• Korean Journal of Food Science and Technology
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• v.37 no.6
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• pp.1005-1011
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• 2005

Widespread distributions of repetitive DNA elements in bacteria genomes are useful for analysis of genomes and should be exploited to differentiate food-borne pathogenic bacteria among and within species. Enterobacterial repetitive intergenic consensus (ERIC) sequence has been used for ERIC-PCR genomic fingerprinting to identify and differentiate bacterial strains from various environmental sources. ERIC-PCH genomic fingerprinting was applied to detect and differentiate four major Gram-negative food-borne bacterial pathogens, Esherichia coli, Salmonella, Shigella, and Vibrio. Target DNA fragments of pathogens were amplified by ERIC-PCR reactions. Dendrograms of subsequent PCR fingerprinting patterns for each strain were constructed, through which relative similarity coefficients or genetic distances between different strains were obtained numerically. Numerical comparisons revealed ERIC-PCR genotyping is effective for differentiation of strains among and within species of food-borne bacterial pathogens, showing ERIC-PCR fingerprinting methods can be utilized to differentiate isolates from outbreak and to determine their clonal relationships among outbreaks.

• Journal of Microbiology and Biotechnology
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• v.11 no.5
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• pp.788-797
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• 2001

The usefulness of three PCR methods were evaluated for the epidemiological typing of Staphylococcus aureus: an enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR), repetitive extragenic palindromic element PCR (REP-PCR), and 16S-23S intergenic spacer PCR (ITS-PCR). The analysis was performed using a collection of S. aureus strains comprised of 6 reference and 79 isolates from patients with various diseases. Among the 85 S. aureus strains tested, 6 references and 6 isolates were found to be susceptible to methicillin, whereas the remaining 73 isolates were resistant to it. PCR methods are of special concern, as conventional phenotypic methods are unable to clearly distinguish among methicillin-resistant S. aureus (MRSA) strains. The ability of the techniques to detect different unrelated types was found to be as follows: ERIC-PCR, 19 types; REP-PCR, 36 types; and ITS-PCR, 14 types. On the basis of combining the ERIC, REP, and ITS fingerprints, the 85 S. aureus strains were grouped into 56 genetic types (designated G1 to G56). The diversities for the 85 S. aureus strains, calculated according to Simpson\`s index, were 0.88 for an ERIC-PCR, 0.93 for a REP-PCR, and 0.48 for an ITS-PCR, and the diversity increased up to 0.97 when an ERIC-PCR and REP-PCR were combined. The above discrimination indices imply that the genetic heterogeneity of S. aureus strains is high. Accordingly, this study demonstrates that DNA sequences from highly conserved repeats of a genome, particularly a combination of ERIC sequences and REP elements, are a convenient and accurate tool for the subspecies-specific discrimination and epidemiologic tracking of S. aureus.

• Korean Journal of Clinical Laboratory Science
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• v.36 no.1
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• pp.1-6
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• 2004

The enterobacterial repetitive intergenic consensus (ERIC)-PCR is a recently described DNA fingerprinting technique based on amplification of repetitive element distributed in bacteria. We applied of ERIC-PCR to clinical isolates of Vibrio parahaemolyticus and other bacteria associated diarrhea. Twenty isolates of V. parahaemolyticus were used for intragenic genotyping, which were isolated from 2001 to 2002 in Chungbuk National University hospital. For interspecies genotyping, V. vulnificus, V. alginolyticus, V. parahaemolyticus, Escherichia coli, Salmonella and Shigella spp. were used. The genotyping were analyzed by ERIC-PCR. The genotyping of V. parahaemolyticus were grouped two major pattern (A, B) and were subdivided into 10 subtypes (A1, A2, B1-B8) by ERIC-PCR. These method distinctly differentiated bacterial species associated diarrhea. Those results show that ERIC-PCR can be reliable and efficient method for genotyping of V. parahaemolyticus and bacteria associated diarrhea.

• Journal of Life Science
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• v.13 no.5
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• pp.699-704
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• 2003

The results typed by random amplification of polymorphic DNA (RAPD) were compared with those obtained by Enterobacterial repititive intergenic consensus (ERIC) fingerprinting and ribotyping-PCR. The discriminatory power of RAPD typing was the best among the methods tested. RAPD typing with two different primers for 13 Listeria spp. reference strains produced 11 patterns each. In contrast, ERIC fingerprinting produced 9 patterns and ribotyping-PCR produced 7 patterns each. Composite of two separate RAPD (Lis 11 and primer 6) results or RAPD (Lis11)/ ribotyping-PCR differentiated all 13 Listeria spp. reference strains. Therefore, composite of 2 separate RAPD (Lis11 and primer 6) or composite of RAPD (Lis11)/ribotyping-PCR is expected the most promising approach for typing field isolated Listeria spp. strains.

• The Korean Journal of Mycology
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• v.27 no.2 s.89
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• pp.119-123
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• 1999

Genetic diversity of Korean isolates of Pseudomonas tolaasii and WLRO (White line reacting organism) was assessed using BOX-, REP-, and ERIC-PCR analysis. P. tolaasii showed nearly identical band patterns among isolates, whereas considerable DNA polymorphism was found among isolates of WLRO. On the basis of dendogram, WLRO is characterized as a complex group with high degree of genetic differentiation. Genetic relatedness based on repetitive DNA regions was low between P. tolaasii and WLRO isolates.

