Simultaneous detection and differentiation of Escherichia coli populations from environmental freshwaters by means of sequence variations in a fragment of the β-D-glucuronidase gene

Applied and Environmental Microbiology

Volumn 66, Issue 4, 2000, Pages 1340-1346

  Farnleitner, Ndreas H ^a   Kreuzinger, Norbert ^a   Kavka, Gerhard G ^b   Grillenberger, Sonja ^c   Rath, Johannes ^d   Mach, Robert L ^a  

^a VIENNA UNIVERSITY OF TECHNOLOGY   (Austria)

^b Federal Agency for Water Management   (Austria)

^c University of Vienna ^*  (Austria)

^d UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GLUCOSIDASE; FRESH WATER;

DETECTION METHOD; FECAL COLIFORM; FRESHWATER; GENETIC ANALYSIS;

ARTICLE; BACTERIUM CULTURE; BACTERIUM DETECTION; BACTERIUM ISOLATE; CONTROLLED STUDY; ESCHERICHIA COLI; GEL ELECTROPHORESIS; GENE SEQUENCE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; SPECIES DIFFERENTIATION; WATER CONTAMINATION;

ELECTROPHORESIS, POLYACRYLAMIDE GEL; ESCHERICHIA COLI; FRESH WATER; GLUCURONIDASE; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS); WATER MICROBIOLOGY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA;

EID: 0342369384     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.66.4.1340-1346.2000     Document Type: Article

References (41)

