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Journal of microbiology and biotechnology v.15 no.3, 2005년, pp.672 - 677   피인용횟수: 1

Diversity and Genotypic Structure of ECOR Collection Determined by Repetitive Extragenic Palindromic PCR Genome Fingerprinting

HWANG KEUM-OK    (Department of Environmental Sciences, Hankuk University of Foreign Studies   ); JANG HYO-MI    (Department of Environmental Sciences, Hankuk University of Foreign Studies   ); CHO JAE-CHANG    (Department of Environmental Sciences, Hankuk University of Foreign Studies  );
  • 초록

    The standard reference collection of strains for E. coli, the ECOR collection, was analyzed by a genome-based typing method. Seventy-one ECOR strains were subjected to repetitive extragenic palindromic PCR genome fingerprinting with BOX primers (BOX-PCR). Using a similarity value of 0.8 or more after cluster analysis of BOX-PCR fingerprinting patterns to define the same genotypes, we identified 28 genotypes in the ECOR collection. Shannon's entropy-based diversity index was 3.07, and the incident-based coverage estimator indicated potentially 420 genotypes among E. coli populations. Chi-square test of goodness-of-fit showed statistically significant association between the genotypes defined by BOX-PCR fingerprinting and the groups previously defined by multi-locus enzyme electrophoresis. This study suggests that the diversification of E. coli strains in natural populations is actively ongoing, and rep-PCR fingerprinting is a convenient and reliable method to type E. coli strains for the purposes ranging from ecology to quarantine.ine.

  • 주제어

    Genotype .   diversity .   ECOR .   BOX-PCR.  

  • 참고문헌 (38)

