• Title/Summary/Keyword: ribotype

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Clonal Analysis of Methicillin-Resistant Staphylococcus aureus Strains in Korea

  • Kim, Jung-Min;Seol, Sung-Yong;Cho, Dong-Taek
    • The Journal of the Korean Society for Microbiology
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    • v.35 no.3
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    • pp.215-224
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    • 2000
  • In this study, the distribution of the mec regulator genes and the presence of the mutation in mecI gene and mec promoter region among 50 MRSA clinical isolates derived from a single university hospital in Korea were analyzed. Among 50 MRSA strains, 13 strains had a deletion of mecI gene, and 37 strains were found to have mutations in mecI gene or mecA promoter region corresponding to a presumptive operator of mecA, i.e., the binding site of the repressor protein. Furthermore, in order to track the evolution of methicillin-resistant Staphylococcus aureus (MRSA) distributed in Korea, we determined the MRSA clonotype by combined use of genetic organization patterns of mec regulator genes, ribotype, and coagulase type. As the result, 48 of 50 MRSA strains could be classified into four distinct clones. Clonotype I is characterized by the coagulase type 3, deletion of mecI gene, and ribotype 1 shared by NCTC10442, the first reported MRSA isolate in England (9 strains). Clonotype II is characterized by the coagulase type 4, C to T substitution at position 202 of mecI gene, and ribotypes 2, 3 and 4 shared by 85/3619 strain isolated in Austria (10 strains). Clonotype III is characterized by the coagulase type 2, mutations of mecA promoter region and/or mecI, and ribotypes 4, 5, and 6 shared by N315 strain isolated in Japan (25 strains). Clonotype IV is characterized by the coagulase type 4, deletion of mecI gene, and ribotype 7 (4 strains). The clonality of two strains could not be determined due to their undefined ribotype.

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Ribotyping of Porphyromonas Gingivalis Isolated from Rapidly Progressive Periodontitis Patients (급속진행성치주염 환자로부터 배양분리한 Porphyromonas gingivalis 균주의 ribotyping)

  • Kim, Jin-Hong;Choi, Bong-Kyu;Choi, Seong-Ho;Cho, Kyoo-Sung;Chai, Jung-Kiu;Kim, Chong-Kwan
    • Journal of Periodontal and Implant Science
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    • v.29 no.4
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    • pp.963-979
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    • 1999
  • This study examined ribotypes of 36 P. gingivalis strains isolated from 10 rapidly progressive periodontitis patients in Korean and revealed the presence of genetic heterogeneity among the patients. Ribotyping was performed by using a oligonucleotide probes based on 16S rRNA after whole genomic DNA had been digested with the restriction endonuclease enzyme Kpn I and Pst I. In addition, the antigenic heterogeneity of fimbrillin and protease activity was analysed to observe the virulency of P. gingivalis. The results were as follows. 1. Using KpnI, 6 ribotypes were detected, whereas 7 ribotypes were identified by using PstI. When combined two enzymes, a total of 8 ribotypes was subgrouped. 2. Ribotype I/e was the most common and detected in 4 among 10 patients. 3. The fimbrillin expressed from P. gingivalis isolates had the molecular size of 41kDa, 43kDa, 49kDa. It was observed that the size of fimbrillin with the same ribotypes could be identical. 4. All the P. gingivalis strains showed strong proteolytic activity and had the molecular size more than 120kDa. In summary, total 8 ribotypes were observed for isolates from rapidly progressive periodontitis patients. Forty percent of the patients harbored isolates exhibiting the same ribotype I/e, and it was observed that more than one ribotype can coexist in an individual patient.

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Distributions of East Asia and Philippines ribotypes of Cochlodinium polykrikoides (Dinophyceae) in the South Sea, Korea (Cochlodinium polykrikoides (Dinophyceae)의 동아시아와 필리핀 유전형의 남해안 분포)

  • PARK, TAE GYU;KIM, JIN JOO;SONG, SEON YOUNG
    • The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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    • v.24 no.3
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    • pp.422-428
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    • 2019
  • Fish killing dinoflagellate Cochlodinium polykrikoides has been separated into four genetically differentiated subpopulations globally based on large-subunit (LSU) ribosomal RNA gene, and two subpopulations have been found in the South Sea, Korea. In this study, distributions of the East Asia and Philippines ribotypes were surveyed in the South Sea for 3 years (2014~2016) using quantitative real-time PCR (qPCR). The East Asia ribotype was detected in all sampling stations of the South Sea (Tongyeong~Wando) by 40~100% positives for 2014~2016, whereas the Philippines ribotype was detected in some areas of Tongyeong~Goheung by 1~2% positives for only 2016 when the Tsushima Warm Current (TWC) was particularly strengthened. These results indicate that the East Asia ribotype is the dominant subpopulation in the South Sea, also some of C. polykrikoides swimming cells might be transported from offshore to the South Sea via TWC.

