic and genotypic methods for typing Campylobacter jejuni and Campylobacter coli in poultry

Human campylobacteriosis, an infection caused by the bacterium Campylobacter, is a major issue in the United States food system, especially for poultry products. According to the Center for Disease Control, campylobacterosis is estimated to affect over 2.4 million people annually. Campylobacter jejuni and Campylobacter coli are 2 species responsible for the majority of campylobacterosis infections. Phenotypic and genotypic typing methods are often used to discriminate between bacteria at the species and subspecies level and are often used to identify pathogenic organisms, such as C. jejuni and C. coli. This review describes the design as well as advantages and disadvantages for 3 current phenotypic techniques (biotyping, serotyping, and multilocus enzyme electrophoresis) and 6 genotypic techniques (multilocus sequence typing, PCR, pulse-field gel electrophoresis, ribotyping, flagellin typing, and amplified fragment length polymorphisms) for typing pathogenic Campylobacter spp.

Intrafamilial Genotyping of Helicobacter pylori from Faecal DNA

Helicobacter pylori infection, often acquired in early childhood, is a global cause of undernutrition, gastritis, peptic ulcer disease and gastric carcinoma. This study tested the feasibility of using H. pylori shed in the faeces as a source of DNA for non-invasive epidemiological studies. H. pylori DNA was chemically recovered and isolated using a specific biotinylated oligonucleotide probe with magnetic capture from 28 H. pylori positive faecal samples obtained from children attending hospital for the investigation of suspected H. pylori infection, together with close family members. Random amplification of polymorphic DNA (RAPD) was subsequently used to discriminate each isolate. 93% of stool samples selected were typeable. Parent, child and sibling samples were compared and similarities determined. Phylogenetic analysis showed that H. pylori DNA obtained from the faeces can be used to genotype individual strains, offering a means of studying intrafamilial transfer of this microorganism.

Prevalence of Helicobacter pullorum in conventional, organic, and free-range broilers and typing of isolates

Helicobacter pullorum represents a potential food-borne pathogen, and avian species appear to be a relevant reservoir of this organism. In this study, the prevalence of H. pullorum was investigated at 30 conventional farms where 169 ceca from 34 flocks were tested, at eight organic farms where 39 ceca from eight flocks were tested, and at seven free-range farms where 40 ceca from eight flocks were tested. All of the ceca were obtained from healthy broiler chickens. Moreover, amplified fragment length polymorphism, pulsed-field gel electrophoresis, and automated ribotyping were employed to estimate the levels of genetic variability of H. pullorum broiler isolates within and between flocks. Overall, Gram-negative, slender, curved rods, identified as H. pullorum by PCR, were isolated at 93.3% of the farms tested. The percentage of positive free-range farms (54.2%) was significantly lower than that of conventional (100%) or organic (100%) farms (P < 0.001). The level of within-flock genetic variability, calculated as the number of flocks colonized by isolates genetically different by all of the typing methods, was 34.9%. Isolates showing identical profiles by each typing method were observed in 11.6% of the flocks, but they were never detected between flocks. However, groups of isolates clustered together with an overall similarity level of ≥85%. Our results suggest that even though a high level of genetic variability is attributable to H. pullorum broiler isolates, their hierarchical genotyping produces data useful for epidemiological investigations.

Prevalence of Helicobacter pylori vacA, cagA and iceA genotypes in South African patients with upper gastrointestinal diseases

Clinical response to Helicobacter pylori infection may be determined by specific virulence-associated genotypes which varies geographically. The aim of this study was to investigate the diversity of putative virulence markers of H. pylori; cagA, vacA and iceA in the Eastern Cape Province of South Africa. One hundred H. pylori strains obtained from dyspeptic patients were used. Gastric biopsies were obtained from 254 dyspeptic patients. H. pylori was cultured and strains were studied. Bacterial genotypes cagA, vacA (s and m subtypes) and iceA were analysed by PCR using specific primers. CagA was identified in 90% of the strains investigated. Fifty-eight of the 100 strains had the vacA signal sequence genotype s1 and 26 had subtype s2. Combined vacA s1/s2 was detected in 16 of the strains. VacA middle region analysis showed that 8 (8%) strains were m1 while 50 were m2. Combined vacA m1/m2 was detected in 36 of the strains. s1m2 (20%) and s2m2 (20%) genotypes were the most common allelic combinations of the vacA gene among the strains. Multiple vacA genotypes were detected in this study. Twenty-six percent of the strains identified had both iceA1 and iceA2. All our strains tested positive for the ureC (glmM) gene. This study reveals a high prevalence of vacA, cagA and iceA2.

PCR melting profile (PCR MP)--a new tool for differentiation of Candida albicans strains

Background

We have previously reported the use of PCR Melting Profile (PCR MP) technique based on using low denaturation temperatures during ligation mediated PCR (LM PCR) for bacterial strain differentiation. The aim of the current study was to evaluate this method for intra-species differentiation of Candida albicans strains.

Methods

In total 123 Candida albicans strains (including 7 reference, 11 clinical unrelated, and 105 isolates from patients of two hospitals in Poland) were examined using three genotyping methods: PCR MP, macrorestriction analysis of the chromosomal DNA by pulsed-field gel electrophoresis (REA-PFGE) and RAPD techniques.

Results

The genotyping results of the PCR MP were compared with results from REA-PFGE and RAPD techniques giving 27, 26 and 25 unique types, respectively. The results showed that the PCR MP technique has at least the same discriminatory power as REA-PFGE and RAPD.

