DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting

genoBASE pylori: A genotype search tool and database of the human gastric pathogen Helicobacter pylori

Helicobacter pylori is the pathogenic bacterium linked to gastric and duodenal ulcers and gastric carcinoma. Genomic diversity of the organism has enabled new insights into its population biology through comparative genomics. genoBASE pylori is an online databank of several virulence-linked and phylogenetic markers of H. pylori strains obtained from different human populations. This knowledgebase is built upon a relational database management system which is connected to visualize the presence of known, pathogenicity markers such as the co-ordinates within the cag pathogenicity island (cagPAI), the cagA gene and motifs surrounding it, the vacA allotypes and the oipA gene frame status, together with genotypic details in the form of DNA profiling traces and candidate gene sequences for individual strains. This flexible search tool allows inter-laboratory comparison of DNA fingerprinting data in the form of fluorescent amplified fragment length polymorphism (FAFLP), enterobacterial repetitive intergenic consensus (ERIC) and repetitive extragenic palindromic (REP) signature profiles. Besides this, the database also displays diversity of strains based on nucleotide sequences of several house keeping genes and two membrane proteins. Being the first of its kind, genoBASE pylori is expected to be a helpful online tool in strengthening the concept of 'geographic genomics' and will be useful to molecular epidemiologists, clinical laboratory scientists and those interested in diagnostic development for H. pylori. The database can be accessed through its website (http://www.cdfd.org.in/amplibase/HP).

Enterococcus populations in Pecorino Abruzzese cheese: biodiversity and safety aspects

The presence of enterococci in Pecorino Abruzzese cheese during ripening was evaluated. Counts were high, especially in fully ripened summer batches. Seventy strains were isolated and identified based on phenotypical and genotypical features as Enterococcus faecium (48.5%), Enterococcus faecalis (40%), and Enterococcus durans (11.5%), with the first species predominant in spring batches and the second predominant in summer batches. High biodiversity was revealed by random amplification of polymorphic DNA and a PCR assay, suggesting the presence of autochthonous strains. E. faecium isolates were the most resistant to the tested antibiotics, especially to erythromycin, chloramphenicol, and penicillin, but all strains were susceptible to vancomycin, as confirmed by the absence of vanA and vanB genes. The presence of some virulence determinants was investigated, revealing the diffusion of aggregation substance (asal) and gelatinase (gelE) genes in 37.5% of E. faecalis strains. However, none of the isolates produced gelatinase in vitro, suggesting the presence of silent genes. The virulence genes were absent in E. durans. Among E. faecium strains, only Lab 41/1 possessed gelE and asal, whose presence previously has been reported only in E. faecalis. Decarboxylating activity was revealed for phenylalanine (27% of the strains) and tyrosine (96%) but not histidine. The presence of a tyrosine decarboxylase-encoding gene was observed for all strains. A comparison of these results with those of previous studies of clinical and food isolates indicates that enterococci from Pecorino Abruzzese cheese have low pathogenic potential.

Helicobacter pylori evolution: lineage- specific adaptations in homologs of eukaryotic Sel1-like genes

Geographic partitioning is postulated to foster divergence of Helicobacter pylori populations as an adaptive response to local differences in predominant host physiology. H. pylori's ability to establish persistent infection despite host inflammatory responses likely involves active management of host defenses using bacterial proteins that may themselves be targets for adaptive evolution. Sequenced H. pylori genomes encode a family of eight or nine secreted proteins containing repeat motifs that are characteristic of the eukaryotic Sel1 regulatory protein, whereas the related Campylobacter and Wolinella genomes each contain only one or two such "Sel1-like repeat" (SLR) genes ("slr genes"). Signatures of positive selection (ratio of nonsynonymous to synonymous mutations, dN/dS = omega > 1) were evident in the evolutionary history of H. pylori slr gene family expansion. Sequence analysis of six of these slr genes (hp0160, hp0211, hp0235, hp0519, hp0628, and hp1117) from representative East Asian, European, and African H. pylori strains revealed that all but hp0628 had undergone positive selection, with different amino acids often selected in different regions. Most striking was a divergence of Japanese and Korean alleles of hp0519, with Japanese alleles having undergone particularly strong positive selection (omegaJ > 25), whereas alleles of other genes from these populations were intermingled. Homology-based structural modeling localized most residues under positive selection to SLR protein surfaces. Rapid evolution of certain slr genes in specific H. pylori lineages suggests a model of adaptive change driven by selection for fine-tuning of host responses, and facilitated by geographic isolation. Characterization of such local adaptations should help elucidate how H. pylori manages persistent infection, and potentially lead to interventions tailored to diverse human populations.

Metabolic and genetic profiling of clinical O157 and non-O157 Shiga-toxin-producing Escherichia coli

A collection of clinical Shiga-toxin-producing Escherichia coli (STEC) strains, mainly belonging to serotypes O26, O103, O111, O145 and O157, was characterised by a polyphasic approach including molecular serotyping, PCR-based detection of virulence factors (stx1, stx2, eae, EHEC-hlyA, saa, katP, espP), carbohydrate fermentation profiles using API50 tests and random amplification of polymorphic DNA (RAPD) fingerprinting. An RAPD protocol based on the combination of 2 primers resulted in sufficiently complex patterns enabling discrimination to the serotype level. Moreover, carbohydrate fermentation profiles obtained after evaluating up to 50 different carbohydrates led to separation of different STEC serotypes. Virulence typing results confirm the association of Shiga toxins and intimin subtypes with specific serotypes and clinical diagnosis. Clinical diagnosis of strains did not correlate with either RAPD profiles or carbohydrate fermentation patterns.

Helicobacter pylori genome variability in a framework of familial transmission

BACKGROUND

Helicobacter pylori infection is exceptionally prevalent and is considered to be acquired primarily early in life through person-to-person transmission within the family. H. pylori is a genetically diverse bacterial species, which may facilitate adaptation to new hosts and persistence for decades. The present study aimed to explore the genetic diversity of clonal isolates from a mother and her three children in order to shed light on H. pylori transmission and host adaptation.

RESULTS

Two different H. pylori strains and strain variants were identified in the family members by PCR-based molecular typing and sequencing of five loci. Genome diversity was further assessed for 15 isolates by comparative microarray hybridizations. The microarray consisted of 1,745 oligonucleotides representing the genes of two previously sequenced H. pylori strains. The microarray analysis detected a limited mean number (+/- standard error) of divergent genes between clonal isolates from the same and different individuals (1 +/- 0.4, 0.1%, and 3 +/- 0.3, 0.2%, respectively). There was considerable variability between the two different strains in the family members (147 +/- 4, 8%) and for all isolates relative to the two sequenced reference strains (314 +/- 16, 18%). The diversity between different strains was associated with gene functional classes related to DNA metabolism and the cell envelope.

CONCLUSION

The present data from clonal H. pylori isolates of family members do not support that transmission and host adaptation are associated with substantial sequence diversity in the bacterial genome. However, important phenotypic modifications may be determined by additional genetic mechanisms, such as phase-variation. Our findings can aid further exploration of H. pylori genetic diversity and adaptation.

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.

