Repetitive element palindromic pcr reppcr as a genetic. Bacterial repetitive extragenic palindromic sequences are. Request pdf use of repetitive element palindromic pcr reppcr for the. The obtained results suggest high heterogeneity of soybean microsymbionts. Emergence of a new antibiotic resistance mechanism in india, pakistan, and the. Molecular and epidemiological analysis of nosocomial. Bacterial repetitive extragenic palindromes reps compose a distinct group of genomic repeats. Bacterial repetitive extragenic palindromic sequences are dna. The term rep sequences encompasses repetitive and palindromic sequences with a length between 21 and 65 bases detected in the extragenic space of some bacterial genomes. We used repetitive element sequencebased pcr reppcr to evaluate the potential of rep and eric elements for typing l. The polymerase chain reaction pcr, first envisaged in 1984 by kary mullis, has revolutionized life sciences and has become an essential technique in many aspects of science, including clinical diagnostics, forensics and genetic engineering. Repetitive element sequence based polymerase chain reaction for. Pcr, as epidemiological tools with which to discriminate among genetically distinct strains within two bacterial fish pathogens, pseudomonas.
Repetitive extragenic palindromic polymerase chain reaction reppcr dna was isolated with an ultraclean microbial dna isolation kit mobio, san diego, ca, usa and used for experiments with the enterobacter spp. They usually occur in high abundance 100 copiesgenome and are often arranged in composite repetitive structures bacterial interspersed mosaic elements bimes. Pdf evaluation of uvc induced changes in escherichia coli. Evaluation of repetitive element sequencebased pcr as a molecular typing method for clostridium difficile. The aim of this study was to evaluate the use of two molecular techniques, repetitive extragenic palindromic polymerase chain reaction rep. Reppcr is a wellknown fast and reproducible method to distinguish closely related organisms on the basis of dna diversity 17.
Ercolini, 2004, repetitive extragenic palindromic pcr reppcr. Repetitive extragenic palindromic pcr reppcr pcr primer is designed complementary to interspersed palindromic repetitive sequences. This study was conducted to determine the esbl production and prevalence of blactxm1, blashv and blatem and ampc genes and repetitive extragenic palindromic polymerase chain reaction reppcr pattern among klebsiella. The repetitive extragenic palindromic rep sequence, also known as the palindrome unit, is a potential regulatory sequence located in the untranslated operon region based on its palindromic properties and the fact that the transcribed rna can form a stable stem. In the present study, we compared an automated repetitive extragenic palindromic sequencebased pcr reppcr method diversilab.
Primers directed at the repetitive extragenic palindromic element were used to characterize isolates of legioneula. African journal of biotechnology dna fingerprinting of. Use of repetitive sequences and the polymerase chain reaction to fingerprint the genomic dna of rhizobium galegae strains and to identify the dna obtained by sonicating the liquid cultures and root nodules. Reppcr has been successfully applied to strain typing both grampositive. Considering that there are a sufficient number of available genomes with described reps, and exploiting the advantage of. Repetitive extragenic palindromic sequence polymerase chain. Thedistribution ofdispersed repetitive dna repetitive extragenic palindromic rep andenterobacterial repetitive intergenic consensus eric sequences in the genomes ofa numberofgramnegative soil bacteria was examined by using conserved primers corresponding to repand ericsequences and the polymerase chainreaction pcr. Dna fingerprinting of thermophilic lactic acid bacteria. Use of rep repetitive extragenic palindromic and enterobacterial repetitive intergenic consensus sequences and the polymerase chain reaction to fingerprint the genomes of rhizobium meliloti.
Thus, reliable typing methods for epidemic control are needed. This media is currently being used in a largescale epidemiological study to genotype sm using repetitive extragenic palindromic pcr reppcr. Diversity of pseudomonas strains isolated with kings b and. The objective of this study was to investigate the potential of repetitive extragenic palindromic anchored polymerase chain reaction rep. Pcr, as epidemiological tools with which to discriminate among genetically distinct strains within two bacterial fish pathogens, pseudomonas anguilliseptica and aeromonas salmonicida. To compare repetitive sequencebased polymerase chain reaction. To analyze the mechanism by which the pora deletion occurred, the regions upstream and downstream of pora from three meningococcal strains h4476, h355, and 860183. Fingerprinting analyses by automated repetitive extragenic palindromicpolymerase chain reaction rep.
Application of repetitive extragenic palindromic elements. Evaluation of repetitive extragenic palindromicpolymerase chain reaction and denatured gradient gel electrophoresis in identifying salmonella serotypes isolated from processed turkeys. Repetitive sequence based polymerase chain reaction reppcr technique has been devised for characterization of bacteria and is widely employed to distinguish species, strains, serotypes, among others. Mitis salivarius with bacitracin msb, golds is a selective media commonly used for the isolation of streptococcus mutans sm, an organism associated with dental caries. Use of repetitive repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus sequences and the polymerase chain reaction to fingerprint the genomes of rhizobium meliloti isolates and other soil bacteria. Use of repetitive sequences and the polymerase chain reaction technique to. In the present study, we compared an automated repetitive extragenic palindromic sequencebased pcr reppcr. Fifty isolates of the most common uk strain of clostridium difficile polymerase chain reaction pcr ribotype 001 were analysed by three pcrbased typing methods in order to determine genomic diversity within this strain that may form the basis of a subtyping method. Comparison of repetitive extragenic palindromic sequencebased pcr with pcr ribotyping and pulsedfield gel.
