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)
  • Published : 2005.06.01

Abstract

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.

Keywords

References

  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 https://doi.org/10.1111/j.1574-6968.2004.tb09597.x
  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. 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
  4. 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 https://doi.org/10.1007/s00203-003-0636-2
  5. Chao, A. and S.-M. Lee. 1992. Estimating the number of classes via sample coverage. J. Am. Stat. Assoc. 87: 210-217 https://doi.org/10.2307/2290471
  6. 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 https://doi.org/10.1128/AEM.67.8.3677-3682.2001
  7. 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 https://doi.org/10.1128/AEM.66.12.5448-5456.2000
  8. Clermont, O., S. Bonacorsi, and E. Bingen. 2000. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl. Environ. Microbiol. 66: 4555-4558 https://doi.org/10.1128/AEM.66.10.4555-4558.2000
  9. 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 https://doi.org/10.1128/AEM.70.10.6309-6314.2004
  10. 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 https://doi.org/10.1128/AEM.70.4.2464-2473.2004
  11. 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
  12. 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 https://doi.org/10.1038/298760a0
  13. Hohwy, J., J. Reinholdt, and M. Kilian. 2001. Population dynamics of Streptococcus mitis in its natural habitat. Infect. Immun. 69: 6055-6063 https://doi.org/10.1128/IAI.69.10.6055-6063.2001
  14. 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 https://doi.org/10.1111/j.1365-2958.1991.tb00755.x
  15. 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
  16. 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
  17. 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
  18. 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 https://doi.org/10.1101/gr.5.4.408
  19. Krawiec, S. and M. Riley. 1990. Organization of the bacterial chromosome. Microbiol. Rev. 54: 502-539
  20. 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 https://doi.org/10.1093/oxfordjournals.molbev.a025895
  21. Legendre, P. and L. Legendre. 1998. Numerical Ecology. Elsevier Science, Amsterdam, The Netherlands
  22. Lupski, J. R. and G. M. Weinstock. 1992. Short, interspersed repetitive DNA sequences in prokaryotic genomes. J. Bacteriol. 174: 4525-4529 https://doi.org/10.1128/jb.174.14.4525-4529.1992
  23. 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 https://doi.org/10.1093/nar/20.13.3479
  24. Milkman, R. 1973. Electrophoretic variation in Escherichia coli from natural sources. Science 182: 1024-1026 https://doi.org/10.1126/science.182.4116.1024
  25. 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 https://doi.org/10.1046/j.1462-2920.2004.00554.x
  26. 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 https://doi.org/10.1128/JCM.42.9.4007-4015.2004
  27. Ochman, H. and R. K. Selander. 1984. Standard reference strains of Escherichia coli from natural populations. J. Bacteriol. 157: 690-693
  28. 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 https://doi.org/10.1099/00207713-50-2-665
  29. 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
  30. 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 https://doi.org/10.1016/S0928-8244(03)00308-0
  31. 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
  32. 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
  33. 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 https://doi.org/10.1093/nar/18.22.6503
  34. 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 https://doi.org/10.1099/ijs.0.02360-0
  35. Valsecchi, E. 1998. Tissue boiling: A short-cut in DNA extraction for large-scale population screenings. Mol. Ecol. 7: 1243-1245 https://doi.org/10.1046/j.1365-294x.1998.00379.x
  36. 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 https://doi.org/10.1128/AEM.70.4.2556-2559.2004
  37. 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 https://doi.org/10.1128/JCM.40.3.959-954.2002
  38. 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