Conclusion

Data presented here show for the first time the evaluation of PCR MP technique for candidial strains differentiation and we propose that this can be used as a relatively simple and cheap technique for epidemiological studies in short period of time in hospital.

Comparative genomics of Helicobacter pylori

Genomic sequences have been determined for a number of strains of Helicobacter pylori (H pylori) and related bacteria. With the development of microarray analysis and the wide use of subtractive hybridization techniques, comparative studies have been carried out with respect to the interstrain differences between H pylori and inter-species differences in the genome of related bacteria. It was found that the core genome of H pylori constitutes 1111 genes that are determinants of the species properties. A great pool of auxillary genes are mainly from the categories of cag pathogenicity islands, outer membrane proteins, restriction-modification system and hypothetical proteins of unknown function. Persistence of H pylori in the human stomach leads to the diversification of the genome. Comparative genomics suggest that a host jump has occurs from humans to felines. Candidate genes specific for the development of the gastric diseases were identified. With the aid of proteomics, population genetics and other molecular methods, future comparative genomic studies would dramatically promote our understanding of the evolution, pathogenesis and microbiology of H pylori.

Restriction fragment length polymorphism of urease C and urease B genes of Helicobacter pylori strains isolated from Brazilian patients with peptic ulcer and chronic gastritis

The aim of the present work is to identify the presence of Helicobacter pylori bacterium in samples of gastric mucosa fragments, obtained by gastric biopsy, from Brazilian patients with peptic ulcer and chronic gastritis and also to determine differences among the prevalent strains in these two diseases by urease C and urease B genes amplification utilizing nested polymerase chain reaction (PCR) and PCR. We encountered 17 genotyping patterns for urease C and 7 for urease B and, although no significant differences were found among the patterns encountered for both diseases, we found predominant groups for each disease. Typing methods of the products obtained by nested PCR and PCR show a functional scheme and are of great importance for epidemiologic studies and H. pylori strain characterization, in addition to allowing correlation among the several strains and their role in the diseases caused by this microorganism.

Capillary electropherograms for restriction fragment length polymorphism of Helicobacter pylori

Rapid identification of Helicobacter pylori strains is of importance for diagnosis and then treatment of duodenal and gastric ulcers. We developed a CE approach for the analysis of RFLP of the PCR products of urease (UreAB) gene and flagellin A (FlaA) gene fragments. Prior to CE analysis, the 2.4-kbp UreAB and 1.5-kbp FlaA PCR products were digested with the restriction enzymes HaeIII and HhaI, respectively. The DNA fragments were then separated by CE in conjunction with laser-induced fluorescence detection using poly(ethylene oxide) in the presence of electroosmotic flow. The DNA fragments range in sizes 259-1831 bp and 12-827 bp for UreAB and FlaA restriction fragments, respectively. Of 27 samples, the CE approach provided five and ten different RFLP patterns of the HaeIII and HhaI digests. The RFLP of PCR products of the two genes allow great sensitivity of identification of H. pylori strains. When compared with slab gel electrophoresis, the present CE approach provides advantages of rapidity (within 6 min per run), simplicity, and automation. The preliminary results have shown great practicality of the CE approach for screening H. pylori strains.

A novel noninvasive genotyping method of Helicobacter pylori using stool specimens

BACKGROUND & AIMS

The source(s) of the infection and the route(s) of transmission of Helicobacter pylori have not yet been clarified. This is to introduce a noninvasive protocol allowing molecular typing of H pylori using stool specimens.

METHODS

The genotyping method is based on 2 H pylori-specific biprobe real-time polymerase chain reaction assays using fragments of the glmM and the recA genes as target sequences. Discrimination between strains results from differences in the melting temperature during melting curve analysis. In case of identical melting temperatures in both assays, sequence analysis of the glmM amplicon was performed to confirm strain identity. The method was validated using gastric biopsy specimens and stool specimens of 97 unrelated individuals suffering from abdominal pain and stool specimens of members of 10 families in Austria (infected index child and family members) and 8 African households.

RESULTS

Of the 97 patients, 27 were infected as shown by culture, histology, and rapid urease test. The sensitivity of each of the assays was 100% in gastric biopsy specimens and 92.2% in stool specimens; the specificity was 100%. The discriminatory capacity of the method was 100%. Clonal identities were found in 9 of 10 (90%) European and 7 of 8 (87.5%) African households. In 2 African households, 2 different clonal lineages each were found.

CONCLUSIONS

The genotyping protocol introduced allows for both accurate detection and discrimination of H pylori strains in stool samples. Large-scale studies using this protocol may contribute to the clarification of the transmission pathways of infection with H pylori.

Rapid determination of Escherichia coli O157:H7 lineage types and molecular subtypes by using comparative genomic fingerprinting

In this study, variably absent or present (VAP) regions discovered through comparative genomics experiments were targeted for the development of a rapid, PCR-based method to subtype and fingerprint Escherichia coli O157:H7. Forty-four VAP loci were analyzed for discriminatory power among 79 E. coli O157:H7 strains of 13 phage types (PT). Twenty-three loci were found to maximize resolution among strains, generating 54 separate fingerprints, each of which contained strains of unique PT. Strains from the three previously identified major E. coli O157:H7 lineages, LSPA6-LI, LSPA6-LI/II, and LSPA6-LII, formed distinct branches on a dendrogram obtained by hierarchical clustering of comparative genomic fingerprinting (CGF) data. By contrast, pulsed-field gel electrophoresis (PFGE) typing generated 52 XbaI digestion profiles that were not unique to PT and did not cluster according to O157:H7 lineage. Our analysis identified a subpopulation comprised of 25 strains from a closed herd of cattle, all of which were of PT87 and formed a cluster distinct from all other E. coli O157:H7 strains examined. CGF found five related but unique fingerprints among the highly clonal herd strains, with two dominant subtypes characterized by a shift from the presence of locus fprn33 to its absence. CGF had equal resolution to PFGE typing but with greater specificity, generating fingerprints that were unique among phenotypically related E. coli O157:H7 lineages and PT. As a comparative genomics typing method that is amenable for use in high-throughput platforms, CGF may be a valuable tool in outbreak investigations and strain characterization.