    1. Amhaz, J. M., A. Andrade, S. Y. Bando, T. L. Tanaka, C. A. Moreira-Filho, and M. B. Martinez. 2004. Molecular typing and phylogenetic analysis of enteroinvasive Escherichia coli using the fliC gene sequence. FEMS Microbiol. Lett. 235: 259-264 
    2. Anton, A. I., A. J. Martinez-Murcia, and F. RodriguezValera. 1999. Intraspecific diversity of the 23S rRNA gene and the. spacer region downstream in Escherichia coli. J. Bacteriol. 181: 2703-2709 
    3. Clermont, O., S. Bonacorsi, and E. Bingen. 2000. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl. Environ. Microbiol. 66: 4555-4558 
    4. Diamant, E., Y. Palti, R. Gur-Arie, H. Cohen, E. M. Hallerman, and Y. Kashi. 2004. Phylogeny and strain typing of Escherichia coli, inferred from variation at mononucleotide repeat loci. Appl. Environ. Microbiol. 70: 2464-2473 
    5. Higgins, C. F., G. F. Ames, W. M. Barnes, J. M. Clement, and M. Hofnung. 1982. A novel intercistronic regulatory element of prokaryotic operons. Nature 298: 760-762 
    6. Kim, T. W., S. H. Jung, J. Y. Lee, S. K. Choi, S. H. Park, J. S. Jo, and H. Y. Kim. 2003. Identification of lactic acid bacteria in kimchi using SDS-PAGE profiles of whole cell proteins. J. Microbiol. Biotechnol. 13: 119-124 
    7. Minana-Galbis, D., M. Farfan, M. C. Fuste, and J. G. Loren. 2004. Genetic diversity and population structure of Aeromonas hydrophila, Aer. bestiarum, Aer. salmonicida and Aer. popoffii by multilocus enzyme electrophoresis (MLEE). Environ. Microbiol. 6: 198-208 
    8. Ochman, H. and R. K. Selander. 1984. Standard reference strains of Escherichia coli from natural populations. J. Bacteriol. 157: 690-693 
    9. Sharples, G. J. and R. G. Lloyd. 1990. A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes. Nucleic Acids Res. 18: 6503-6508 
    10. Welinder-Olsson, C., M. Badenfors, T. Cheasty, E. Kjellin, and B. Kaijser. 2002. Genetic profiling of enterohemorrhagic Escherichia coli strains in relation to clonality and clinical signs of infection. J. Clin. Microbiol. 40: 959-964 
    11. Hulton, C. S., C. F. Higgins, and P. M. Sharp. 1991. ERIC sequences: A novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol. Microbiol. 5: 825-834 
    12. Rademaker, J. L. W., F. J. Louws, and F. J. de Bruijn. 1998. Characterization of the diversity of ecologically important microbes by rep-PCR fingerprinting, pp. 1-26. In A. D. L. Akkermans, J. D. van Elsas, and F. J. de Bruijn (eds.), Molecular Microbial Ecology Manual, suppl. 3. Kluwer Academic Publishers, Dordrecht, The Netherlands 
    13. Gilson, E., J. M. Clement, D. Brutlag, and M. Hofnung. 1984. A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. EMBO J. 3: 1417-1421 
    14. Krawiec, S. and M. Riley. 1990. Organization of the bacterial chromosome. Microbiol. Rev. 54: 502-539 
    15. Selander, R. K., D. A. Caugant, H. Ochman, J. M. Musser, M. N. Gilmour, and T. S. Whittam. 1986. Methods of multi locus enzyme electrophoresis for bacterial population genetics and systematics. Appl. Environ. Microbiol. 51: 873-884 
    16. Cho, J. C. and J. M. Tiedje. 2000. Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl. Environ. Microbiol. 66: 5448-5456 
    17. Hohwy, J., J. Reinholdt, and M. Kilian. 2001. Population dynamics of Streptococcus mitis in its natural habitat. Infect. Immun. 69: 6055-6063 
    18. Kim, S. H., K. B. Lee, J. S. Lee, and Y. H. Cho. 2003. Genomic diversification by phage-derived genomic islands in Pseudomonas aeruginosa. J. Microbiol. Biotechnol. 13: 783-832 
    19. Legendre, P. and L. Legendre. 1998. Numerical Ecology. Elsevier Science, Amsterdam, The Netherlands 
    20. Rademaker, J. L., B. Hoste, F. J. Louws, K. Kersters, J. Swings, L. Vauterin, P. Vauterin, and F. J. de Bruijn. 2000. Comparison of AFLP and rep-PCR genomic fingerprinting with DNA-DNA homology studies: Xanthomonas as a modeL system. Int. J. Syst. Evol. Microbiol. 50: 665-677 
    21. Kim, S. O., O. Y. Lim, S. H. Kim, J. Y. Kim, Y. H. Kang, and B. K. Lee. 2003. Pulsed-field gel electrophoresis and mutation typing of gyrA gene of quinolone-resistant Salmonella enterica serovar paratyphi A isolated from outbreak and sporadic cases, 1998-2002, Korea. J. Microbiol. Biotechnol. 13: 155-158 