Bloom-forming dinoflagellate Akashiwo sanguinea(Dinophyceae) in Jangmok Harbour of Geoje Island, Korea: Morphology, phylogeny and effects of temperature and salinity on growth (거제도 장목항에서 적조원인생물 Akashiwo sanguinea(Dinophyceae): 형태, 분자계통학적 특성 및 온도와 염분에 따른 성장 특성)

  • Han, Kyong Ha;Li, Zhun;Youn, Joo Yeon;Kang, Byeong Jun;Kim, Hyun Jung;Seo, Min Ho;Soh, Ho Young;Shin, Hyeon Ho
    • Korean Journal of Environmental Biology
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    • v.37 no.2
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    • pp.119-128
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    • 2019
  • The morphological characteristics of the bloom-forming dinoflagellate Akashiwo sanguinea isolated from Jangmok Harbour, Geoje in Korea was examined using light and scanning electron microscope (SEM), and its large subunit (LSU) rDNA was sequenced. Additionally, investigation was done on the effects of temperature and salinity on the growth of A. sanguinea. The cells were dorso-ventrally compressed up to 54.7-70.3 ㎛ long and 31.5-48.5 ㎛ wide. The epicone was conical while the hypocone was separated into two lobes. The nucleus was positioned at the center of the cell. The yellow-brown chloroplasts radiated close to the cell center. SEM observation indicated that A. sanguinea has an e-shaped apical groove. Molecular phylogeny based on LSU rDNA gene sequences revealed that the A. sanguinea strains isolated from Jangmok Harbor were classified in the clade of ribotype A. The maximum growth rate (0.50 day-1) was observed at 20℃ and 20 psu, while the maximum cell density (1,372 cells mL-1) was observed at 25℃ and 30 psu. This indicates that the blooms of A. sanguinea ribotype A in Korean coastal area are affected by water temperature, rather than the salinity.

A Molecular Phylogenetic Study on Korean Alexandrium catenella and A. tamarense Isolates (Dinophyceae) Based on the Partial LSD rDNA Sequence Data

  • Kim, Keun-Yong;Kim, Chang-Hoon
    • Journal of the korean society of oceanography
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    • v.39 no.3
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    • pp.163-171
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    • 2004
  • Sequences of the large subunit ribosomal (LSD) rDNA D1-D2 region of Alexandrium catenella(=A. sp. cf. catenella) and A. tamarense isolates, which were collected along the Korea coasts, were analyzed to understand their phylogenetic relationships and geographical distributions. All A. catenella and A. tamarense isolates belonged to the A. tamarense/catenella/fundyense complex and were grouped with the North American and temperate Asian ribotypes, respectively, regardless of the presence or absence of a ventral pore in the first apical plate. A consistent and peculiar characteristic that differentiated the Alexandrium isolates was amplification of a second PCR product with a lower molecular weight in addition to the predicted one; ten A. catenella isolates belonging to the temperate Asian ribotype yielded this additional PCR product. Sequence alignment revealed that the shorter PCR product resulted from an unusual large deletion of 87 bp in the LSD rDNA D1 domain. The North American and temperate Asian ribotypes were prevalent along the Korean coasts without geographical separation. Given the high genetic homogeneity among widely distributed Alexandrium populations, each ribotype appeared to be pandemic rather than to constitute a distinct regional population.

Detection, Characterization and Antibiotic Susceptibility of Clostridioides (Clostridium) difficile in Meat Products

  • Muratoglu, Karlo;Akkaya, Esra;Hampikyan, Hamparsun;Bingol, Enver Baris;Cetin, Omer;Colak, Hilal
    • Food Science of Animal Resources
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    • v.40 no.4
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    • pp.578-587
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    • 2020
  • Clostridioides (Clostridium) difficile is a Gram (+), anaerobic, spore forming, rod shaped bacterium that can produce toxin. The objective of this study is to reveal the presence of C. difficile in meat products, to analyze the ribotype diversity by PCR and to evaluate the antibiotic susceptibility of isolated strains. The organism was isolated in 22 out of 319 (6.9%) examined meat product samples and 9 out of 22 (40.9%) isolates were identified as RT027 and all isolates had the ability of toxin production. In terms of antibiotic susceptibility, all isolates were susceptive to amoxicillin-clavulanic acid, tetracycline and vancomycin and 21 (95.4%) isolates to metronidazole. On the other hand, imipenem and cefotaxim resistance was observed in all. In conclusion, the results of this comprehensive study conducted in Turkey deduced the presence of C. difficile in different meat products. Therefore, these products can be evaluated as a potential contamination source of C. difficile from animals to humans especially for elders, youngsters, long terms wide spectrum antibiotic used and immuno-suppressed individuals.