Helicobacter pylori evolution and phenotypic diversification in a changing host

Helicobacter pylori colonizes the stomachs of more than 50% of the world's population, making it one of the most successful of all human pathogens. One striking characteristic of H. pylori biology is its remarkable allelic diversity and genetic variability. Not only does almost every infected person harbour their own individual H. pylori strain, but strains can undergo genetic alteration in vivo, driven by an elevated mutation rate and frequent intraspecific recombination. This genetic variability, which affects both housekeeping and virulence genes, has long been thought to contribute to host adaptation, and several recently published studies support this concept. We review the available knowledge relating to the genetic variation of H. pylori, with special emphasis on the changes that occur during chronic colonization, and argue that H. pylori uses mutation and recombination processes to adapt to its individual host by modifying molecules that interact with the host. Finally, we put forward the hypothesis that the lack of opportunity for intraspecies recombination as a result of the decreasing prevalence of H. pylori could accelerate its disappearance from Western populations.

Fatal relapse of a purulent pleurisy caused by Campylobacter fetus subsp. fetus

Campylobacter fetus is associated with invasive disease, while other Campylobacter species, such as C. coli and C. jejuni, are a common cause of bacterial diarrhea. Bacteremia has been well described, but pleurisy remains very uncommon. We report the recurrent isolation of a C. fetus subsp. fetus strain during two episodes of pleural effusion with a fatal outcome.

Occurrence and persistence of Listeria spp. in the environment of ewe and cow's milk cheese dairies in Portugal unveiled by an integrated analysis of identification, typing and spatial–temporal mapping along production cycle

Eight dairies, located in two distant geographic regions of Portugal, were screened along the production cycle in order to evaluate the presence and distribution of Listeria spp. in their environment. Three dairies in each region were positive for the presence of listeriae and 213 isolates were obtained. Based on an integrated analysis of RAPD fingerprints with three primers, molecular identification and genomic typing of isolates was performed followed by spatial and temporal mapping on dairy plants. The occurrence of Listeria species by region was noticeable different. Listeria monocytogenes prevailed in South Portugal dairies and L. innocua presented the highest occurrence in Azores, whereas L. seeligeri and L. ivanovii were detected in distinct regions. Dairies were at risk of contamination, from more than one source, whatever the stage in the production cycle and the surface materials used. For the three prevalent species, most of the genomic types were dairy and sampling time specific. Nonetheless, more than one type could be found in each dairy at a particular site and, in a few cases, even for different species. Some dairies also shared types, mainly for L. innocua and usually at the same stage of the production cycle. For L. monocytogenes, PCR serotyping was applied and 52% of genomic types were serotype 4b. An equal frequency of genomic types (24%) was found for serotypes 1/2b or 3b and 1/2a or 3a. The global pattern of types within a dairy is not constant, suggesting cycles of elimination and recontamination along the production cycle.

Heterogeneity in the activity of Mexican Helicobacter pylori strains in gastric epithelial cells and its association with diversity in the cagA gene

Helicobacter pylori CagA is translocated into gastric epithelial cells by a type IV secretion system and interacts with the Src homology 2 phosphatase, altering cell morphology. Multiple EPIYA motifs in CagA are associated with increased activity in cells and with gastric cancer. The aim of this work was to study the heterogeneity in activity in cells of multiple H. pylori single colonies isolated from a single patient and its association with polymorphism in cagA. The presence of cagA, cagE, cagT, and cag10 was studied with 318 H. pylori isolates from the antra and corpora of 18 patients. AGS gastric epithelial cells were infected with 75 isolates, and interleukin-8 (IL-8) secretion, cytoskeletal changes, CagA translocation, and tyrosine phosphorylation were measured. The cagA 3'-variable region was sequenced for 30 isolates to determine the number and types of EPIYA motifs. Isolates from an individual stomach were usually genetically related and had quantitatively similar phenotypic effects on cells (IL-8 induction and cytoskeletal changes). However, strains from different patients with similar CagA EPIYA motif patterns varied widely in these phenotypes. Among isolates with an EPIYA-ABC pattern, the phenotype was variable: IL-8 induction ranged from 200 to 1,200 pg/ml, and morphological changes occurred in 20 to 70% of cells. In several cases, cagA sequence diversity appeared to explain the lack of CagA activity, as isolates with an EPIYA-ACC pattern or a modified B motif had reduced cell activity. cag pathogenicity island-positive H. pylori isolates displayed a high level of heterogeneity in the capacity to induce IL-8 secretion and morphological changes; an absent or modified B motif was associated with low activity.

Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates

Background

Clinical isolates of the gastric pathogen Helicobacter pylori display a high level of genetic macro- and microheterogeneity, featuring a panmictic, rather than clonal structure. The ability of H. pylori to survive the stomach acid is due, in part, to the arginase-urease enzyme system. Arginase (RocF) hydrolyzes L-arginine to L-ornithine and urea, and urease hydrolyzes urea to carbon dioxide and ammonium, which can neutralize acid.

Results

The degree of variation in arginase was explored at the DNA sequence, enzyme activity and protein expression levels. To this end, arginase activity was measured from 73 minimally-passaged clinical isolates and six laboratory-adapted strains of H. pylori. The rocF gene from 21 of the strains was cloned into genetically stable E. coli and the enzyme activities measured. Arginase activity was found to substantially vary (>100-fold) in both different H. pylori strains and in the E. coli model. Western blot analysis revealed a positive correlation between activity and amount of protein expressed in most H. pylori strains. Several H. pylori strains featured altered arginase activity upon in vitro passage. Pairwise alignments of the 21 rocF genes plus strain J99 revealed extensive microheterogeneity in the promoter region and 3' end of the rocF coding region. Amino acid S232, which was I232 in the arginase-negative clinical strain A2, was critical for arginase activity.

Conclusion

These studies demonstrated that H. pylori arginase exhibits extensive genotypic and phenotypic variation which may be used to understand mechanisms of microheterogeneity in H. pylori.

Occurrence of ssl genes in isolates of Staphylococcus aureus from animal infection

The occurrence of 7 of the 11 known ssl genes that are found within the vSaalpha genomic island of Staphylococcus aureus and encode the novel Ssl family of exoproteins was examined in isolates from cows (42 isolates), goats (4 isolates), sheep (1 isolate), rabbits (3 isolates) and chickens (2 isolates). Based on seven S. aureus genome sequences for human strains NCTC 8325, N315, Mu50, COL, MRSA 252, MW2 and MSSA-476, and bovine strain RF122, along with the ssl reference gene sequences from strains NCTC 6571, FRI326 and NCTC 8325, ClustalW-generated alignments were used to design PCR primers for unique regions of the ssl genes that are present in the allelic variants of each, except for the ssl4 gene for which specific primers for the set2 and set9 allelic variants were designed individually. The genotypes of isolates were determined using random amplified polymorphic DNA (RAPD) typing. All of the animal-associated S. aureus isolates contained an ssl locus, but there were minor variations in the number of ssl genes present. Forty-nine of the animal isolates possessed a vSaalpha genomic island containing the ssl3 (set8), ssl5 (set3/set10), ssl7 (set1/set11), ssl8 (set12), ssl9 (set5/set13) and ssl10 (set4/set14) genes. One bovine and one goat isolate lacked the ssl3 gene. The ssl9 gene was absent in one bovine isolate. The goat isolate lacking the ssl3 gene was the only animal isolate that possessed the set2 allele of the ssl4 gene. PCR for the set9 allele of the ssl4 gene was inconclusive. Isolates that showed identical RAPD fingerprints had the same complement of ssl genes, but the ssl gene pattern was not RAPD-type specific. Southern blot hybridization showed similar ssl gene RFLPs in isolates of the same RAPD type.