J. Análise das impressões digitais de DNA e de fatores de virulência de linhagens de Helicobacter pylori

RACIONAL: Helicobacter pylori é hoje aceito como o principal agente etiológico de gastrite em seres humanos e fator de risco para úlcera péptica e câncer gástrico. A evolução da infecção está relacionada a diversos fatores, inclusive bacterianos, como presença do gene cagA e o genótipo vacA s1m1, associados ao desenvolvimento de úlcera e adenocarcinoma gástrico. A técnica de RAPD ("random amplified polimorphic") tem sido amplamente utilizada para obtenção de impressões digitais de DNA para examinar a similaridade entre linhagens. OBJETIVOS: Avaliar a presença de cagA e alelos do vacA em amostras de H. pylori e associar os achados com a doença apresentada e também investigar possível clonicidade entre os fatores de virulência e as doenças com a impressão digital de DNA gerada pelo RAPD-PCR. MÉTODOS: Foram incluídas 112 amostras provenientes de pacientes com diferentes laudos endoscópicos: gastrite (n = 41), esofagite de refluxo (n = 14), úlcera gástrica (n = 19) e úlcera duodenal (n = 38). A análise dos fatores de virulência da bactéria foi feita por PCR e as impressões digitais de DNA foram estabelecidas pelo método de RAPD-PCR. RESULTADOS: Os resultados obtidos indicam que houve uma associação significativa entre úlcera duodenal e o mosaico vacA s1m1. Analisando-se os padrões de bandas geradas pelo RAPD-PCR, sete diferentes dendogramas foram construídos e não foi possível detectar associação significativa entre os agrupamentos, sugerindo que as amostras não possuem perfil clonal. CONCLUSÃO: Os resultados reforçam a importância do gene vacA como um marcador de virulência do H. pylori. O RAPD da impressão digital de DNA realizado foi incapaz de associar o padrão de bandas com as enfermidades e os genótipos de vacA e cagA.

The use of killer sensitivity patterns for biotyping yeast strains: the state of the art, potentialities and limitations

In recent years molecular techniques have been the most useful tools for the unequivocal identification of undetermined strains at the species level. In many instances, however, a further discrimination at the strain level (biotyping) is required, such as during epidemiological investigations, in which the distribution of pathogenic microorganisms is studied, and for patent protection purposes. Although molecular methods are routinely used also for yeast biotyping, several nonmolecular techniques have been proposed. One of these, the determination of the killer sensitivity pattern (KSP) towards a panel of selected killer toxins has proven to be a good auxiliary method. Despite the plethora of studies published, the potential and limitations of the determination of KSPs have never been critically evaluated. In this review the use of this nonmolecular technique as a biotyping tool is discussed and compared with some currently used DNA-based procedures. In addition, methodological, mechanistic and ecological implications are evaluated.

Helicobacter pylori detection and antimicrobial susceptibility testing

The discovery of Helicobacter pylori in 1982 was the starting point of a revolution concerning the concepts and management of gastroduodenal diseases. It is now well accepted that the most common stomach disease, peptic ulcer disease, is an infectious disease, and all consensus conferences agree that the causative agent, H. pylori, must be treated with antibiotics. Furthermore, the concept emerged that this bacterium could be the trigger of various malignant diseases of the stomach, and it is now a model for chronic bacterial infections causing cancer. Most of the many different techniques involved in diagnosis of H. pylori infection are performed in clinical microbiology laboratories. The aim of this article is to review the current status of these methods and their application, highlighting the important progress which has been made in the past decade. Both invasive and noninvasive techniques will be reviewed.

Clarithromycin resistance in Helicobacter pylori strains isolated from French children: prevalence of the different mutations and coexistence of clones harboring two different mutations in the same biopsy

BACKGROUND

The aim of our study was to assess the different mutations involved in clarithromycin-resistant Helicobacter pylori strains isolated from French children and their temporal trends.

METHODS

The point mutations of H. pylori were detected by PCR followed by RFLP technique in 50 clarithromycin-resistant strains collected between 1993 and 2004 in France.

RESULTS

Clarithromycin resistance was observed in 23% (50/217) of H. pylori isolates. Two mutations A2143G and A2142G in the 23S rRNA genes of H. pylori were detected. The former was found in 45/50 (90%) of isolates. The rate of resistance increased with time from 18.6% in the period 1993-1996 to 41.6% in 2001-2004. No significant difference was observed in the distribution of mutations during the same periods. No correlation was found between any mutation and age, sex, and ethnic origin of children. Furthermore, no significant differences in minimal inhibitory concentrations level were observed according to the different point mutations. In all cases, only one point mutation was present, except in two cases where two different mutations were found in two different clones from the same biopsy.