    22. Valsecchi, E. 1998. Tissue boiling: A short-cut in DNA extraction for large-scale population screenings. Mol. Ecol. 7: 1243-1245 
    23. Bae, J. W., J. J. Kim, C. O. Jeon, K. Kim, J. J. Song, S. G. Lee, H. Poo, C. M. Jung, Y. H. Park, and M. H. Sung. 2003. Application of denaturing gradient gel electrophoresis to estimate the diversity of commensal thermophiles. J. Microbiol. Biotechnol. 13: 1008-1012 
    24. Cho, J. C. and J. M. Tiedje. 2001. Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl. Environ. Microbiol. 67: 3677-3682 
    25. Whittam, T. S., M. L. Wolfe, I. K. Wachsmuth, F. Orskov, I. Orskov, and R. A. Wilson. 1993. Clonal relationships among Escherichia coli strains that cause hemorrhagic colitis and infantile diarrhea. Infect. Immun. 61: 1619-1629 
    26. Milkman, R. 1973. Electrophoretic variation in Escherichia coli from natural sources. Science 182: 1024-1026 
    27. De Baets, L., I. Van der Taelen, M. De Filette, D. Pierard, L. Allison, H. De Greve, J. P. Hernalsteens, and H. Imberechts. 2004. Genetic typing of shiga toxin 2 variants of Escherichia coli by PCR-restriction fragment length polymorphism analysis. Appl. Environ. Microbiol. 70: 6309-6314 
    28. Vernozy-Rozand, C., M. P. Montet, Y. Bertin, F. Trably, J. P. Girardeau, C. Martin, V. Livrelli, and L. Beutin. 2004. Serotyping, stx2 subtyping, and characterization ofthe locus of enterocyte effacement island of shiga toxin-producing Escherichia coli and E. coli O157:H7 strains isolated from the environment in France. Appl. Environ. Microbiol. 70: 2556-2559 
    29. Koeuth, T., J. Versalovic, and J. R. Lupski. 1995. Differential subsequence conservation of interspersed repetitive Streptococcus pneumoniae BOX elements in diverse bacteria. Genome Res. 5: 408-418 
    30. Mora, A., M. Blanco, J. E. Blanco, M. P. Alonso, G. Dhabi, F. Thomson-Carter, M. A. Usera, R. Bartolome, G. Prats, and J. Blanco. 2004. Phage types and genotypes of shiga toxinproducing Escherichia coli 0157:H7 isolates from humans and animals in Spain: Identification and characterization of two predominating phage types (PT2 and PT8). J. Clin. Microbiol. 42: 4007-4015 
    31. Martin, B., O. Humbert, M. Camara, E. Guenzi, J. Walker, T. Mitchell, P. Andrew, M. Prudhomme, G. Alloing, and R. Hakenbeck. 1992. A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniae. Nucleic Acids Res. 20: 3479-3483 
    32. Regua-Mangia, A. H., B. C. Guth, J. R. da Costa Andrade, K. Irino, A. B. Pacheco, L. C. Ferreira, V. Zahner, and L. M. Teixeira. 2004. Genotypic and phenotypic characterization of enterotoxigenic Escherichia coli (ETEC) strains isolated in Rio de Janeiro city, Brazil. FEMS Immunol. Med Microbiol. 40: 155-162 
    33. Beyene, D., S. Kassa, F. Ampy, A. Asseffa, T. Gebremedhin, and P. van Berkum. 2004. Ethiopian soils harbor natural populations of rhizobia that form symbioses with common bean (Phaseolus vulgaris L.). Arch. Microbiol. 181: 129-136 
    34. Lecointre, G, L. Rachdi, P. Darlu, and E. Denamur. 1998. Escherichia coli molecular phylogeny using the incongruence length difference test. Mol. Biol. Evol. 15: 1685-1695 
    35. Lupski, J. R. and G. M. Weinstock. 1992. Short, interspersed repetitive DNA sequences in prokaryotic genomes. J. Bacteriol. 174: 4525-4529 
    36. Selander, R. K., T. K. Korhonen, V. Vaisanen-Rhen, P. H. Williams, P. E. Pattison, and D. A. Caugant. 1986. Genetic relationships and clonal structure of strains of Escherichia coli causing neonatal septicemia and meningitis. Infect. Immun. 52: 213-222 
    37. Stackebrandt, E., W. Frederiksen, G. M. Garrity, P. A. Grimont, P. Kampfer, M. C. Maiden, X. Nesme, R. Rossello-Mora, J. Swings, H. G. Truper, L. Vauterin, A. C. Ward, and W. B. Whitman. 2002. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 52: 1043-1047 
    38. Chao, A. and S.-M. Lee. 1992. Estimating the number of classes via sample coverage. J. Am. Stat. Assoc. 87: 210-217 
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    1. 2006. "" Journal of microbiology and biotechnology, 16(11): 1773~1777     

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