• Environmental Analysis Health and Toxicology
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• v.23 no.1
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• pp.1-9
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• 2008

유산균인 비피도박테리아는 사람과 동물에서 유익한 프로바이오틱 미생물로 알려져 있다. 본 연구에서는 이러한 비피도박테리아 균주의 분류를 위한 repetitive DNA element PCR fingerprinting (ERIC-또는 TAP-PCR)의 사용을 평가하였다. 사람분변으로부터 분리한 알려지지 않은 비피도박테리움 균주와 한국생명공학연구원 생물자원센터로부터 분양받은 표준균주를 가지고 분류 및 동정에 ERIC-PCR과 TAP-PCR을 이용한 RAPD-fingerprinting을 수행하였다. 그 결과 비피도박테리움 균주에 대한 속과 종단위의 분류가 가능하였으며, 실험에 사용된 모든 비피도박테리움 균주는 RAPD-fingerprinting 분석을 통해 유전적 다양성을 확인하였다. 또한 ERIC2와 TAP1 프라이머를 이용한 실험에서는 Bifidobacterium adolescenits 특이 유전자 단편을 확인하였으며 이는 B. adolescenits 균주의 동정에 유용할 것으로 사료된다.

• Korean Journal of Microbiology
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• v.50 no.2
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• pp.114-118
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• 2014

A total of 122 ESBL-producing intestinal bacteria were collected from regional hospitals in the Chungcheong area. Combination disk test (CDT) was performed for antimaicrobial susceptability using cefotaxime and cefotaxime/clavulanate according to Clinical Laboratory Standard Institute (CLSI). Mutiplex PCR using specific primers was performed for a detection of ESBL-genotypes and enterobacterial repetitive intergenic consensus (ERIC)-PCR was carried out for the tracking of molecular epidemiology. In the confirmation test using CDT, 73 out of 76 (96.1%) ESBL-producing Escherichia coli and 43 out of 46 (93.4%) ESBL-producing Klebsiella pnemoniae were positive. In the multiplex PCR, 60.5% of E. coil were positive for CTX-M-2 type gene and 56.5% of K. pneumoniae were positive for VEB -1 type gene. In the ERIC-PCR, E. coil isolates formed 5 clusters and K. pneumoniae isolates were grouped into 4 clusters depending on region. Genotypes of clinical isolates are useful for detection and differentiation of ESBL producing intestinal bacteria. The ERIC-PCR method is thought to be helpful for establishing a regional surveillance system for infection due to its formation of different clusters depending on region.

• Journal of Food Hygiene and Safety
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• v.18 no.4
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• pp.229-236
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• 2003

The five different foodborne pathogenic bacterial genera of Escherichi, Salmonella, Shigella, Vibrio and Listeria are important sources of foodpoison. However, the method was not developed to simultaneously differentiate these five bacteria at molecular level. The optimized concentrations of the four major PCR cocktail components of $MgCl_2$, dNTPs, primers and template DNA were determined when ERIC (enterobacterial repetitive intergenic consensus)-PCR reactions were carried out to differentiate the five differnet foodborne pathogenic bacteria. The optimized concentration of $MgCl_2$ was determined to be 2 mM in order to obtain a consistent fingerprinitng pattern. The similar fingerprinting pattern was obtained when ERIC primers and dNTPs were added up to the concentrations of 2 ${\mu}M$ and 200 ${\mu}M$, respectively. As for template DNA, the numbers of PCR fragments were not affected, but their intensities were increased as the concentrations of the DNA were increased.

• Journal of Microbiology and Biotechnology
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• v.27 no.10
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• pp.1778-1782
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• 2017

To identify and discriminate the bacterial species at the subspecific level, rep-PCR is a reliable genomic fingerprinting tool. Fourteen strains of bacteria were isolated from different food sources, identified as Leuconostoc citreum using 16S rRNA gene sequencing, and amplified using rep-primers (REP, ERIC, and $(GTG)_5$). Fingerprinting patterns generated bands in the range of 300-6,000 bp with REP, 150-6,000 bp with ERIC, and 200-1,700 bp with $(GTG)_5$ primers. In UPGMA dendrogram analysis, 14 strains were clustered into three clades (I, II, and III) with all the primers, thus differentiating them at the molecular level. The present study revealed the differentiation of L. citreum strains using rep-PCR.

• Journal of agriculture & life science
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• v.50 no.2
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• pp.53-59
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• 2016

Bacterial fruit blotch(BFB) of cucurbits caused by Acidovorax citrulli(Acc) continues to diminish fruit yields. The aim of this study was to address whether two genetically distinct populations of Acc are present in watermelon-growing fields in Korea. For this purpose, we used the enterobacterial repetitive intergenic consensus polymerase chain reaction(ERIC-PCR) profiling and substrate-utilization profiles. According to the results of ERIC-PCR, group I and II strains showed clearly differentiated PCR-based fingerprinting profiles. Differences between group I and II strains included amplification of unique, group-specific DNA fragments such as the 1.3-, 0.28-, and 0.25-kb fragments in ERIC-PCR. Acc stains belonging to group I did not use L-leucine, whereas group II strains did use the substrate. Our results support the genetic differentiation of Acc strains into two groups and demonstrate that Acc strains from both groups are previously existed in watermelon-growing fields in Korea. Information about the genetic diversity of Acc under the present study will help scientists and managers form strategies to control BFB.