High-frequency phage-mediated gene transfer among Escherichia coli cells, determined at the single-cell level

Recent whole-genome analysis suggests that lateral gene transfer by bacteriophages has contributed significantly to the genetic diversity of bacteria. To accurately determine the frequency of phage-mediated gene transfer, we employed cycling primed in situ amplification-fluorescent in situ hybridization (CPRINS-FISH) and investigated the movement of the ampicillin resistance gene among Escherichia coli cells mediated by phage at the single-cell level. Phages P1 and T4 and the newly isolated E. coli phage EC10 were used as vectors. The transduction frequencies determined by conventional plating were 3x10(-8) to 2x10(-6), 1x10(-8) to 4x10(-8), and <4x10(-9) to 4x10(-8) per PFU for phages P1, T4, and EC10, respectively. The frequencies of DNA transfer determined by CPRINS-FISH were 7x10(-4) to 1x10(-3), 9x10(-4) to 3x10(-3), and 5x10(-4) to 4x10(-3) for phages P1, T4, and EC10, respectively. Direct viable counting combined with CPRINS-FISH revealed that more than 20% of the cells carrying the transferred gene retained their viabilities. These results revealed that the difference in the number of viable cells carrying the transferred gene and the number of cells capable of growth on the selective medium was 3 to 4 orders of magnitude, indicating that phage-mediated exchange of DNA sequences among bacteria occurs with unexpectedly high frequency.

Genetic analysis of Helicobacter pylori strain populations colonizing the stomach at different times postinfection

Genetic diversity of the human gastric pathogen Helicobacter pylori in an individual host has been observed; whether this diversity represents diversification of a founding strain or a mixed infection with distinct strain populations is not clear. To examine this issue, we analyzed multiple single-colony isolates from two to four separate stomach biopsies of eight adult and four pediatric patients from a high-incidence Mexican population. Eleven of the 12 patients contained isolates with identical random amplified polymorphic DNA, amplified fragment length polymorphism, and vacA allele molecular footprints, whereas a single adult patient had two distinct profiles. Comparative genomic hybridization using whole-genome microarrays (array CGH) revealed variation in 24 to 67 genes in isolates from patients with similar molecular footprints. The one patient with distinct profiles contained two strain populations differing at 113 gene loci, including the cag pathogenicity island virulence genes. The two strain populations in this single host had different spatial distributions in the stomach and exhibited very limited genetic exchange. The total genetic divergence and pairwise genetic divergence between isolates from adults and isolates from children were not statistically different. We also analyzed isolates obtained 15 and 90 days after experimental infection of humans and found no evidence of genetic divergence, indicating that transmission to a new host does not induce rapid genetic changes in the bacterial population in the human stomach. Our data suggest that humans are infected with a population of closely related strains that vary at a small number of gene loci, that this population of strains may already be present when an infection is acquired, and that even during superinfection genetic exchange among distinct strains is rare.

Conjugative transfer of chromosomally encoded antibiotic resistance from Helicobacter pylori to Campylobacter jejuni

Many strains of Helicobacter pylori are naturally competent for transformation and able to transfer chromosomal DNA among different isolates using a conjugation-like mechanism. In this study, we sought to determine whether H. pylori can transfer DNA into Campylobacter jejuni, a closely related species of the Campylobacterales group. To monitor the transfer, a chromosomally encoded streptomycin resistance cassette prearranged by a specific mutation in the rpsL gene of H. pylori was used. Mating of the bacteria on plates or in liquid broth medium produced C. jejuni progeny containing the streptomycin marker. DNA transfer was unidirectional, from H. pylori to C. jejuni, and the progeny were genetically identical to C. jejuni recipient strains. DNase I treatment reduced but did not eliminate transfer, and DNase I-treated cell supernatants did not transform, ruling out phage transduction. Recombinants also did not occur when the mating bacteria were separated by a membrane, suggesting that DNA transfer requires cell-to-cell contact. Transfer of the streptomycin marker was independent of the H. pylori comB transformation system, the cag pathogenicity island, and another type IV secretion system called tfs3. These findings indicated that a DNase I-resistant, conjugation-like mechanism may contribute to horizontal DNA transfer between different members of the Campylobacteriales group. The significance of this DNA uptake by C. jejuni in the context of acquiring antibiotic resistance is discussed.

Sensitivity of two techniques to detect Escherichia coli O157 in naturally infected bovine fecal samples

The aim of this study was to investigate the sensitivity and reliability of two techniques commonly used for the isolation of Escherichia coli O157: (i) buffered peptone water (BPW) containing vancomycin, cefsulodin and cefixime followed by immunomagnetic separation (IMS-VCC) and (ii) modified E. coli (EC) broth supplemented with novobiocin (m ECn), both followed by culturing on cefixime tellurite sorbitol McConkey (ctSMAC) agar plates. Over a 2-year period, 24 feedlots located over a large geographical area (approximately 600 x 450 km) were screened for the presence of E. coli O157. A total of 194 E. coli O157 isolates were identified; 151 (77.4%) using IMS-VCC and 108 (55.4%) using m ECn. The recovery rates of IMS-VCC varied from 100% to 47%, whereas for m ECn ranged from 100% to 16%. All isolates were grouped, using randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR), into 3 major clusters that comprised 39 different subtypes, providing evidence of considerable genetic heterogeneity. The results from this study revealed false negatives in IMS-VCC technique, most probably due to the high genetic diversity of environmental E. coli O157 isolates and antibiotic sensitivity. Using only IMS-VCC as a method for detection may result in significant underestimation of the pathogen. Performing two different enrichment steps in parallel can lead to markedly improved recovery rates of E. coli O157 isolates from naturally infected samples.

The use of multiplex PCR to detect and differentiate food- and beverage-associated microorganisms: a review

Regarding food safety, rapid detection of microbial species is crucial to develop effective preventive and/or adjustment measures. Classical methods for determining the presence of certain species are time-consuming and labor-intensive, hence, molecular methods, which offer speed, sensitivity and specificity, have been developed to address this problem. Multiplex PCR (MPCR) is widely applied in the various fields of microbiology for the rapid differentiation of microbial species without compromising accuracy. This paper describes the method and reports on the state-of-the-art application of this technique to the identification of microorganisms vehiculated with foods and beverages. The identification of both pathogens and probiotics and the species important for food fermentation or deterioration will be discussed. Applications of MPCR in combination with other techniques are also reviewed. Potentials, pitfalls, limitations and future prospects are summarised.

Strategy to characterize the number and type of repeating EPIYA phosphorylation motifs in the carboxyl terminus of CagA protein in Helicobacter pylori clinical isolates

Cytotoxin-associated gene A (CagA) diversity with regard to EPIYA-A, -B, -C, or -D phosphorylation motifs may play an important role in Helicobacter pylori pathogenesis, and therefore determination of these motifs in H. pylori clinical isolates can become a useful prognostic tool. We propose a strategy for the accurate determination of CagA EPIYA motifs in clinical strains, based upon one-step PCR amplification using primers that flank the EPIYA coding region. We thus analyzed 135 H. pylori isolates derived from 75 adults and 60 children Greek patients. A total of 34 cases were found to be EPIYA PCR negative and were consequently verified as cagA negative by cagA-specific PCR, empty-site cagA PCR, and Western blotting. Sequencing of the remaining 101 PCR-positive amplicons confirmed that an accurate prediction of the number of EPIYA motifs on the basis of size distribution of the PCR products was feasible in all cases. Furthermore, our assay could identify closely related H. pylori subclones within the same patient, harboring different numbers of EPIYA repeats. The prevalence of CagA proteins with three EPIYA motifs (ABC) or four EPIYA motifs (ABCC) was the same within the adult and children groups. However, CagA species with more than four EPIYA motifs were observed exclusively within adults (8.6%), suggesting that CagA-positive strains may acquire additional EPIYA-C motifs throughout adulthood. Our strategy requires no initial cagA screening of the clinical isolates and can accurately predict the number of EPIYA repeats in single or multiple closely related subclones bearing different numbers of EPIYA motifs in their CagA, which may coexist within the same patient.