Riboprint and Virulence Gene Patterns for Bacillus cereus and Related Species

  • Kim, Young-Rok;Batt, Carl A.
    • Journal of Microbiology and Biotechnology
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    • v.18 no.6
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    • pp.1146-1155
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    • 2008
  • A total of 72 Bacillus cereus strains and 5 Bacillus thuringiensis strains were analyzed for their EcoRI ribogroup by ribotyping and for the presence or absence of seven virulence-associated genes. From these 77 strains, 42 distinctive ribogroup were identified using EcoRI, but the two species could not be discriminated by their EcoRI ribogroup. The 77 strains were also examined by PCR for the presence of seven virulence-associated genes, cerAB, pi-plc, entFM, bceT, hblA, hblC, and hblD. All five Bacillus thuringiensis strains were positive for these genes. Although differences in the patterns of virulence genes were observed among the different B. cereus strains, within any given ribogroup the patterns of the seven virulence genes was the same. Pulsed-field gel electrophoresis (PFGE) analysis in combination with available chromosomal maps for a selected group of B. cereus strains revealed significant differences in their chromosome size and the placement of virulence genes. Evidence for significant rearrangements within the B. cereus chromosome suggests the mechanism through which the pattern of virulence-associated genes varies. The results suggest linkage between ribogroups and virulence gene patterns as well as no apparent containment of the latter within any particular species boundary.

Molecular Phylogenetic Relationships Within the Genus Alexandrium(Dinophyceae) Based on the Nuclear-Encoded SSU and LSU rDNA D1-D2 Sequences

  • Kim, Choong-Jae;Sako Yoshihiko;Uchida Aritsune;Kim, Chang-Hoon
    • Journal of the korean society of oceanography
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    • v.39 no.3
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    • pp.172-185
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    • 2004
  • LSU rDNA D1-D2 and SSU rDNA genes of 23 strains in seven Alexandrium (Halim) species, A. tamarense (Lebour) Balech, A. catenella (Whedon et Kofoid), A. fraterculus (Balech) Balech, A. affine (Inoue et Fukuyo) Balech, A. insuetum Balech, A. pseudogonyaulax (Biecheler) Horiguchi ex Yuki et Fukuyo and A. tamiyavanichii Balech, were sequenced and the data were used for molecular phylogenetic analysis. The sequence data revealed 11 and 7 ribotypes in the LSU rDNA D1-D2 region and 4 and 17 ribotypes in the SSU rDNA region of A. catenella and A. tamarense, respectively. Other Alexandrium species had also 1 to 5 ribotypes in the two regions. With the exception of CMC2 and CMC3 of A. catenella, all A. tamarense and A. catenella strains had a common ribotype, a functionally expressed rRNA gene (here termed type A), in both gene regions. In addition to the functionally expressed gene, several pseudogenes were obtained that were found to be good tools to analyze the population designation of regional isolates by grouping them according to shared ribotypes. From the phylogenetic analysis of the sequence data determined in this study and retrieved from GenBank, the genus Alexandrium was divided into 14 groups: 1) A. tamarense, 2) A. excavatum, 3) A. catenella, 4) Tasmanian A. tamarense, 5) A. affine (and/or A. concavum), 6) Thai A. tamarense, 7) A. tamiyavanichii, 8) A. fraterculus, 9) A. margalefii, 10) A. andersonii, 11) A. ostenfeldii, 12) A. minutum (or A. lusitanicum), 13) A. insuetum, and 14) A. pseudogonyaulax. The SSU rDNA gene sequence of A. fundyense was so similar to those of A. tamarense used in this study that the two species were difficult to discriminate each other. A. tamiyavanichii was closest to the A. tamarense strain isolated in Thailand and close to the long chain-forming species of A. affine and A. fraterculus. The phylogenetic tree showed that A. margalefii, A. andersonii, A. ostenfeldii, A. minutum and A. insuetum constituted the basal relative complex, and that A. pseudogonyaulax is an ancestral taxon in the genus Alexandrium.