H. pylori DNA Fingerprinting Using the Arbitrarily Primed PCR (AP-PCR) or Random Amplified Polymorphic DNA (RAPD) Method

2003 ◽  
pp. 117-132 ◽  
Author(s):  
Douglas E. Berg ◽  
Janaki Lelwala-Guruge ◽  
Engin T. Incecik ◽  
Kalpana Srivastava ◽  
Natalia S. Akopyants
Keyword(s):  
Dna Fingerprinting ◽  
Random Amplified Polymorphic Dna ◽  
H Pylori ◽  
Arbitrarily Primed Pcr ◽  
Rapd Method

scholarly journals Effectiveness of Enterobacterial Repetitive Intergenic Consensus PCR and Random Amplified Polymorphic DNA Fingerprinting for Helicobacter pylori Strain Differentiation

2006 ◽  
Vol 72 (7) ◽  
pp. 4713-4716 ◽  
Author(s):  
S. Alison Finger ◽  
Billie Velapatiño ◽  
Margaret Kosek ◽  
Livia Santivañez ◽  
Daiva Dailidiene ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Gene Transfer ◽  
Dna Fingerprinting ◽  
Efficient Method ◽  
Random Amplified Polymorphic Dna ◽  
Kappa Statistic ◽  
Enterobacterial Repetitive Intergenic Consensus ◽  
Strain Differentiation ◽  
H Pylori ◽  
Fingerprinting Methods

ABSTRACT 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.

scholarly journals Reproducible DNA fingerprinting with the random amplified polymorphic DNA (RAPD) method

1994 ◽  
Vol 22 (10) ◽  
pp. 1921-1922 ◽  
Author(s):  
Maria Rita Micheli ◽  
Rodolfo Bova ◽  
Esterina Pascale ◽  
Ettore D'Ambrosio
Keyword(s):  
Dna Fingerprinting ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Method

scholarly journals Dissemination of Two Methicillin-Resistant Staphylococcus aureus Clones Exhibiting Negative Staphylase Reactions in Intensive Care Units

1999 ◽  
Vol 37 (3) ◽  
pp. 504-509 ◽  
Author(s):  
Po-Ren Hsueh ◽  
Lee-Jene Teng ◽  
Pan-Chyr Yang ◽  
Hui-Ju Pan ◽  
Yu-Chi Chen ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Intensive Care ◽  
Intensive Care Units ◽  
Random Amplified Polymorphic Dna ◽  
Cellular Fatty Acid ◽  
University Hospital ◽  
Methicillin Resistant ◽  
Type Iv ◽  
Routine Identification ◽  
Arbitrarily Primed Pcr

From December 1997 to March 1998, 25 methicillin-resistantStaphylococcus aureus (MRSA) isolates exhibiting negative Staphylase (Oxoid Ltd., Basingstoke, England) reactions were identified from various clinical specimens from 13 patients in six intensive care units (ICUs) or in wards following a stay in an ICU at the National Taiwan University Hospital. The characteristics of these isolates have not been previously noted in other MRSA isolates from this hospital. Colonies of all these isolates were grown on Trypticase soy agar supplemented with 5% sheep blood and were nonhemolytic and unpigmented. Seven isolates, initially reported as Staphylococcus haemolyticus (5 isolates) and Staphylococcus epidermidis (2 isolates) by the routine identification scheme and with the Vitek GPI system (bioMerieux Vitek, Inc., Hazelwood, Mo.), were subsequently identified as S. aureus by positive tube coagulase tests, standard biochemical reactions, and characteristic cellular fatty acid chromatograms. The antibiotypes obtained by the E test, coagulase types, restriction fragment length polymorphism profiles of the staphylococcal coagulase gene, and random amplified polymorphic DNA patterns generated by arbitrarily primed PCR of the isolates disclosed that two major clones disseminated in the ICUs. Clone 1 (16 isolates) was resistant to clindamycin and was susceptible to trimethoprim-sulfamethoxazole (TMP-SMZ) and was coagulase type II. Clone 2 (eight isolates) was resistant to clindamycin and TMP-SMZ and was coagulase type IV. These two epidemic clones from ICUs are unique and underline the need for caution in identifying MRSA strains with colonial morphologies not of the typical type and with negative Staphylase reactions.

scholarly journals Nitazoxanide, a Potential Drug for Eradication ofHelicobacter pylori with No Cross-Resistance to Metronidazole

1998 ◽  
Vol 42 (11) ◽  
pp. 2836-2840 ◽  
Author(s):  
Francis Mégraud ◽  
Alessandra Occhialini ◽  
Jean François Rossignol
Keyword(s):  
Pilot Study ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Acquired Resistance ◽  
Anaerobic Bacteria ◽  
Antimicrobial Properties ◽  
Cross Resistance ◽  
Treatment Regimens ◽  
H Pylori