Analysis of serum antibody profile against H pylori VacA and CagA antigens in Turkish patients with duodenal ulcer

AIM

To investigate the frequency of seropositivity against CagA, VacA proteins and to determine their independent effects on the development of duodenal ulcer (DU) in Turkish patients.

METHODS

The study was designed as a prospective one from a tertiary referral hospital. Dyspeptic patients who were referred to our endoscopy unit for upper gastrointestinal endoscopy between June 2003 and March 2004 and diagnosed to have DU or nonulcer dyspepsia (NUD) were included. Biopsies from the antrum and body of the stomach were taken in order to assess the current H pylori status by histology, rapid urease test and culture. Fasting sera were obtained from all patients and H pylori status of all sera was determined by IgG antibodies using an enzyme-linked immunosorbent assay (ELISA) kit. All seropositive patients were further analysed using Western blot assays detecting IgG antibodies against CagA and VacA proteins. The c2 test was used for statistical comparison of the values and age-sex adjusted multiple regression analysis was used to determine the independent effects of CagA and VacA seropositivities on the development of DU.

RESULTS

Sixty-three patients with DU and 62 patients with NUD were eligible for the final analysis. Seropositivity for anti-CagA was detected in 51 of 62 (82%), and in 55 of 63 (87%) patients with NUD and DU, respectively (P = no significance), and seropositivity for anti-VacA was found in 25 of 62 (40% ) and in 16 of 63 (25%) patients, with NUD and DU, respectively.

CONCLUSION

These findings suggest that none of these virulence factors is associated with the development of DU in the studied Turkish patients with dyspepsia.

Phenotypic and molecular typing of Vibrio cholerae O1 and O139 isolates from India

OBJECTIVES

To determine whether Vibrio cholerae strains with similar phage types are also genetically homogeneous or heterogeneous by molecular typing methods like PFGE and RAPD-PCR employed in this study.

METHODS

A total of 26 V. cholerae O1 and O139 strains received from different parts of India were analyzed by using conventional phage typing method, antibiogram and molecular typing methods such as PFGE and RAPD-PCR.

RESULTS

Both O1 and O139 strains were resistant against two antibiotics (Ampicillin and Furazolidone) were detected. All of these strains were clustered in a single phage type, i.e., Type 27 for V. cholerae O1 and Type 1 for V. cholerae O139. Extensive molecular characterization by RAPD and PFGE showed that six sets of O1 and O139 strains, each comprising two strains, had identical PFGE and RAPD profiles. Only one O139 strain (PL-4) had unique RAPD and PFGE profile among all the 26 V. cholerae strains used in this study.

CONCLUSION

Apart from serology, the strains of V. cholerae can be discriminated by this conventional phage typing system that offers the basic information on identification, biotyping and discrimination of strains. But, a high level of heterogeneity was observed in RAPD and PFGE profiles indicating the clonal diversity of V. cholerae O1 and O139 strains. It was concluded that these strains were phenotypically identical through phage typing system and antibiogram but genetically dissimilar, as shown in molecular typing systems.

Bacterial populations as perfect gases: genomic integrity and diversification tensions in Helicobacter pylori

Microorganisms that persist in single hosts face particular challenges. Helicobacter pylori, an obligate bacterial parasite of the human stomach, has evolved a lifestyle that features interstrain competition and intraspecies cooperation, both of which involve horizontal gene transfer. Microbial species must maintain genomic integrity, yet H. pylori has evolved a complex nonlinear system for diversification that exists in dynamic tension with the mechanisms for ensuring fidelity. Here, we review these tensions and propose that they create a dynamic pool of genetic variants that is sufficiently genetically diverse to allow H. pylori to occupy all of the potential niches in the stomach.

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.

Genotypic diversity in a localized population of Ralstonia solanacearum as revealed by random amplified polymorphic DNA markers

AIMS

To assess genotypic diversity within Ralstonia solanacearum isolates of a single field.

METHODS AND RESULTS

A total of 44 field isolates and 22 in vitro generated clones of R. solanacearum were studied for genotypic diversity by random amplified polymorphic DNA (RAPD) technique. Genomic DNA of these isolates and clones was extracted by proteinase-K-SDS lysis mini-prep method. RAPD analysis was done with 30 decamer primers. The data were analysed using NTSYSpc 2.02h software. Forty-two out of 44 field isolates and all the clonal isolates were identified as distinct genotypes at 70% similarity level.

CONCLUSION

Very high level of genome variability was observed within the field and clonal isolates of R. solanacearum. This might be a reason for the wide host range of this bacterium and for quick breakdown of wilt resistance in host plants.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results suggest that it would be difficult to design specific diagnostic protocol for R. solanacearum even for a localized population and to breed cultivars with broad-spectrum resistance.

Oenococcus kitaharae sp. nov., a non-acidophilic and non-malolactic-fermenting oenococcus isolated from a composting distilled shochu residue

Six strains of lactic acid bacteria were isolated in Japan from a composting distilled shochu residue. The six isolates grew poorly on MRS agar and slowly in MRS broth. The 16S rRNA gene sequences did not show high levels of similarity to those of the recognized species of lactic acid bacteria, and formed a subcluster within the cluster comprising obligately heterofermentative lactic acid bacteria closely related to Oenococcus oeni. The levels of DNA–DNA relatedness revealed that the isolates belonged to the same taxon and were genetically separate from O. oeni. Furthermore, various phenotypic characteristics such as the optimum pH for growth, malolactic fermentation and resistance to 10 % ethanol revealed that the isolates are distinguishable from O. oeni. On the basis of their phylogenetic and phenotypic characteristics, the isolates represent a novel species, for which the name Oenococcus kitaharae sp. nov. is proposed. The type strain is NRIC 0645T (=JCM 13282T=DSM 17330T).

Effectiveness of enterobacterial repetitive intergenic consensus PCR and random amplified polymorphic DNA fingerprinting for Helicobacter pylori strain differentiation

We compared the robustness and discriminatory power of the enterobacterial repetitive intergenic consensus (ERIC) and random amplified polymorphic DNA (RAPD) fingerprinting methods for detecting cases of mixed Helicobacter pylori infection in Peruvian shantytown residents. H. pylori isolates from 63 participants were cultured, and five single colonies and a pool of additional colonies from each participant were analyzed by ERIC-PCR and by RAPD tests with four 10-nucleotide primers (one primer per reaction). There was 94% agreement between the ERIC and RAPD profiles in classifying sets of isolates as uniform versus closely related but not identical versus probably unrelated, indicating a high kappa statistic of 0.8942. Subtle differences in related ERIC or RAPD patterns likely reflect gene transfer between strains, recombination, and/or mutation, whereas markedly different patterns reflect infection by unrelated strains. At least half of infected shantytown residents seemed to carry more than one H. pylori strain, although in 19 of 31 persons, the strains were closely related. Three RAPD tests, each with a different primer, were needed to achieve the sensitivity of one ERIC test. ERIC-PCR constitutes a resource- and time-efficient method for H. pylori strain differentiation.