CONCLUSION

The mutation A2143G is predominant in clarithromycin-resistant H. pylori strains isolated from children in France. We report for the first time the presence of two clarithromycin-resistant clones harboring two different mutations of the 23S rRNA genes present in the same biopsy specimen and genotypically identical as demonstrated by RAPD fingerprinting.

Genetic diversity of the HpyC1I restriction modification system in Helicobacter pylori

Helicobacter pylori is unique because of the unusually high number and diversity of its restriction modification (R-M) systems. HpyC1I R-M was recently characterized and contains an endonuclease which is an isoschizomer of the endonuclease BccI. This R-M is involved in adherence to gastric epithelial cells, a crucial step in bacterial pathogenesis. This observation illustrates the fact that R-M systems have other putative biological functions in addition to protecting the bacterial genome from external DNA. The genomic diversity of HpyC1I R-M was evaluated more precisely on a large collection of H. pylori strains by PCR, susceptibility to BccI digestion and sequencing. The results obtained support the mechanism of gain and loss of this R-M system in the H. pylori genome, and suggest that it is an ancestral system which gradually disappears during H. pylori evolution, following successive steps: (1) inactivation of the endonuclease gene, followed or accompanied by: (2) inactivation of the methyltransferase genes, and then: (3) definitive loss, leaving only short endonuclease remnant sequences.

Campylobacter spp. subtype analysis using gel-based repetitive extragenic palindromic-PCR discriminates in parallel fashion to flaA short variable region DNA sequence analysis

AIMS

The repetitive extragenic palindromic-PCR (rep-PCR) subtyping technique, which targets repetitive extragenic DNA sequences in a PCR, was optimized for Campylobacter spp. These data were then used for comparison with the established genotyping method of flaA short variable region (SVR) DNA sequence analysis as a tool for molecular epidemiology.

METHODS AND RESULTS

Uprime Dt, Uprime B1 or Uprime RI primers were utilized to generate gel-based fingerprints from a set of 50 Campylobacter spp. isolates recovered from a variety of epidemiological backgrounds and sources. Analysis and phenogram tree construction, using the unweighted pair group method with arithmetic mean, of the generated fingerprints demonstrated that the Uprime Dt primers were effective in providing reproducible patterns (100% typability, 99% reproducibility) and at placing isolates into epidemiological relevant groups. Genetic stability of the rep-PCR Uprime Dt patterns under nonselective, short-term transfer conditions revealed a Pearson's correlation approaching 99%. These same 50 Campylobacter spp. isolates were analysed by flaA SVR DNA sequence analysis to obtain phylogenetic relationships.

CONCLUSIONS

The Uprime Dt primer-generated rep-PCR phenogram was compared with a phenogram generated from flaA SVR DNA sequence analysis of the same isolates. Comparison of the two sets of resulting genomic relationships revealed that both methods segregated isolates into similar groups.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results indicate that rep-PCR analysis performed using the Mo Bio Ultra Clean Microbial Genomic DNA Isolation Kit for DNA isolation and the Uprime DT primer set for amplification is a useful and effective tool for accurate differentiation of Campylobacter spp. for subtyping and epidemiological analyses.

Helicobacter cinaedi cellulitis and bacteremia in immunocompetent hosts after orthopedic surgery

At various times after orthopedic operations (more than a few weeks, with an average of 29.9 days), 11 patients had a sudden onset of high temperature (average 38.9 degrees C) and local cellulitis at different sites on the operated sides. The wounds had completely healed, without complicated infections, when the cellulitis occurred. The clinical picture of cellulitis in all patients was atypical: diffuse salmon-pink skin color, local heat, swelling, spontaneous pain, and tenderness but no eruptions. No patient had any underlying immunocompromising conditions or had been given immunosuppressive agents. Gram-negative spiral bacteria were isolated from blood cultures and were identified as Helicobacter cinaedi on the basis of 16S rRNA gene sequencing and DNA-DNA hybridization using standard strains. By means of phylogenetic analysis, we divided these clinical isolates into two clones. The H. cinaedi strain isolated via fecal cultures from two patients without intestinal symptoms was the same clone as the blood isolate. All isolates were quite susceptible to various antibiotics, and clinical and inflammatory symptoms of bacteremia and cellulitis improved after treatment with penicillins and cephalosporins. A relatively high incidence of recurrence of the same disease was observed, however. Almost all patients responded immunologically to the infection, as evidenced by the production of serum antibody against H. cinaedi. We thus suggest that H. cinaedi should not be regarded as simply an opportunistic pathogen but that it may be a pathogen in immunocompetent hosts and may cause infections together with bacteremia and cellulitis.

Use of RAPD and killer toxin sensitivity in Saccharomyces cerevisiae strain typing

AIMS

Two different strain characterization techniques, random amplified polymorphic DNA (RAPD) and killer toxin sensitivity (KTS), were compared to assess their typing performance using a set of 30 certified Saccharomyces cerevisiae strains.

METHODS AND RESULTS

A sequential random resampling procedure was employed to subdivide the 32 descriptors in eight sets, in order to compare the differential performances of the two techniques with diverse number of characters. Results showed that RAPD performs better than killer, although the complete differentiation of the strains under study could be obtained only by combining profiles from the two techniques.

CONCLUSIONS

The combination of different typing techniques was useful when discriminating similar organisms. In such cases, the introduction of a second typing technique can be more advantageous than increasing the number of characters obtained with a single method.

SIGNIFICANCE AND IMPACT OF THE STUDY

The distribution of among-strains pairwise distances and the relative performance of the two techniques has implications for the study of biodiversity, taxonomy and microbial ecology.