Diversity of pseudomonas strains isolated with kings b. Pulsedfield gel electrophoresis pfge is considered the gold standard for molecular epidemiological study. Application of repetitive extragenic palindromic reppcr and. Within the pcr ribotype 001 isolates, repetitive extragenic palindromic sequencebased pcr allows the identification of four subgroups sub. Repetitive extragenic palindromic reppcr and enterobacterial repetitive intergenic consensus ericpcr analysis was applied to the identification and. Utility of wholecell repetitive extragenic palindromic sequencebased pcr. Repetitive element pcr journal of clinical microbiology asm. Utility of wholecell repetitive extragenic palindromic sequence. The three methods used were repetitive extragenic palindromic elements rep. Multilocus sequence typing mlst and repetitive extragenic palindromic polymerase chain reaction reppcr, characterization of shigella spp. Subtyping of clostridium difficile polymerase chain reaction pcr ribotype 001 by repetitive extragenic palindromic pcr genomic fingerprinting article in journal of hospital infection 601. This study reports the microbiologic, clinical, and epidemiologic features and the therapeutic outcomes of the infections caused by carbapenem and pandrugresistant klebsiella emerged in our hospital. To study the genetic diversity, we analysed molecular data from 79 singlespore isolates of the p.
All study isolates belonging to genetic clusters iii and vi were selected to evaluate the specificity of the enterobacterial repetitive intergenic consensus eric and repetitive extragenic palindromic rep polymerase chain reaction pcr for the identification of clonal isolates belonging to the e. Repetitive sequencebased pcr reppcr dna fingerprinting. This study was conducted to determine the esbl production and prevalence of blactxm1, blashv and blatem and ampc genes and repetitive extragenic palindromic polymerase chain reaction reppcr pattern among klebsiella pneumoniae isolates in. Typing of ochrobactrum anthropi clinical isolates using. Subtyping of clostridium difficile polymerase chain reaction.
We have determined that repetitive repetitive extragenic palindromic rep and enterobacterial repetitive intergenic consensus eric sequences used in conjunction with the polymerase chain reaction technique rep and eric pcr provide an effective means of differentiating between and classifying genetically related bradyrhizobium japonicum serocluster 123 strains. Mobile elements are involved in genomic rearrangements and virulence acquisition, and hence, are important elements in bacterial genome evolution. Pora is an important component in a vaccine against infection with neisseria meningitidis. Several studies have shown that reppcr has the ability to fingerprint strains of escherichia coli and k. Comparison of pulsed field gel electrophoresis and repetitive sequence polymerase chain reaction as genotyping methods for detection of genetic diversity and.
The distribution of dispersed repetitive dna repetitive extragenic palindromic rep and enterobacterial repetitive intergenic consensus eric sequences in the genomes of a number of gramnegative soil bacteria was examined by using conserved primers corresponding to rep and eric sequences and the polymerase chain reaction pcr. Sep 01, 2005 read specificity of enterobacterial repetitive intergenic consensus and repetitive extragenic palindromic polymerase chain reaction for the detection of clonality within the enterobacter cloacae complex, diagnostic microbiology and infectious disease on deepdyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips. Pdf evaluation of uvc induced changes in escherichia. It has been established that all studied strains are able to form active symbiotic relationships with soybean. Pcr products generated from the second and the third set of reactions yielded. Read specificity of enterobacterial repetitive intergenic consensus and repetitive extragenic palindromic polymerase chain reaction for the detection of clonality within the enterobacter cloacae complex, diagnostic microbiology and infectious disease on deepdyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips. The reppcr repetitive element palindromicpolymerase chain reaction. Repetitive extragenic palindromic polymerase chain reaction reppcr uses oligo primers with the conserved rep sequences originally found in escherichia coli. Detection of coliform bacteria in water by polymerase chain reaction and.
Pfge and reppcr provide comparable genotyping results for investigating streptococcus mutans diversity and transmission. Listeria monocytogenes strains possess short repetitive extragenic palindromic rep elements and enterobacterial repetitive intergenic consensus eric sequences. Rapd 6, 25, 30, and repetitive extragenomic palindromic elementspolymerase chain reaction reppcr, are used as reliable techniques compared to the highly inaccurate and timeconsuming. Feb 01, 2011 read comparison of repetitive extragenic palindromic sequence. Evaluation of repetitive element sequencebased pcr as a. Polymerase chain reaction based techniques such as denaturing gradient gel electrophoresis dgge. The function of rep elements is not completely determined but there are important processes in which rep sequences are involved. Use of repetitive sequences and the polymerase chain. Understand the principles of the polymerase chain reaction. Infections with carbapenemresistant enterobacteria are an emerging threat. Lanes m show dna reference marker sizes gibco brl in. Utilisation of enterobacterial repetitive intergenic.