Prevalence of Escherichia coli O157 in Saskatchewan cattle: characterization of isolates by using random amplified polymorphic DNA PCR, antibiotic resistance profiles, and pathogenicity determinants

The prevalence of Escherichia coli O157 associated with feedlot cattle in Saskatchewan was determined in a 10-month longitudinal study (3 feedlots) and a point prevalence study (20 feedlots). The prevalence of E. coli O157 at the three different sites in the horizontal study varied from 2.5 to 45%. The point prevalence of E. coli O157 among Saskatchewan cattle from 20 different feedlots ranged from 0% to a high of 57%. A statistically significant (P = 0.003) positive correlation was determined to exist between the density of cattle and the E. coli O157 prevalence rate. A significant correlation (P = 0.006) was also found between the E. coli O157 percent prevalence and the number of cattle housed/capacity ratio. All 194 E. coli O157 isolates obtained were highly virulent, and random amplified polymorphic DNA PCR analysis revealed that the isolates grouped into 39 different E. coli O157 subtypes, most of which were indigenous to specific feedlots. Two of the most predominant subtypes were detected in 11 different feedlots and formed distinct clusters in two geographic regions in the province. Antimicrobial susceptibility testing of the E. coli O157 isolates revealed that 10 were multidrug resistant and that 73 and 5 were resistant to sulfisoxazole and tetracycline, respectively.

Lactobacillus paracasei A survives gastrointestinal passage and affects the fecal microbiota of healthy infants

This study focuses on the potentiality of a putative probiotic strain, Lactobacillus paracasei A, to survive gastrointestinal (GI) passage and modulate the resident microbiota of healthy infants. In a placebo-controlled study, 26 children aged 12-24 months received 100 g/day of either fermented milk containing strain A or pasteurized yogurt for four weeks. Fecal samples were analyzed before starting the administration, after 1, 3 and 4 weeks of consumption and after washout. The fate of strain A was followed by means of a newly developed PCR targeting a strain-specific genomic marker. The composition and dynamics of fecal microbial communities during the study were analyzed by culturing on selective media and by the PCR-denaturing gradient gel electrophoresis (DGGE) technique using universal and group-specific (Lactobacillus and Bifidobacterium) primers. The variation in enzymatic activities in infant feces during probiotic consumption was also analyzed. Strain A survived in fecal samples in most (92%) of the infants examined after 1 week of consumption, and temporarily dominated the intestinal Lactobacillus community. The administration of L. paracasei A led to a significant increment in the Lactobacillus population, while a moderate effect upon the main bacterial groups in the GI ecosystem was observed. Strain A also affected the diversity of the Lactobacillus and Bifidobacterium populations. The fecal bacterial structure of 1 - 2-year-old infants seems to combine neonate and adult-like features. The microbiota of these subjects promptly responded to probiotic consumption, later restoring the endogenous equilibrium.

Lactobacillus durianis Leisner et al. 2002 is a later heterotypic synonym of Lactobacillus vaccinostercus Kozaki and Okada 1983

The taxonomic status of the species Lactobacillus durianis and Lactobacillus vaccinostercus is briefly summarized and experimental evidence concerning their similarity is presented. Highly similar 16S rRNA gene sequences (99.8 % similarity over 1523 bp), partial recA gene sequences (99.5 % similarity over 600 bp) and partial hsp60 gene sequences (99.1 % similarity over 924 bp) suggest that the two species are closely related. Moreover, a high DNA–DNA binding level (87 %) and similar genomic DNA G+C contents (41–44 mol% for both species) as well as similar biochemical characteristics support the evidence that they constitute a single species. Consequently, according to Rules 38 and 42 of the Bacteriological Code, the name Lactobacillus vaccinostercus, the oldest legitimate name, must be maintained and the name Lactobacillus durianis should be considered a later heterotypic synonym.

Gain and loss of multiple genes during the evolution of Helicobacter pylori

Sequence diversity and gene content distinguish most isolates of Helicobacter pylori. Even greater sequence differences differentiate distinct populations of H. pylori from different continents, but it was not clear whether these populations also differ in gene content. To address this question, we tested 56 globally representative strains of H. pylori and four strains of Helicobacter acinonychis with whole genome microarrays. Of the weighted average of 1,531 genes present in the two sequenced genomes, 25% are absent in at least one strain of H. pylori and 21% were absent or variable in H. acinonychis. We extrapolate that the core genome present in all isolates of H. pylori contains 1,111 genes. Variable genes tend to be small and possess unusual GC content; many of them have probably been imported by horizontal gene transfer. Phylogenetic trees based on the microarray data differ from those based on sequences of seven genes from the core genome. These discrepancies are due to homoplasies resulting from independent gene loss by deletion or recombination in multiple strains, which distort phylogenetic patterns. The patterns of these discrepancies versus population structure allow a reconstruction of the timing of the acquisition of variable genes within this species. Variable genes that are located within the cag pathogenicity island were apparently first acquired en bloc after speciation. In contrast, most other variable genes are of unknown function or encode restriction/modification enzymes, transposases, or outer membrane proteins. These seem to have been acquired prior to speciation of H. pylori and were subsequently lost by convergent evolution within individual strains. Thus, the use of microarrays can reveal patterns of gene gain or loss when examined within a phylogenetic context that is based on sequences of core genes.

Genotypic analysis of Acinetobacter bloodstream infection isolates in a Turkish university hospital

Acinetobacter baumannii is a significant pathogen of bloodstream infections in hospital patients that frequently causes single clone outbreaks. We aimed to evaluate the genetic relatedness and antimicrobial susceptibility of Acinetobacter spp. bloodstream isolates, in order to obtain insight into their cross-transmission. This prospective study was conducted at the Erciyes University Hospital. During a 1-y period, all patients with nosocomial BSI caused by Acinetobacter spp. were included in the study. All data with regard to the patients, underlying diseases and risk factors for BSI and the severity of disease were collected. Blood culture isolates of Acinetobacter spp. were identified according to their morphology and biochemical reactions. The antimicrobial susceptibility was determined using the Kirby-Bauer disk diffusion test according to the NCCLS; the genetic relatedness of isolates was determined by RAPD-PCR analysis and pulsed-field gel electrophoresis (PFGE). 41 patients acquired a nosocomial bloodstream infection caused by A. baumanii during this period. 88% of these infections (36 of 41) occurred while the patients were treated in the intensive care unit. Nearly 80% of the isolates belonged to 3 genotypes, suggesting cross-transmission in ICU settings where infection control practices are poor. All Acinetobacter isolates were multidrug-resistant and the crude mortality of patients infected with A. baumanii was 80.5%. We concluded that the genetic relatedness of Acinetobacter spp. causing BSI was very high, indicating cross-transmission within the ICU setting. Essential components of an infection control programme to prevent nosocomial transmission of A. baumannii are early detection of colonized patients, followed by strict attention to standard precautions and contact isolation.