Antimicrobial peptides are among the antagonistic metabolites produced by Bifidobacterium against Helicobacter pylori

Sixty acid-resistant Bifidobacterium isolates were recovered from human faeces and identified by genus-specific PCR and RAPD-PCR. Helicobacter pylori strains were isolated from gastric biopsies and identified by species-specific PCR. Twenty-four of the 60 Bifidobacterium isolates were considered to be different strains by RAPD-PCR. Six of the twenty-four different strains were shown to inhibit H. pylori. These antagonistic effects were related to heat-stable proteinaceous compounds, resistant to heating at 100 degrees C for 10 min, but sensitive to proteases. H. pylori stains showed variable resistance to therapeutic antibiotics (metronidazole and clarithromycin), while all the selected bifidobacteria showed intrinsic resistance to metronidazole. These potentially probiotic bifidobacteria were able to inhibit the growth of both antibiotic sensitive and resistant H. pylori strains. Thus, the synthesis of antimicrobial peptides could be one of the mechanisms of bifidobacteria to combat H. pylori infections.

Molecular characterization of hand flora and environmental isolates in a community setting

We analyzed 69 bacterial isolates, comprising seven species of gram-negative bacterial rods and three species of coagulase-negative staphylococci, recovered from both the hands of caretakers and their environment in households sampled in upper Manhattan. Repetitive sequence-based PCR and dendrogram analysis were used to determine strain similarity. Greater than 25% of individual species of Acinetobacter, Enterobacter, and coagulase-negative staphylococci recovered from the hands and immediate environment within each household shared the same genotype. This study is the first to demonstrate the frequency of bacteria shared within community households. These strains may serve as potential reservoirs for either community- or hospital-acquired infections.

Heterogeneity of cag genotypes and clinical outcome of Helicobacter pylori infection

Helicobacter pylori infecting strains may include colony subtypes with different cytotoxin-associated gene (cag) genotypes. We sought to determine whether the cag heterogeneity of infecting strains is related to the clinical outcome of infection. Gastric biopsies for culture and histologic study were taken from 19 patients infected with cagA-positive strains (6 with duodenal ulcer, 8 with atrophic gastritis, and 5 with nonatrophic gastritis). For each biopsy, DNA was extracted from 10 single colonies and from a sweep of colonies. Polymerase chain reaction (PCR) for cagA and cagE (both located in the right half of cag) and virB11 (located in the left half of cag) was performed. Random amplified polymorphic DNA PCR (RAPD-PCR) and sequencing of glmM PCR product were performed to verify strain identity of colonies with different cag genotypes. In all patients, PCR from sweeps were positive for cagA, showing that all specimens contained cagA-positive H. pylori subtypes. In 11 patients, PCR products from all colonies were positive for cagA, cagE, and virB11, but in 8 patients, PCR products from varying numbers of colonies were negative for 1 or more cag genes. RAPD-PCR and sequencing of glmM PCR product confirmed the strain identities of colonies with different cag genotypes. We detected cag deletions in 6 of 8, 2 of 5, and 0 of 6 patients with atrophic gastritis, nonatrophic gastritis, and duodenal ulcer, respectively (P = .02). In conclusion, changes in cag genotype in single colony isolates from subjects infected with cagA-positive H. pylori strains are more common in atrophic than in nonatrophic gastritis or duodenal ulcer. These findings are consistent with host-induced (acid secretion?) adaptive changes in cag genotype during infection.

Antimicrobial resistance and characterization of Helicobacter pylori strains isolated from Mexican adults with clinical outcome

Eradication of Helicobacter pylori infection in Mexico is of great importance due to the elevated seroprevalence, however, there is yet very little information about antibiotic resistance rates in H. pylori isolates in our country. We analyzed susceptibility to three antimicrobials used in therapy of 49 H. pylori strains isolated from patients with active chronic gastritis, active chronic gastritis with lymphoid follicles, intestinal metaplasia and gastric cancer. All isolated strains were susceptible to amoxicillin, 28 (58%) were resistant to metronidazole and 2 (4%) were resistant to both clarithromycin and metronidazole. Sequence analysis of the 23S rRNA of the two clarithromycin-resistant strains showed the A2142G mutation in one and A2143G and T2182C mutations in the other. Metronidazole resistance was associated with cagA negative strains with a frequency of 82% (9/11). No significant correlation was found between vacA s/m alleles and metronidazole resistance.

Use of the restriction enzyme EcoRI for pulsed-field gel electrophoretic analysis of Helicobacter pylori

Pulsed-field gel electrophoretic (PFGE) analysis of Helicobacter pylori isolates is not commonly employed because of the inability to compare the typing with other typing systems. We adapted the PFGE analysis for H. pylori by using EcoRI and slightly modified our laboratory methods to improve the typing of isolates (typeability was 97%).

Long-term follow-up of Helicobacter pylori eradication therapy in Vietnam: reinfection and clinical outcome

AIM

To assess the long-term Helicobacter pylori reinfection rates, as well as the clinical outcome in peptic ulcer disease patients in Vietnam.

METHOD

At a 1-year evaluation of H. pylori eradication treatment in 226 peptic ulcer patients, long-term H. pylori status was assessed with serology and/or culture, peptic ulcer status by gastroscopy, and DNA-fingerprinting performed with random amplified polymorphic DNA and restriction fragment polymorphism.

