Specific genomic fingerprints of Escherichia coli strains with repetitive sequences and PCR as an effective tool for monitoring freshwater environments

• Autorzy: Baldy-Chudzik K , Stosik M.
• Języki publikacji: EN

Abstrakty

EN

The Rep-PCR fingerprinting method has been applied to identify genomic diversity of 252 E. coli strains derived in the area of a flowing-water basin. The received results show that applying UPGMA and Nearest Neighbour-Joining clustering methods to statistical analysis of rep-PCR fingerprints has made it possible to discriminate and group the strains, revealing a characteristic structure of E. coli population for particular stands of sample drawing. The proposed procedure of the analysis may be useful for routinely monitoring water quality.

Słowa kluczowe

EN

water quality; genomic diversity; fingerprinting method; freshwater environment; monitoring; Escherichia coli

• Wydawca: -
• Czasopismo: Polish Journal of Environmental Studies
• Rocznik: 2005
• Tom: 14
• Numer: 5
• Opis fizyczny: p.551-557,fig.,ref.

Twórcy

autor

Baldy-Chudzik K

• University of Zielona Gora, Monte Cassino 21B, 65-561 Zielona Gora, Poland

autor

Stosik M.

Bibliografia

• 1. NIEMIR. M., HEIKKILA M. P., LAHTI K., KALSO S., NIEMELÄ S. I. Comparison of methods for determining the numbers and species distribution of coliform bacteria in well water samples. J. Appl. Microbiol. 90, 850, 2001.
• 2. GORDON D., M. Geographical structure and host specificity in bacteria and the implication for tracing the source of coliform contamination. Microbiol. 147, 1079, 2001.
• 3. KARIUKI S., GILKS C., KIMARI J., OLANDA A., MUYODI F., WAIYAKI P., HART C., A. Genotype analysis of Escherichia coli strains isolated from children and chicken living in close contact. Appl. Environ. Microbiol. 65, 472, 1999.
• 4. CARSON C. A., SHEAR B. L., ELLERSIECK M. R., ASFAW A. Identification of fecal Escherichia coli from human and animals by ribotyping. Appl. Environ. Microbiol. 67, 1503, 2001.
• 5. PARVEEN S., PORTER K. M., ROBINSON K., EDMINSTON L., TAMPLIN M. L. Discrimination analysis of ribotype profiles of Escherichia coli for differentiating human and nonhuman sources of fecal pollution. Appl. Environ. Microbiol. 65, 3142, 1999.
• 6. BERNHARD A. E., FIELD K. G. A PCR assay to discriminate human and animal feces on the basis of host differences in Bacteroides-Prevotella genes encoding 16S rRNA. Appl. Environ. Microbiol. 66, 4571, 2000.
• 7. CARSON C. A., SHEAR B. L., ELLERSIECK M. R., SCHNELL J. D. Comparison of ribotyping and repetitive extragenic palindromic-PCR for identification of fecal Escherichia coli from human and animals. Appl. Environ. Microbiol. 69, 1836, 2003.
• 8. DOMBEK P. E., JOHNSON L. K., ZIMMERLEY S. J., SADOWSKY M. J. Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources. Appl. Environ. Microbiol. 66, 2572, 2000.
• 9. OLIVE D. M., BEAN P. Principles and applications of methods for DNA-based typing of microbial organisms. J. Clin. Microbiol. 37, 1661, 1999.
• 10. HULTON C. S. J., HIGGINS C. F., SHARP P. M. ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol. Microbiol. 5, 825, 1991.
• 11. VERSALOVIC J., KOEUTH T., LUPSKI J. R. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 19, 6823, 1991.
• 12. GILSON E., CLEMENT J. M., BRUTLAG D., HOFNUNG M. A. A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. EMBO J. 3, 1417, 1984.
• 13. VERSALOVIC J., SCHNEIDER M., DE BRUIJN F. J., LUPSKI J. R. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol. Cell. Biol. 5, 25, 1994.
• 14. Evaluation of the environmental in Lubuskie province in 2000. Provincial Inspectorate of Environmental Protection in Zielona Góra, Library of environmental monitoring Zielona Góra – Gorzów Wielkopolski. (in Polish) 2001.
• 15. Polish standards PN-77 (C-04615 (07, Determination of the fecal coliform by the fermentative test-tube method. 1990.
• 16. RADEMAKER J. L., DE BRUIJN F. J. Characterization and classification of microbes by rep-PCR genomic fingerprinting and computer-assisted pattern analysis. IN: DNA markers: protocols, applications and overviews. WilleyLiss, INC., New York, pp151-171, 1997.
• 17. LECLERC H., MOSSEL D. A. A., EDBERG S. C., STRUIJK C. B. Advances in the bacteriology of the coliform group: Their suitability as markers of microbial water safety. Annu. Rev. Microbiol. 55, 201, 2001.
• 18. BALDY-CHUDZUK K., NIEDBACH J., STOSIK M. Heterogeneity of Escherichia coli derived from artiodactyla animals analyzed with the use of rep-PCR fingerprinting, Folia Microbiol. 48, 162, 2003.
• 19. GORDON D. M., FITZ-GIBBON F. The distribution of enteric bacteria from Australian mammals: host and geographical effects. Microbiol 145, 2663, 1999.
• 20. HARTEL P. G., SUMMER J. D., HILL J. L., COLLINS J. V., ENTRY J. A., SEGERS W. I. Geographic variability of Escherichia coli ribotypes from animals in Idaho and Georgia. J. Environ. Qual. 31, 1273, 2002.