Host Lewis phenotype-dependent Helicobacter pylori Lewis antigen expression in rhesus monkeys

Both human and H. pylori populations are polymorphic for the expression of Lewis antigens. Using an experimental H. pylori challenge of rhesus monkeys of differing Lewis phenotypes, we aimed to determine whether H. pylori populations adapt their Lewis phenotypes to those of their hosts. After inoculation of four monkeys with a mixture of seven strains identified by RAPD-polymerase chain reaction, H. pylori Lewis expression was followed in 86 isolates obtained over 40 wk. Host Lewis(a/b) secretion status was characterized by immunological assays. Fingerprints of the predominating strain (J166) were identical in all four animals after 40 wk, but its Lewis phenotype had substantial variability in individual hosts. At 40 wk, J166 populations from two Lewis(a-b+) animals predominantly expressed Lewis(y). In contrast, J166 populations had switched to a Lewis(x) dominant phenotype in the two Lewis(a+b-) animals; a frame shift in futC, regulating conversion of Lewis(x) to Lewis(y), accounted for the phenotypic switch. The results indicate that individual cells in H. pylori populations can change Lewis phenotypes during long-term colonization of natural hosts to resemble those of their hosts, providing evidence for host selection for bacterial phenotypes.

Volatile sulfur compounds produced by Helicobacter pylori

GOALS

To assess the volatile sulfur compounds produced by three strains of Helicobacter pylori in broth cultures mixed with sulfur-containing amino acids.

BACKGROUND

Halitosis has been reported in H. pylori-positive patients, and volatile sulfur compounds such as hydrogen sulfide and methyl mercaptan are known to be responsible for inducing oral malodor. Whether H. pylori produces these volatile sulfur compounds has yet to be established.

STUDY

Three strains of H. pylori (ATCC 43504, SS 1, DSM 4867) were cultured with 5 mM cysteine and methionine. After 72 hours of incubation, the headspace air was aspirated and injected directly into a gas chromatograph. The concentrations of hydrogen sulfide and methyl mercaptan were analyzed and compared between experimental and control cultures

RESULTS

In broth containing 5 mM cysteine, hydrogen sulfide was increased by ATCC 43504 (P < 0.01) and SS 1 (P < 0.05), while methyl mercaptan was elevated only by SS 1 (P < 0.05). In broth containing 5 mM methionine, methyl mercaptan increases were significant for SS 1 (P < 0.05) and DSM 4867 (P < 0.05). In broth containing 5 mM cysteine and 5 mM methionine, the concentration of hydrogen sulfide was higher than in controls for all three strains (P < 0.01); that of methyl mercaptan was higher only for SS 1 (P < 0.01). Cysteine addition to cultures containing methionine increased hydrogen sulfide and methyl mercaptan for ATCC 43504 (P < 0.05) and SS 1 (P < 0.05). Conversely, addition of methionine to cultures containing cysteine increased methyl mercaptan only for DSM 4867 (P < 0.01).

CONCLUSIONS

The production of volatile sulfur compounds by H. pylori is not only very complicated but also strain-specific. Nevertheless, H. pylori was shown to produce hydrogen sulfide and methyl mercaptan, which suggests that this microorganism can contribute to the development of halitosis.

Reinfection after successful eradication of Helicobacter pylori: a 2-year prospective study in Alaska Natives

BACKGROUND

Limited information exists regarding risk factors for reinfection after cure of Helicobacter pylori infection.

AIM

To determine the 2-year reinfection rate of H. pylori in a cohort of urban Alaska Natives.

METHODS

Participants over 18 years of age undergoing oesophagogastroduodenoscopy had (13)C urea breath test, culture, CLOtest and histology performed. Those diagnosed with H. pylori who tested urea breath test-negative at 8 weeks after treatment were followed prospectively at 4 months, 6 months, 1 year and 2 years. Subjects experiencing H. pylori reinfection as defined by a positive urea breath test were compared with those who did not become reinfected using univariable and multivariable analysis. Risk of reinfection over time was estimated by the Kaplan-Meier method.

RESULTS

Helicobacter pylori reinfection occurred in 14 of 98 subjects successfully treated. The cumulative reinfection rate was 5.1% (95% CI: 0.7%-9.5%) at 4 months, 7.2% (2.0-12.3%) at 6 months, 10.3% (4.2-16.3%) at 1-year and 14.5% (7.5-21.6%) at 2 years. In multivariable analysis, a history of previous peptic ulcer disease or presence of ulcer at time of study oesophagogastroduodenoscopy were the only risk factors associated with reinfection (P = 0.01).

CONCLUSIONS

Based on the findings from our study, subjects with a history of or current peptic ulcer disease should be followed, after successful treatment for H. pylori, with periodic urea breath test to detect reinfection, as reinfection would put them at high risk for ulcer recurrence.

CMY-16, a novel acquired AmpC-type beta-lactamase of the CMY/LAT lineage in multifocal monophyletic isolates of Proteus mirabilis from northern Italy

We report multifocal detection (four different cities in northern Italy) of Proteus mirabilis isolates resistant to both oxyimino- and 7-alpha-methoxy-cephalosporins and producing a novel acquired AmpC-like beta-lactamase. The enzyme, named CMY-16, is a variant of the CMY/LAT lineage, which differs from the closest homologues, CMY-4 and CMY-12, by a single amino acid substitution (A171S or N363S, respectively) and from CMY-2 by two substitutions (A171S and W221R). Expression of the cloned bla(CMY-16) gene in Escherichia coli decreased susceptibility to penicillins, cephalosporins, and aztreonam. Tazobactam was more effective than clavulanate at antagonizing the enzyme activity. Genotyping, by random amplification of polymorphic DNA and pulsed-field gel electrophoresis of genomic DNA digested with SfiI, showed that isolates were clonally related to each other, although not identical. The bla(CMY-16) gene was not transferable to E. coli by conjugation or transformation. In all isolates, it was chromosomally located and inserted in a conserved genetic environment. PCR mapping experiments revealed that the bla(CMY-16) was flanked by ISEcp1 and the blc gene, similar to other genes of this lineage from plasmids of Salmonella enterica, Klebsiella spp., and E. coli. Overall, these results revealed multifocal spreading of a CMY-16-producing P. mirabilis clone in northern Italy. This finding represents the first report of an acquired AmpC-like beta-lactamase in Proteus mirabilis from Italy and underscores the emergence of similar resistance determinants in the European setting.

Molecular characterization of Haemophilus ducreyi isolates from different geographical locations

The technique of random amplified polymorphic DNA (RAPD) was adapted and optimized to study Haemophilus ducreyi isolates. A panel of 43 strains isolated from chancroid patients from different countries in Africa, Europe, North America, and Asia were characterized. The strains were also studied with respect to lipooligosaccharide (LOS) migration and immunoblotting patterns and the presence of cytolethal distending toxin genes. The RAPD method with the OPJ20 primer generated nine banding patterns (1 to 9). The majority of the isolates were clustered into two major profiles, 14 and 13 strains into profiles 1 and 2, respectively, and just a few strains revealed patterns 3 and 4. The isolates from Thailand were exceptional in that they showed greater diversity and were represented by six different RAPD patterns, i.e., patterns 3 and 5 to 9. The LOS migration and immunoblotting analyses revealed two different patterns, which indicated long and short forms of LOS; the former was found in 20/23 tested strains. Two strains that expressed the short form of LOS were grouped into RAPD pattern 4. The absence of cdtABC genes was observed in only 4/23 strains, and three of these isolates were assigned to RAPD pattern 4. Our results showed limited genotypic and phenotypic variations among H. ducreyi strains, as supported by the conserved RAPD and LOS profiles shared by the majority of the studied strains. However, the RAPD method identified differences between strains, including those from different geographic areas, which indicate the potential of RAPD as an epidemiological tool for the typing of H. ducreyi isolates in countries where chancroid is endemic.