RESULT

Follow-up was performed a mean 11 months after the post-treatment evaluation on day 30 after beginning of treatment. The overall reinfection rate was 23.5%, with 58.8% of the strains being identical to the pre-treatment isolates and 41.2% being different. Peptic ulcer was found in 22.9% of the reinfected patients and in 6.3% of the non-reinfected. At the long-term follow-up of successful eradication cases, 89.8% of the patients were free of peptic ulcer disease. The corresponding result was 58.7% in patients in whom H. pylori eradication failed.

CONCLUSION

Following successful H. pylori eradication, reinfection with H. pylori in patients in Vietnam was found to be higher than in industrialized countries but the long-term recurrence of peptic ulcer disease was still low. Helicobacter pylori eradication treatment is therefore of value also in developing countries as the rate of peptic ulcer disease was low at the 1-year follow-up.

Genotypic and phenotypic stability of Helicobacter pylori markers in a nine-year follow-up study of patients with noneradicated infection

The cagA gene, alleles of the vacA gene,random amplified polymorphic DNA (RAPD), and neutrophil activating capacity (HpNAC) were used to examine paired H. pylori isolates from 10 noneradicated individuals 9 years apart. Paired isolates from each patient were indistinguishable with regard to vacA alleles, RAPD, and HpNAC. Isolates from nine patients showed concordance for the cagA gene, which was not detected in the recent isolate of the tenth patient. Antibodies to CagA were, however, demonstrated in the serum specimens 9 years apart and were also present in two other patients whose paired isolates were cagA-, indicating the existence of both cagA+ and cagA-organisms, with the latter predominating in some patients. The present study suggests a greater stability of phenotypic and genotypic markers of H. pylori than previously regarded. This might be true for a community with low infection and transmission rates. Complementary techniques like microarrays might, however, disclose evolutionary changes not identified here.

Evaluation of randomly amplified polymorphic DNA and pulsed field gel electrophoresis techniques for molecular typing of Dermatophilus congolensis

This study aimed to evaluate molecular typing methods useful for standardization of strains in experimental work on dermatophilosis. Fifty Dermatophilus congolensis isolates, collected from sheep, cattle, horse and a deer, were analyzed by randomly amplified polymorphic DNA (RAPD) method using twenty-one different primers, and the results were compared with those obtained by typing with a pulsed field gel electrophoresis (PFGE) method using the restriction digest enzyme Sse8387I. The typeability, reproducibility and discriminatory power of RAPD and Sse8387I-PFGE typing were calculated. Both typing methods were highly reproducible. Of the two techniques, Sse8387I-PFGE was the least discriminating (Dice Index (DI), 0.663) and could not distinguish between epidemiologically related isolates, whereas RAPD showed an excellent discriminatory power (DI, 0.7694-0.9722). Overall, the degree of correlation between RAPD and PFGE typing was significantly high (r, 0.8822). We conclude that the DNA profiles generated by either RAPD or PFGE can be used to differentiate epidemiologically unrelated isolates. The results of this study strongly suggest that at least two independent primers are used for RAPD typing in order to improve its discriminatory power, and that PFGE is used for confirmation of RAPD results.

DNA typing for Helicobacter pylori isolates from eradication-failed patients: comparison of the isolates before and after therapy

BACKGROUND

Failure of Helicobacter pylori eradication occurs frequently despite use of multiple microbial agents.

AIM

We aimed to study differences between H. pylori strains isolated before and after eradication failure.

METHODS

We treated 87 patients with peptic ulcer using triple therapy consisting of omeprazole plus combinations of clarithromycin, amoxicillin, or metronidazole. We studied the status of cagA, vacA, and iceA by PCR, and examined the differences in H. pylori isolates by pulsed-field gel electrophoresis and arbitrary primer polymerase chain reaction. The minimum inhibitory concentration of clarithromycin, amoxicillin, or metronidazole was determined by an agar dilution method.

RESULTS

Eradication therapy failed in 12 patients (14%); H. pylori isolates were obtained from all of these both before and after therapy. After eradication therapy, 10 patients were colonized with the same strain as before therapy, while the other two patients were colonized with different strains from those before therapy. In the former group, one isolate changed from metronidazole-sensitive to -resistant, one changed from clarithromycin- and metronidazole-sensitive to -resistant, and four were resistant to clarithromycin or metronidazole both before and after therapy. The other four isolates remained sensitive to clarithromycin and metronidazole after therapy. In the two patients who yielded apparently different isolates after therapy, they changed from clarithromycin- and metronidazole-sensitive to -resistant.

CONCLUSION

Eradication of H. pylori by first-line therapy is an important goal in the treatment of H. pylori-positive peptic ulcer, and that appropriate antimicrobial sensitivity testing should be conducted in patients with eradication failure.

Analysis of Helicobacter pylori genotypes and correlation with clinical outcome in Turkey

The predominant Helicobacter pylori strains circulating among geographic locations differ in regard to genomic structure. The association of the cagA-positive, vacA s1 genotypes with peptic ulcer disease (PUD) and gastric cancer was reported in Western countries but not in East Asian countries. Strains from Western countries predominantly possessed cagA type 2a, vacA s1a or s1b/m1a, or vacA m2a genotypes, whereas strains from East Asia possessed cagA type 1a, vacA s1c/m1b, or vacA m2b genotypes. Whether the Turkish strains possessed such genotypes was investigated and correlated with the disease outcome. Seventy-three patients from Turkey were enrolled. H. pylori was detected in 65 (89%) patients (22 with gastritis, 33 with PUD, and 10 with gastric cancer) by any of the following tests: Campylobacter-like organism test, culture, or PCR. Among the H. pylori-positive patients, presence of the cagA gene (78%) was significantly associated with PUD (P < 0.00001), gastric cancer (P < 0.001), and vacA s1a genotypes (P < 0.0001). Multiple vacA genotypes were more prevalent in PUD and gastric cancer patients than in patients with gastritis. Restriction fragment length polymorphism analysis of the cagA gene revealed three different patterns with no significant association with clinical outcome. Turkish strains examined predominantly possessed cagA type 2a, vacA s1a/m1a, or vacA m2a genotypes, which were typical genotypes in strains from Western countries. This fact might be one of the reasons for the low prevalence of severe gastroduodenal diseases in Turkey compared to the East Asian countries.

