Development of a rapid quantitative PCR assay for direct detection and quantification of culturable and non-culturable Escherichia coli from agriculture watersheds

Journal of Microbiological Methods

Volumn 69, Issue 3, 2007, Pages 480-488

  Khan, Izhar U H ^a   Gannon, Vic ^b   Kent, Rob ^a   Koning, Wendell ^c   Lapen, David R ^d   Miller, Jim ^e   Neumann, Norman ^f   Phillips, Rob ^a   Robertson, Will ^g   Topp, Edward ^h   van Bochove, Eric ^h   Edge, Thomas A ^a  

^a ENVIRONMENT CANADA   (Canada)

^b PUBLIC HEALTH AGENCY OF CANADA   (Canada)

^c ALBERTA ENVIRONMENT AND PARKS   (Canada)

^d OTTAWA RESEARCH AND DEVELOPMENT CENTRE   (Canada)

^e LETHBRIDGE RESEARCH CENTRE   (Canada)

^f UNIVERSITY OF CALGARY   (Canada)

^g HEALTH CANADA   (Canada)

^h AGRICULTURE AND AGRI FOOD CANADA   (Canada)

Author keywords

Agriculture water; Escherichia coli; ITS region; Real time quantitative PCR

Indexed keywords

INTERNAL TRANSCRIBED SPACER; OLIGONUCLEOTIDE; RNA 16S;

AGRICULTURE; ARTICLE; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM DETECTION; CONTROLLED STUDY; DNA EXTRACTION; DNA FLANKING REGION; DNA PURIFICATION; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; WATER SAMPLING; WATERSHED;

AGRICULTURE; ANIMALS; CATS; CATTLE; CHILD; COLONY COUNT, MICROBIAL; CULTURE MEDIA; DNA, BACTERIAL; DNA, RIBOSOMAL SPACER; DOGS; ESCHERICHIA COLI; FRESH WATER; GUINEA PIGS; HUMANS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S; SEQUENCE ANALYSIS, DNA; TIME FACTORS;

ESCHERICHIA COLI;

EID: 34247620209     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2007.02.016     Document Type: Article

References (40)