Staphylococcus aureus isolates from Irish domestic refrigerators possess novel enterotoxin and enterotoxin-like genes and are clonal in nature

A previous study carried out by the National Food Centre in Dublin on bacterial contamination of Irish domestic refrigeration systems revealed that 41% were contaminated with Staphylococcus aureus. One hundred fifty-seven S. aureus isolates were screened by multiplex PCR analysis for the presence of 15 staphylococcal enterotoxin and enterotoxin-like genes (sea-see, seg-sei, selj-selo, and selq) and the toxic shock toxin superantigen tst gene. Of the refrigerator isolates, 64.3% possessed more than one staphylococcal enterotoxin or staphylococcal enterotoxin-like gene. All bar one of the 101 staphylococcal enterotoxin or staphylococcal enterotoxin-like gene-positive strains possessed the egc locus bearing the seg, sei, selm, seln, and selo genes. Twelve random amplified polymorphic DNA (RAPD) types accounted for 119 (75.8%) of the strains, two of these types accounting for 25 (RAPD type 1, 15.9%) and 52 (RAPD type 5, 33.1%), respectively. All of the RAPD type 5 isolates possessed the egc gene cluster only. The RAPD type 5 amplicon profile was identical to that of S. aureus isolates associated with osteomyelitis in broiler chickens in Northern Ireland that also possessed the egc locus only. However, the RAPD type 5 domestic refrigerator and chicken isolates differed in penicillin G sensitivity, production of Protein A and staphylokinase, and crystal violet agar growth type. These findings highlight that the average Irish household refrigerator harbors potential enterotoxin-producing S. aureus that may or may not be of animal origin and, accordingly, is a potential reservoir for staphylococcal food poisoning.

Validation of string test for diagnosis of Helicobacter pylori infections

The method of recovering Helicobacter pylori DNA or viable cells absorbed on a string that a person has swallowed and that is retrieved an hour later (string test) should be a useful alternative to traditional analysis of cells or DNA obtained by endoscopy, which is invasive, uncomfortable, relatively costly, and ill-suited for community-based and pediatric studies. Here we assayed the sensitivity and validity of the string test versus conventional endoscopic biopsy for detecting and analyzing H. pylori infection. Forty-four people with gastric complaints were studied using both H. pylori culture and urease gene (ureB) PCR. H. pylori organisms cultured from strings and biopsy specimens from the same patients were fingerprinted by the randomly amplified polymorphic DNA (RAPD) method. Biopsy sections were also hematoxylin and eosin and silver stained for H. pylori detection. H. pylori was cultured from 80% of strings and detected by PCR from 91% of strings from participants whose biopsies had been H. pylori positive by culture, PCR, and/or histology. Strains recovered from strings and biopsy specimens yielded identical or closely related RAPD profiles in each of the 24 cases tested. We conclude that the string test is a useful method for H. pylori recovery and analysis when relatively noninvasive procedures are needed.

Association of antibiotic resistance and higher internalization activity in resistant Helicobacter pylori isolates

OBJECTIVES

Helicobacter pylori resistance to antibiotics is the main factor for therapy failure, while other features remain largely unknown. The aims of this study are to investigate the relationship of antibiotic resistance and in vitro internalization activity between cure and failure isolates and to determine whether failures are associated with persistence of the same predominant strain.

METHODS

Fifty-three isolates from forty-seven patients (cure group, n = 31; failure group, n = 16) receiving one of two lansoprazole-based therapies before and/or after therapy were investigated. Antibiotic susceptibility was determined by Etest. Genotyping was determined by cagA, babA, vacA and RAPD analyses. Target cells of internalization assay were AGS cells.

RESULTS

Five of six paired pre- and post-treatment isolates had the same predominant genetic profiles and exhibited similarly high internalization activities. The A2143G point mutation of the 23S rRNA gene conferred clarithromycin resistance. Moreover, increased antibiotic resistance after therapy was found for these five cases. Pre-treatment isolates from the failure group (n = 11) had higher level of internalization activity than those from the cure group (n = 31) (P = 0.00005). Antibiotic-resistant strains were significantly associated with higher internalization activity than were susceptible strains (metronidazole, P < 0.005; clarithromycin, P < 0.005).

CONCLUSIONS

Our results suggest that resistant H. pylori strains are associated with antibiotic resistance and superior internalization activity, protecting them against antibiotic treatment.

Conjugative plasmid DNA transfer in Helicobacter pylori mediated by chromosomally encoded relaxase and TraG-like proteins

One of the striking characteristics of Helicobacter pylori is the extensive genetic diversity among clinical isolates. This diversity has been attributed to an elevated mutation rate, impaired DNA repair, DNA transfer and frequent recombination events. Plasmids have also been identified in H. pylori but it remained unknown whether conjugation can contribute to DNA transfer between clinical isolates. To examine whether H. pylori possesses intrinsic capability for conjugative plasmid transfer, shuttle vectors were introduced into H. pylori containing an oriT sequence of the conjugative IncPalpha plasmid RP4 but no mobilization (mob) genes. It was shown that these vectors could stably replicate and be mobilized among clinical H. pylori strains. It was also demonstrated that traG and relaxase (rlx) homologues carried on the H. pylori chromosome were important for plasmid transfer. Primer extension studies and mutagenesis further confirmed that the relaxase homologue rlx1 in H. pylori encodes a functional enzyme capable of acting on the RP4 oriT. Furthermore, the findings of this study indicate that traG and rlx1 act independently of the previously described type IV secretion systems, including that encoded by the cag pathogenicity island and the comB transformation apparatus, in mediating conjugative plasmid DNA transfer between H. pylori strains.

Damage effect of different genotype of Helicobacter pylori on human gastric epithelial cell line GES-1 in high- and low-risk areas of gastric cancer

AIM: To investigate the damage effect of the different genotypes of Helicobacter pylori (H. pylori) on human gastric epit-helial cell line GES-1 in high- and low-risk areas of ga-stric cancer, and to explore its related mechanism.

METHODS: H. pylori were identified by hematoxylin-eosin (HE) staining, Gimsa staining, and Warthin-Starry silver staining. The DNA was obtained by proteinase K and phenol-chloroform extraction method. The cagA, vacAs1/s2, m1a, m1b, and m2 gene were amplified by polymerase chain reaction (PCR). The damage eff-ects of H. pylori with differential sub-genotypes and 2 other non-differential genotypes on GES-1 cells were observed by cell and H. pylori co-culture. The expression of 8-OHdG in GES-1 cells was detected by S-P immun-ohistochemistry.

RESULTS: GES-1 cells were seriously damaged by H. pylori. With the prolongation of the co-culture time, the morphology of GES-1 cells were changed from spindle to round, and the nuclei showed chromatin pyknosis and clustered on the inner border of karyon. The cytoplasm condensed and blebbing appeared. The numbers of the dead and damaged cells were increas-ing. The damage effect of H. pylori with differential ge-notypes on GES-1 cells was more serious than that of the non-differential genotypes. The expression of 8-OHdG were almost all negative (0.5% positive) in GES-1 cells of the normal controls, while the positive rate was 98.5% in the H. pylori treatment cells (P < 0.01).

CONCLUSION: H. pylori with cagA⁺, vacAs1⁺/m1b⁺ ge-notypes in the high-risk area of gastric cancer have more serious damage effects on gastric cancer cell line GES-1, and they can promote the transformation of normal gastric epithelial cells to malignant cells by up-regulation of 8-OHdG expression.