High prevalence of multiple strain colonization of Helicobacter pylori in Korean patients: DNA diversity among clinical isolates from the gastric corpus, antrum and duodenum

BACKGROUND

The aims of our study were to determine the correlation of the strain variation and degree of homogeneity of infecting Helicobacter pylori (H. pylori) with their disease outcomes, and the relevance of duodenal H. pylori expression of cagA and/or vacA gene to the development of duodenal ulcer in Korean patients.

METHODS

One hundred and twenty bacterial colonies isolated from different anatomical sites of the stomach and duodenum were used. The study population was consisted of 40 Korean patients, 21 with duodenal ulcer, 7 with gastric ulcer, 3 with combined gastric and duodenal ulcer, and 9 with chronic gastritis. Genomic characteristics of each strain were analyzed by random amplified polymorphic DNA (RAPD) fingerprinting. The cagA and vacA genes were detected by polymerase chain reaction (PCR).

RESULTS

PCR-based RAPD was proved to be a reliable method for the discrimination of individual bacterial genomic characteristics. Genomic fingerprinting showed a varying degree of inter- and intra-patient variation. Thirteen patients (32.5%) were colonized by a single strain throughout the corpus, antrum and duodenum, whereas the other 27 (67.5%) harbored multiple H. pylori strains. Thirty-six isolates (90.0%) each from the corpus and antrum, and 34 (85.0%) from the duodenum, expressed the cagA gene. The prevalence of duodenal H. pylori expression of the cagA gene was not different between patients with chronic gastritis and those with duodenal ulcer. All isolates were positive for both genes vacA s1 and vacA s1a.

CONCLUSION

These results suggested that many of the H. pylori-infected Korean patients were actually colonized with mixed populations of different H. pylori strains and that the prevalence of duodenal H. pylori expression of the cagA and/or vacA gene was not correlated with the development of duodenal ulcer in Korean patients.

Concordance of Helicobacter pylori strains within families

Helicobacter pylori infection is typically acquired in early childhood, and a predominantly intrafamilial transmission has been postulated. To what extent family members share the same strains is poorly documented. Our aim was to explore patterns of shared strains within families by using molecular typing. Family members of H. pylori-infected 10- to 12-year-old index children identified in a school survey were invited to undergo gastroscopy. Bacterial isolates were typed with random amplified polymorphic DNA and PCR-restriction fragment length polymorphism of the genes ureA-B, glmM, or flaA. The presence or absence of the cag pathogenicity island, a bacterial virulence factor, was determined by PCR. GelCompar II software, supplemented with visual inspection, was used in the cluster analysis. In 39 families, 104 individuals contributed 208 bacterial isolates from the antrum and corpus. A large proportion, 29 of 36 (81%) of the offspring in a sibship, harbored the same strain as at least one sibling. Mother-offspring strain concordance was detected in 10 of 18 (56%) of the families. Of 17 investigated father-offspring relations in eight families, none were strain concordant. Spouses were infected with the same strains in 5 of 23 (22%) of the couples. Different strains in the antrum and corpus were found in 8 of 104 (8%) of the subjects. Our family-based fingerprinting study demonstrates a high proportion of shared strains among siblings. Transmission between spouses seems to be appreciable. The data support mother-child and sib-sib transmission as the primary transmission pathways of H. pylori.

Stability of randomly amplified polymorphic DNA fingerprinting in genotyping clinical isolates of Helicobacter pylori

AIM: H pylori genomes are highly diversified. This project was designed to genotype H pylori isolates by the polymerase chain reaction (PCR)-based randomly amplified polymorphic DNA (RAPD) fingerprinting technique and to verify its stability by Southern blotting and DNA sequencing.

METHODS: Clinical isolates of H pylori were cultured from gastric antra and cardia of 73 individuals, and genomic DNA was prepared for each isolate. RAPD was carried out under optimized conditions. 23S rDNA was regarded as an internal control, and a 361 bp rDNA fragment (RDF) was used as a probe to screen the RAPD products by Southern blotting. Ten RDFs from different clinical isolates and the flanking regions (both upstream and downstream) of four RDFs were amplified and sequenced.

RESULTS: H pylori isolates from different individuals had different RAPD profiles, but the profiles for isolates cultured from different gastric sites of a given individual were identical in all but one case. Isolates from 27 individuals were RDF positive by Southern blotting. Sequences of the RDFs and their flanking regions were almost the same between the RDF positive and negative isolates as determined by Southern blotting. There was no binding site for random PCR primer inside the sequences.

CONCLUSION: RAPD is very useful in genotyping H pylori grossly on a large scale. However, it seems unstable in amplification of low yield fragments, especially those that do not appear as visible bands on the agarose gel stained with EB, since the primer is partially matched to the template.