ABSTRACT Nitazoxanide, a thiazolide compound, and its desacetyl derivative, tizoxanide, have antimicrobial properties against anaerobic bacteria, as well as against helminths and protozoa. Because the treatment ofHelicobacter pylori infection may be jeopardized by metronidazole resistance, nitazoxanide and tizoxanide were tested in vitro against these bacteria. The MICs of these two compounds were determined by agar dilution and were compared to those of metronidazole. Exposure to subinhibitory concentrations of nitazoxanide was also carried out by the method of Szybalski (W. Szybalski and V. Bryson, J. Bacteriol. 64:489–499, 1952). The MICs of nitazoxanide and tizoxanide for 103 strains ranged from 0.25 to 8 μg/ml, with the MIC at which 50% of strains are inhibited (MIC50) being 1 μg/ml and the MIC90 being 4 μg/ml, and no resistant strain was detected, whereas strains resistant to metronidazole were detected. When 10 strains were successively subcultured on medium containing nitazoxanide, no significant change in the MICs of this compound was observed. A pilot study of nitazoxanide for the treatment of H. pyloriinfection was carried out with 86 patients in association with 20 mg of omeprazole. An eradication rate of 83% (95% confidence interval, 64% to 94%) was obtained in a per-protocol analysis in the group receiving 1 g of nitazoxanide orally twice daily, and a few side effects were observed. The failures could not be explained by the selection of resistant strains since the MICs of nitazoxanide were similar for six pairs of isolates (proven to be the same strain by random amplified polymorphic DNA analysis in four cases) cultured before and after the treatment failure. Nitazoxanide exhibits good antimicrobial activity against H. pylori without the problem of acquired resistance which is encountered with metronidazole and has been demonstrated to have a satisfactory effect in a dose-ranging pilot study. It is therefore a good candidate to be included in treatment regimens aimed at the eradication of H. pylori.

scholarly journals Clonality Analysis ofHelicobacter pyloriin Patients Isolated from Several Biopsy Specimens and Gastric Juice in a Japanese Urban Population by Random Amplified Polymorphic DNA Fingerprinting

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Nariaki Toita ◽  
Shin-ichi Yokota ◽  
Nobuhiro Fujii ◽  
Mutsuko Konno
Keyword(s):  
Gastric Juice ◽  
Urban Population ◽  
Random Amplified Polymorphic Dna ◽  
Clonal Diversity ◽  
Japanese Patients ◽  
Upper Gastrointestinal Endoscopy ◽  
Rapd Fingerprinting ◽  
Biopsy Specimens ◽  
Single Host ◽  
H Pylori

Background. The number ofHelicobacter pyloriclones infecting a single host has been discussed in numerous reports. The number has been suggested to vary depending on the regions in the world.Aim. The purpose of this study was to examine the number of clones infecting a single host in a Japanese urban population.Materials and Methods. Thirty-one Japanese patients undergoing upper gastrointestinal endoscopy were enrolled in this study.H. pyloriisolates (total 104 strains) were obtained from biopsy specimens (antrum, corpus, and duodenum) and gastric juice. Clonal diversity was examined by the random amplified polymorphic DNA (RAPD) fingerprinting method.Results. The RAPD fingerprinting patterns of isolates from each patient were identical or very similar. And the isolates obtained from several patients with 5- to 9-year intervals showed identical or very similar RAPD patterns.Conclusion. Each Japanese individual of an urban population is predominantly infected with a singleH. pyloriclone.

Development of DNA fingerprinting keys for the identification of radish cultivars

2004 ◽  
Vol 44 (1) ◽  
pp. 95 ◽  
Author(s):  
A. Pradhan ◽  
G. Yan ◽  
J. A. Plummer
Keyword(s):  
Dna Fingerprinting ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Morphological Characteristics ◽  
Group Method ◽  
Base Pairs ◽  
Difference Matrix ◽  
Pair Group ◽  
Young Leaves ◽  
Polymerase Chain

Identification of cultivars is extremely important both for cultivation and breeding of crop plants. Cultivar identification based on morphological characteristics can be difficult and complicated. Polymerase chain reaction technologies, such as random amplified polymorphic DNA (RAPD) analysis, can readily and quickly identify cultivars using seeds and young leaves. Sixty individuals representing 7 radish cultivars were examined for RAPD marker polymorphism. Based on the polymorphism generated, 5 primers were selected, out of the 14��examined, to fingerprint the cultivars. The 5 primers produced a total of 52 fragments, 6 monomorphic and 46�polymorphic fragments, ranging in size from 206 to 2258 base pairs. A total and mean character difference matrix was calculated based on the RAPD data and a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA). Three DNA fingerprinting keys were developed for the 7 cultivars and 5 markers derived from 3 primers was the minimum required to distinguish cultivars. Results demonstrated that RAPD markers could be effectively used for the identification of radish cultivars.

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