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.

Comparison of genotyping methods by application to Salmonella livingstone strains associated with an outbreak of human salmonellosis

During 2000 and 2001, an outbreak of human salmonellosis occurred in Sweden and Norway, caused by Salmonella livingstone. In this study, the genotypic differences between three strains obtained from food sources during the outbreak, two human strains and 27 more or less unrelated strains were analysed, using the three methods; automated ribotyping, pulsed field gel electrophoresis (PFGE) and randomly amplified polymorphic DNA (RAPD). Each method was evaluated regarding its discriminatory ability, reproducibility and typeability. Simpson's discriminatory index calculated for each method was 0.556 for automated ribotyping, 0.766 for PFGE and 0.236 for RAPD. The reproducibility, defined as the minimum similarity between individual replicates in a cluster analysis, was 96% for automated ribotyping and PFGE, and 90% for RAPD. All the strains were typeable with each method. When combining results for the three genotyping methods, it was found that RAPD did not increase the discriminatory index and was therefore excluded from further analysis. Using a combination of the results obtained from ribotyping and PFGE (D=0.855), two strains that had been isolated from feed factories during 1998 were shown to be identical to the outbreak strain, indicating a possible route of contamination due to a clone of Salmonella livingstone persisting in feed producing facilities. No connection to poultry was established.

Diverse phenotypes resulting from polyphosphate kinase gene (ppk1) inactivation in different strains of Helicobacter pylori

Connections among biochemical pathways should help buffer organisms against environmental stress and affect the pace and trajectory of genome evolution. To explore these ideas, we studied consequences of inactivating the gene for polyphosphate kinase 1 (ppk1) in strains of Helicobacter pylori, a genetically diverse gastric pathogen. The PPK1 enzyme catalyzes synthesis of inorganic polyphosphate (poly P), a reservoir of high-energy phosphate bonds with multiple roles. Prior analyses in less-fastidious microbes had implicated poly P in stress resistance, motility, and virulence. In our studies, ppk1 inactivation caused the expected near-complete absence of poly P (>250-fold decrease) but had phenotypic effects that differed markedly among unrelated strains: (i) poor initial growth on standard brain heart infusion agar (five of six strains tested); (ii) weakened colonization of mice (4 of 5 strains); (iii) reduced growth on Ham's F-12 agar, a nutritionally limiting medium (8 of 11 strains); (iv) heightened susceptibility to metronidazole (6 of 17 strains); and (v) decreased motility in soft agar (1 of 13 strains). Complementation tests confirmed that the lack of growth of one Deltappk1 strain on F-12 agar and the inability to colonize mice of another were each due to ppk1 inactivation. Thus, the importance of ppk1 to H. pylori differed among strains and the phenotypes monitored. We suggest that quantitative interactions, as seen here, are common among genes that affect metabolic pathways and that H. pylori's high genetic diversity makes it well suited for studies of such interactions, their underlying mechanisms, and their evolutionary consequences.

Pathogen evolution in vivo: genome dynamics of two isolates obtained 9 years apart from a duodenal ulcer patient infected with a single Helicobacter pylori strain

The survival and microevolution of Helicobacter pylori strains in the niches of the stomach after eradication therapy have largely been unexplored. We analyzed genomic signatures for two successive isolates obtained 9 years apart from a duodenal ulcer patient who underwent eradication therapy for H. pylori. These isolates were genotyped based on 50 different parameters involving three different fingerprinting approaches and several evolutionarily significant and virulence-associated landmarks in the genome, including nine informative gene loci, the cag pathogenicity island and its right junction, members of the plasticity region cluster, and vacA and iceA alleles. Our observations reveal that the two isolates were derived from the same strain that colonized the patient for almost a decade and were almost identical. Microevolution, however, was observed in the cagA gene and its right junction, the vacA m1 allele, and a member of the plasticity region cluster (JHP926). These results suggest that H. pylori has a great ability to survive and reemerge as a microevolved strain posteradication, thereby hinting at the requirement for follow-up of patients after therapy.

Genetic divergence of Campylobacter fetus strains of mammal and reptile origins

Campylobacter fetus is a gram-negative bacterial pathogen of both humans and animals. Two subspecies have been identified, Campylobacter fetus subsp. fetus and Campylobacter fetus subsp. venerealis, and there are two serotypes, A and B. To further investigate the genetic diversity among C. fetus strains of different origins, subspecies, and serotypes, we performed multiple genetic analyses by utilizing random amplification of polymorphic DNA (RAPD), pulsed-field gel electrophoresis (PFGE), and DNA-DNA hybridization. All 10 primers used for the RAPD analyses can distinguish C. fetus strains of reptile and mammal origin, five can differentiate between C. fetus subsp. fetus and C. fetus subsp. venerealis strains, and four showed differences between type A and type B isolates from mammals. PFGE with SmaI and SalI digestion showed varied genome patterns among different C. fetus strains, but for mammalian C. fetus isolates, genome size was well conserved (mean, 1.52 +/- 0.06 Mb for SmaI and 1.52 +/- 0.05 Mb for SalI). DNA-DNA hybridization demonstrated substantial genomic-homology differences between strains of mammal and reptile origin. In total, these data suggest that C. fetus subsp fetus strains of reptile and mammal origin have genetic divergence more extensive than that between the two subspecies and that between the type A and type B strains. Combining these studies with sequence data, we conclude that there has been substantial genetic divergence between Campylobacter fetus of reptile and mammal origin. Diagnostic tools have been developed to differentiate among C. fetus isolates for taxonomic and epidemiologic uses.

Slow genetic divergence of Helicobacter pylori strains during long-term colonization

The genetic variability of Helicobacter pylori is known to be high compared to that of many other bacterial species. H. pylori is adapted to the human stomach, where it persists for decades, and adaptation to each host results in every individual harboring a distinctive bacterial population. Although clonal variants may exist within such a population, all isolates are generally genetically related and thus derived from a common ancestor. We sought to determine the rate of genetic change of H. pylori over 9 years in two asymptomatic adult patients. Arbitrary primed PCR confirmed the relatedness of individual subclones within a patient. Furthermore, sequencing of 10 loci ( approximately 6,000 bp) in three subclones per time and patient revealed only two base pair changes among the subclones from patient I. All sequences were identical among the patient II subclones. However, PCR amplification of the highly divergent gene amiA revealed great variation in the size of the gene between the subclones within each patient. Thus, both patients harbored a single strain with clonal variants at both times. We also studied genetic changes in culture- and mouse-passaged strains, and under both conditions no genetic divergence was found. These results suggest that previous estimates of the rate of genetic change in H. pylori within an individual might be overestimates.

Tn7 distribution in Helicobacter pylori: a selective paradox

The presence of class 1, 2 and 3 integrons in Helicobacter pylori, which in other species are usually related to antimicrobial resistance, were looked for in 40 epidemiologically-unrelated isolates. The presence of the class 2 integrase, which led to the discovery of Tn7, was found in 15 of 35 different clones identified by lspA-glmM polymorphism. MIC values for trimethoprim and streptomycin were not affected by the presence or absence of dfrA1 and aadA1 genes. The polyclonal spread of Tn7 showed the ability of H. pylori to harbour antimicrobial resistance mechanisms, usually located on plasmids, and also suggested that other important mechanisms of resistance may also be acquired, which would result in failure of chemotherapy.