Reppcr is defined as repetitive extragenic palindromic sequence polymerase chain reaction genetics very rarely. Repetitive extragenic palindromicpolymerase chain reaction reppcr uses oligo primers with the conserved rep sequences originally found in escherichia coli. Deletion of pora by recombination between clusters of. Typing of listeria monocytogenes strains by repetitive. How is repetitive extragenic palindromic sequence polymerase chain reaction genetics abbreviated. Molecular epidemiological analysis and risk factors for. Pdf use of rep repetitive extragenic palindromic and. Reppcr repetitive extragenic palindromic sequence polymerase chain reaction.
Repetitive extragenic palindromic reppcr and enterobacterial repetitive. Pdf application of repetitive extragenic palindromic elements. Detection of multiple strains of pasteurella multocida in fowl cholera outbreaks by polymerase chain reactionbased typing s. For example, the repetitive extragenic palindromic rep elements are 38bp. Synthetic repetitive extragenic palindromic rep sequence. Reppcr stands for repetitive extragenic palindromic sequence polymerase chain reaction genetics. Typing of ochrobactrum anthropi clinical isolates using automated repetitive extragenic palindromicpolymerase chain reaction dna fingerprinting and matrixassisted laser desorptionionizationtimeofflight mass spectrometry, bmc microbiology, 2014, pp. Subtyping of clostridium difficile polymerase chain. Repetitive extragenic palindromicpcr reppcr pcr primer is designed complementary to interspersed palindromic repetitive sequences. Fingerprinting analyses by automated repetitive extragenic palindromic polymerase chain reaction reppcr and matrixassisted laser desorptionionizationtime of flight malditof mass spectrometry are also compared. Osf repetitive extragenic palindromic pcr reppcr of oral.
Use of repetitive sequences and the polymerase chain reaction. Evaluation of repetitive extragenic palindromicpolymerase chain reaction and denatured gradient gel electrophoresis in identifying salmonella. Repetitive extragenic palindromic sequencebased reppcr profiles of the pcr ribotype 001 isolates. Evaluation of repetitive extragenic palindromicpolymerase. Synthetic repetitive extragenic palindromic rep sequence as. Specificity of enterobacterial repetitive intergenic. Evaluation of repetitive extragenic palindromic polymerase chain reaction and denatured gradient gel electrophoresis in identifying salmonella serotypes isolated from processed turkeys. Osf repetitive extragenic palindromic pcr reppcr of.
Utility of wholecell repetitive extragenic palindromic. Pcr in differentiating fecal escherichia coli isolates of human, domestic. Thedistribution ofdispersed repetitive dnarepetitive extragenic palindromic rep andenterobacterial repetitive intergenic consensus eric sequences in the genomes ofa numberofgramnegative soil bacteria was examined by using conserved primers corresponding to repand ericsequences and the polymerase chainreaction pcr. In bimes, regularly spaced reps are present in alternating orientations. However, pora negative meningococci were isolated from patients, thereby potentially limiting the role of poramediated immunity. Repetitive sequencebased pcr reppcr dna fingerprinting of. The phenotypic and genotypic features of soybean nodule bacteria with different growth rates common in soils of ukraine have been studied. The initial discovery of repetitive extragenic palindromic rep elements occurred in. Abstract the aim of this study was to evaluate the use of two molecular techniques, repetitive extragenic palindromic polymerase chain reaction reppcr and repetitive intergenic consensus pcr ericpcr, as epidemiological tools with which to discriminate among genetically distinct strains within two bacterial fish pathogens, pseudomonas anguilliseptica and aeromonas salmonicida. The distribution of dispersed repetitive dna repetitive extragenic palindromic rep.
Evaluation of uvc induced changes in escherichia coli dna using repetitive extragenic palindromicpolymerase chain reaction reppcr. The three methods used were repetitive extragenic palindromic elements rep, conserved repetitive dna elements box, and. Comparison of repetitive extragenic palindromic sequence. Read comparison of repetitive extragenic palindromic sequence. Repetitive extragenic palindromic pcr reppcr is less timeconsuming and more suitable for analyzing large numbers of bacterial strains in human populations.
Original article multilocus sequence typing mlst and. Tajabadi ebrahimi 2 abstract tarkhineh is one of the traditional foods in iran and a rich source of probiotic bacteria. Repetitive extragenic palindromic sequence polymerase. Molecular typing of klebsiella pneumoniae isolates using.
Primers directed at the repetitive extragenic palindromic element were used to characterize isolates of legioneula pneumophila. Detection of multiple strains of pasteurella multocida in. The study used the repetitive extragenic palindromic elementspolymerase chain reaction protocol to fingerprinting dna sequence diversity. It is repetitive extragenic palindromic sequence polymerase chain reaction. Use of repetitive repetitive extragenic palindromic and. The insertion of some specific insertion sequences had been associated with repetitive extragenic palindromic rep elements.
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