High-level beta-lactam resistance associated with acquired multidrug resistance in Helicobacter pylori

Four clinical Helicobacter pylori isolates with high-level resistance to beta-lactams exhibited low- to moderate-level resistance to the structurally and functionally unrelated antibiotics ciprofloxacin, chloramphenicol, metronidazole, rifampin, and tetracycline. This pattern of multidrug resistance was transferable to susceptible H. pylori by natural transformation using naked genomic DNA from a clinical multidrug-resistant isolate. Acquisition of the multidrug resistance was also associated with a change in the genotype of the transformed multidrug-resistant H. pylori. DNA sequence analyses of the gene encoding penicillin binding protein 1A (PBP 1A) showed 36 nucleotide substitutions resulting in 10 amino acid changes in the C-terminal portion (the putative penicillin binding domain). Acquisition of beta-lactam resistance was consistently associated with transfer of a mosaic block containing the C-terminal portion of PBP 1A. No changes of genes gyrA, rpoB, rrn16S, rdxA, and frxA, and nine other genes (ftsI, hcpA, llm, lytB, mreB, mreC, pbp2, pbp4, and rodA1) encoding putative PBPs or involved in cell wall synthesis were found among the transformed resistant H. pylori. Antibiotic accumulations of chloramphenicol, penicillin, and tetracycline were all significantly decreased in the natural and transformed resistant H. pylori compared to what was seen with susceptible H. pylori. Natural transformation also resulted in the outer membrane protein profiles of the transformed resistant H. pylori becoming similar to that of the clinical resistant H. pylori isolates. Overall, these results demonstrate that high-level beta-lactam resistance associated with acquired multidrug resistance in clinical H. pylori is mediated by combination strategies including alterations of PBP 1A and decreased membrane permeability.

Molecular fingerprinting of Helicobacter pylori strains from duodenal ulcer patients

AIMS

To characterize the molecular fingerprinting of Helicobacter pylori population isolated in duodenal ulcer patients treated with triple therapy.

METHODS AND RESULTS

Gastric biopsy specimens from corpus and antrum, were cultured for H. pylori isolation. Helicobacter pylori eradication was evaluated after 4 and 16 weeks. DNAs of all isolates were characterized by random amplified polymorphic DNA typing and cagA gene was also detected. After the therapy, five patients harboured the microorganism at 4 weeks and two of them remained H. pylori positive at 16 weeks. The analysis of DNA fingerprinting of strains isolated from antrum and corpus of patients susceptible to treatment, showed similar patterns. Instead, when the therapy was not effective, strains isolated from sequential biopsies from initial and after 4 and 16 weeks, showed distinct fingerprintings and retained the cagA status, over time.

CONCLUSIONS

The drugs used for therapy could exercise an effect in genotypical rearrangement among H. pylori cells.

SIGNIFICANCE AND IMPACT OF THE STUDY

The variableness among H. pylori strains represents a way to challenge environmental stress.

Heterogeneity of cag genotypes in Helicobacter pylori isolates from human biopsy specimens

The Helicobacter pylori chromosomal cluster of genes known as the cytotoxin-associated gene (cag) island may have different compositions in infecting strains. In this study, we analyzed 150 single colonies obtained from gastric biopsy specimens from 10 patients infected with cagA-positive H. pylori strains and sweep isolates (isolates harvested with sweep in different points of the plate) from 6 patients infected with cagA-negative strains. Three loci in the cag island (cagA, cagE, and virB11) and the conserved gene glmM (ureC) were investigated by PCR. The levels of anti-H. pylori and anti-CagA antibodies in patient sera were also measured. For subjects infected with cagA-negative strains, all sweep isolates were also negative for cagE and virB11, suggesting the complete absence of the cag island. For subjects infected with cagA-positive strains, most of the isolates were positive for all three genes studied, whereas 24.7% of the isolates had a partial or total deletion of the cag island. cagA, cagE, and virB11 were, respectively, present in 87.3, 77.3, and 90% of the colonies. The deletion of virB11 was always associated with the deletion of cagA and/or cagE. H. pylori colonies with different cag genotypes were isolated within a single gastric biopsy specimen from 3 of the 10 patients and were further characterized by random amplified polymorphic DNA (RAPD) analysis and by sequencing of an arbitrarily selected gene segment. Although the colonies had different cag genotypes, their RAPD profiles were highly similar within each patient, and the nucleotide sequences of the selected gene segment were identical. All of the patients had detectable antibodies against H. pylori, and 9 of 10 had anti-CagA antibodies. In conclusion, we show that a single infecting H. pylori strain may include variable proportions of colony subtypes with different cag genotypes. The extension of our analysis to patients with well-characterized gastric diseases may provide significant information on the relationship between cag genotypes and clinical outcomes of H. pylori infections.

Performance of PCR-restriction fragment length polymorphism analysis of the Helicobacter pylori ureB gene in differentiating gene variants

Recently, PCR-restriction fragment length polymorphism (PCR-RFLP) of the urease genes of Helicobacter pylori was evaluated in a meta-analysis; acceptable discriminatory indices of the ureAB and C genes were found. In the present investigation, we found a discriminatory index of 0.95 for 191 unrelated clinical H. pylori isolates with PCR-RFLP typing of the ureB gene (933 bp), combining the results obtained with restriction enzymes HaeIII and Sau3A, and a mixture of the enzymes. We therefore find that PCR-RFLP typing of the ureB gene of H. pylori with restriction enzymes HaeIII and Sau3A is comparable to typing of other H. pylori urease genes.