1. Abrams, E. S., and V. P. Stanton. Jr. 1992. Use of denaturing gel electrophoresis to study conformational transitions in nucleic acids. Methods Enzymol. 212:71-104.
2. Alonso, J. L., K. Soriano, I. Amoros, and M. A. Ferrus. 1998. Quantitative determination of E. coli and fecal coliforms in water using a chromogenic medium. J. Environ. Sci. Health Part A Toxic-Hazard. Subst. Environ. Eng. 33:1229-1248.
3. American Public Health Association. 1992. Standard methods for the examination of water and wastewater. 18th ed. American Public Health Association, Washington, D.C.
4. Ausubel, R. B., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl. 1994. Current protocols in molecular biology. John Wiley & Sons, Inc., New York, N.Y.
5. Bej, A. K., J. L. DiCesare, L. Haff, and R. M. Atlas. 1991. Detection of Escherichia coli and Shigella spp. in water by using the polymerase chain reaction and gene probes for uid. Appl. Environ. Microhiol. 57:1013-1017.
6. Bettelheim, K. A. 1991. The genus Escherichia, p. 2697-2735. In A. Balows, H. G. Trüper, M. Dworkin, W. Harder, and K.-H. Schleifer (ed.), The prokaryotes, 2nd ed. Springer Verlag, New York, N.Y.
7. Bogosian, G., P. J. L. Morris, and J. P. O'Neil. 1998. A mixed culture recovery method indicates that enteric bacteria do not enter the viable but nonculturable state. Appl. Environ. Microhiol. 64:1736-1742.
8. Boyd, E. F., C. W. Hill, S. M. Rich, and D. L. Hartl. 1996. Mosaic structure of plasmids from natural populations of Escherichia coli. Genetics 143:1091-1100.
9. Brenner, K. P., C. C. Rankin, M. Sivaganesan, and P. V. Scarpino. 1996. Comparison of the recoveries of Escherichia coil and total coliforms from drinking water by the MI agar method and the U.S. Environmental Protection Agency-approved membrane filter method. Appl. Environ. Microbiol. 62:203-208.
10. Byamukama, D. 1998. Faecal pollution in Nakivubo channel, Uganda. Comparison of indicator organisms and isolation methods. M.Sc. thesis. International Institute of Infrastructure, Hydrology and Environment, Delft, The Netherlands.
11. Caugant, D. A., B. R. Levin, and R. K. Selander. 1981. Genetic diversity and temporal variation in the E. coli population of a human host. Genetics 98:467-490.
12. Cauganl, D. A., B. R. Levin, and R. K. Selander. 1984. Distribution of multilocus genotypes of Escherichia coli within and between host families. J. Hyg. Camb. 92:377-384.
13. Green, L., R. D. Miller, D. E. Dykhuizen, and D. L. Hartl. 1984. Distribution of DNA insertion element IS5 in natural isolates of Escherichia coli. Proc. Natl. Acad. Sci. USA 81:4500-4504.
14. International Organization of Standardization. 1990. Water quality - detection and enumeration of coliforms, thermotolerant coliform organisms and presumptive Escherichia coli. Part 1. 9308-1 (E). International Organization of Standardization, Geneva, Switzerland.
15. Iqbal, S., J. Robinson, D. Deere, J. R. Saunders, C. Edwards, and J. Porter. 1997. Efficiency of the polymerase chain reaction amplification of the uid gene for the detection of Escherichia coli in contaminated water. Lett. Appl. Microbiol. 24:498-502.
16. Kariuki, S., C. Gilks, J. Kimari, A. Obanda, J. Muyodi, P. Waiyaki, and C. A. Hart. 1999. Genotype analysis of Escherichia coli strains isolated from children and chickens living in close contact. Appl. Environ. Microhiol. 65:472-476.
17. Kühn, I. 1985. Biochemical fingerprinting of Escherichia coli: a simple method for epidemiological investigations. J. Microbiol. Methods 3:159-170.
18. Lerman, L. S., and K. Silverstein. 1987. Computational simulation of DNA melting and its application to denaturing gradient gel electrophoresis. Methods Enzymol. 155:482-501.
19. Lin, J. J., J. Kuo, and J. Ma. 1996. A PCR-based DNA fingerprinting technique: AFLP for molecular typing of bacteria. Nucleic Acids Res. 24: 3649-3650.
20. Manafi, M., and W. Kneifel. 1989. A combined chromogenic-fluorogenic medium for the simultaneous detection of coliform groups and E. coli in water. Zentralbl. Hyg. Umweltmed. 189:225-234. (In German.)
21. Milkmann, R., and M. McKane Bridges. 1993. Molecular evolution of the Escherichia coli chromosome. IV. Sequence comparisons. Genetics 133:455-468.
22. Muyzer, G., E. C. De Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
23. Muyzer, G., T. Brinkhoff, U. Nübel, C. Santegoeds, H. Schäfer, and C. Wawer. 1998. Denaturing gradient gel electrophoresis (DGGE) in microbial ecology, p. 1-17. In A. D. L. Akkermans, J. D. Van Elsas, and F. J. De Bruijn (ed.), Molecular microbial ecology manual. Kluwer Academic Publishers, Dordrecht, The Netherlands.
24. Muyzer, G., and K. Smalla. 1998. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Leeuwenhock 73:127-141.
25. Myers, R. M., S. G. Fischer, L. S. Lerman, and T. Maniatis. 1985. Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res. 13:3131-3145.
26. Nübel, U., B. Engelen, A. Felske, J. Snaidr, A. Wieshuber, R. I. Amann, W. Ludwig, and H. Backhaus. 1996. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 176:5636-5643.
27. Ørskov, F., and I. Ørskov. 1992. Escherichia coli serotyping in man and animals. Can. J. Microbiol. 38:699-704.
28. Parveen, S., K. M. Portier, K. Robinson, L. Edmiston, and M. L. Tamplin. 1999. Discriminant analysis of ribotype profiles of Escherichia coli for differentiation of human and nonhuman sources of fecal pollution. Appl. Environ. Microbiol. 65:3142-3147.
29. Routman, E., R. D. Miller, J. Phillips-Conroy, and D. L. Hartl. 1985. Antibiotic resistance and population structure in Escherichia coli from free-ranging African yellow baboons. Appl. Environ. Microbiol. 50:749-754.
30. Selander, R. K., D. A. Caugant, and T. S. Whittam. 1987. Genetic structure and variation in natural populations of Escherichia coli, p. 1625-1648. In F. C. Neidhardt et al. (ed.), Escherichia coli and Salmonella typhimurium: cellular and molecular biology. American Society for Microbiology, Washington, D.C.
31. Sheffield, V. C., D. R. Cox, L. S. Lerman, and R. M. Myers. 1989. Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by polymerase chain reaction results in improved detection of single-base changes. Proc. Natl. Acad. Sci. USA 86:232-236.
32. Sommerville, C. C., I. T. Knight, W. L. Straube, and R. R. Colwell. 1989. Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl. Environ. Microbiol. 55:548-554.
33. Toranzos, G. A., and G. A. McFeters. 1997. Detection of indicator microorganisms in environmental freshwaters and drinking waters, p. 184-194. In C. J. Hurst, G. R. Knudsen, M. J. McInerney, L. D. Stetzenbach, and M. V. Walter (ed.), Manual of environmental microbiology. American Society for Microbiology, Washington, D.C.
34. Towner, K. J., and A. Cockayne. 1993. Molecular methods for microbial identification and typing. Chapman and Hall, London, United Kingdom.
35. Turner, S. J., G. D. Lewis, and A. R. Bellamy. 1997. A genomic polymorphism located downstream of the gcvP gene of Escherichia coli that correlates with ecological niche. Mol. Ecol. 6:1019-1032.
36. Turner, S. J., G. D. Lewis, and A. R. Bellamy. 1997. Detection of sewage-derived Escherichia coli in rural stream using multiplex PCR and automated DNA detection. Wat. Sci. Technol. 35:337-342.
37. Wang, G., T. S. Whittam, C. M. Berg, and D. E. Berg. 1993. RAPD (arbitrary primer) PCR is more sensitive than multilocus enzyme electrophoresis for distinguishing related bacterial strains. Nucleic Acids. Res. 21:5930-5933.
38. Watanabe, H., and N. Okamura. 1991. The genus Shigella, p. 2755-2759. In A. Balows, H. G. Trüper, M. Dworkin, W. Harder, and K.-H. Schleifer (ed.), The prokaryotes, 2nd ed. Springer Verlag, New York, N.Y.
39. Whittam, T. S. 1989. Clonal dynamics of Escherichia coli in its natural habitat. Antonie Leeuwenhoek 55:23-32.
40. Whittam, T. S. 1996. Genetic variation and evolutionary processes in natural populations of Escherichia coli, p. 2708-2720. In F. C. Neidhardt et al. (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. American Society for Microbiology, Washington, D.C.
41. Wintzingerode, F., U. B. Göbel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229.