1. American Public Health Association. Standard Methods for the Examination of Water and Wastewater. 20th ed. (1998), American Public Health Association, Washington, D.C
2. Artz R.E.R., Avery L.M., Jones D.L., and Killham K. Potential pitfalls in the quantitative molecular detection of Escherichia coli O157:H7 in environmental matrices. Can. J. Microbiol. 52 (2006) 482-488
3. Bej A.K., Steffan R.J., DiCesare J., Haff L., and Atlas R.M. Detection of coliform bacteria in water by polymerase chain reaction and gene probes. Appl. Environ. Microbiol. 56 (1990) 307-314
4. Bej A.K., DiCesare J.L., Haff L., and Atlas R.M. Detection of Escherichia coli and Shigella spp. in water by using the polymerase chain reaction and gene probes for uid. Appl. Environ. Microbiol. 57 (1991) 1013-1017
5. Bergallo M., Costa C., Gribaudo G., Tarallo S., Baro S., Negro P.A., and Cavallo R. Evaluation of six methods for extraction and purification of viral DNA from urine and serum samples. New Microbiol. 29 (2006) 111-119
6. Brenner K.P., Rankin C.C., Roybal Y.R., Stelma G.N., Scarpino P.V., and Dufour A.P. New medium for the simultaneous detection of total coliforms and Escherichia coli in water. Appl. Environ. Microbiol. 59 (1993) 3534-3544
7. Candrian U., Furrer B., Hofelein C., Meyer R., Jermini M., and Luthy J. Detection of Escherichia coli and identification of enterotoxigenic strains by primer-directed enzymatic amplification of specific DNA sequences. Int. J. Food Microbiol. 12 (1991) 339-351
8. Ciebin B.W., Brodsky M.H., Eddington R., Hornsnell G., Choney A., Palmateer G., Ley A., Joshi R., and Shears G. Comparative evaluation of modified m-FC and m-TEC media for membrane filter enumeration of Escherichia coli in water. Appl. Environ. Microbiol. 61 (1995) 3940-3942
9. Davis K.C., Nakatsu C.H., Turco R., Weagent S.D., and Bhunia A.K. Analysis of environmental Escherichia coli isolates for virulence genes using the TaqMan PCR system. J. Appl. Microbiol. 95 (2003) 612-620
10. Feng P., Lum R., and Chang G.W. Identification of uidA gene sequences in β-d-glucuronidase-negative Escherichia coli. Appl. Environ. Microbiol. 57 (1991) 320-323
11. Foulds I.V., Granacki A., Xiao C., Krull U.J., Castle A., and Horgen P.A. Quantification of microcystin-producing cyanobacteria and E. coli in water by 5′-nuclease PCR. J. Appl. Microbiol. 93 (2002) 825-834
12. Frahm E., and Obst O. Application of the fluorogenic probe technique (TaqMan PCR) to the detection of Enterococcus spp. and Escherichia coli in water samples. J. Microbiol. Methods 52 (2003) 123-131
13. García-Martínez J., Bescós I., Rodríguez-Sala J.J., and Rodríguez-Valera F. RISSC: a novel database for ribosomal 16S-23S RNA genes spacer regions. Nucleic Acids Res. 29 (2001) 178-180
14. Grant M.A., Weagent S.D., and Feng P. Glutamate decarboxylase genes as a prescreening marker for detection of pathogenic Escherichia coli groups. Appl. Environ. Microbiol. 67 (2001) 3110-3114
15. Hartman L.J., Coyne S.R., and Norwood D.A. Development of a novel internal positive control for TaqmanR based assays. Mol. Cell. Probes 19 (2005) 51-59
16. Haughland R.A., Seifring S.C., Wymer L.J., Brenner K.P., and Dufour A.P. Comparison of Enterococcus measurements in freshwater at two recreational beaches by quantitative polymerase chain reaction and membrane filter culture analysis. Water Res. 39 (2005) 559-568
17. Health and Welfare Canada. Guidelines for Canadian Recreational Water Quality (1992), Minister of Supply and Services Canada, Ottawa, Ontario Cat. H49-70/1991E, 101pp.
18. Heid C.A., Stevens J., Livak K.J., and Williams P.M. Real time quantitative PCR. Genome Res. 6 (1996) 986-994
19. Horachova K., Mlejnkova H., and Mlejnek P. Direct detection of bacterial fecal indicators in water samples using PCR. Water Sci. Technol. 54 (2006) 135-140
20. Ibekwe A.M., and Grieve C.M. Detection and quantification of Escherichia coli O157:H7 in environmental samples by real-time PCR. J. Appl. Microbiol. 94 (2003) 421-431
21. Ibekwe A.M., Watt P.M., Grieve C.M., Sharma V.K., and Lyons S.R. Multiplex fluorogenic real-time PCR for detection and quantification of Escherichia coli O157:H7 in dairy wastewater wetlands. Appl. Environ. Microbiol. 68 (2002) 4853-4862
22. Iqbal S., Robinson J., Deere D., Saunders J.R., Edwards C., and Porter J. Efficiency of the polymerase chain reaction amplification of the uid gene for detection of Escherichia coli in contaminated water. Lett. Appl. Microbiol. 24 (1997) 498-502
23. Juck D., Ingram J., Prevost M., Coallier J., and Greer C. Nested PCR protocol for the rapid detection of Escherichia coli in potable water. Can. J. Microbiol. 42 (1996) 862-866
24. Khan I.U., and Yadav J.S. Real-time PCR assays for genus-specific detection and quantification of culturable and non-culturable mycobacteria and pseudomonads in metalworking fluids. Mol. Cell. Probes 18 (2004) 67-73
25. Kuhnert P., Capaul S.E., Nicolet J., and Frey J.O. Phylogenetic positions of Clostridium chauvoei and Clostridium septicum based on 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 46 (1996) 1174-1176
26. Lleo M.M., Bonato B., Tafi M.C., Signoretto C., Pruzzo C., and Canepari P. Molecular vs culture methods for the detection of bacterial faecal indicators in groundwater for human use. Lett. Appl. Microbiol. 40 (2005) 289-294
27. Ludwig W., and Schleifer K.H. How quantitative is quantitative PCR with respect to cell counts?. Syst. Appl. Microbiol. 23 (2000) 556-562
28. Martins M.T., Rivera I.G., Clark D.L., Stewart M.H., Wolfe R.L., and Olson B.H. Distribution of uidA gene sequences in Escherichia coli isolates in water sources and comparison with the expression of β-glucuronidase activity in 4-methylumbelliferyl-β-d-glucuronide media. Appl. Environ. Microbiol. 59 (1993) 2271-2276
29. McDaniels A.E., Rice E.W., Reyes A.L., Johnson C.H., Haugland R.A., and Stelma G.N. Confirmational identification of Escherichia coli, a comparison of genotypic and phenotypic assays for glutamate decarboxylase and β-d-glucuronidase. Appl. Environ. Microbiol. 62 (1996) 3350-3354
30. Moe C.L. Waterborne transmission of infectious agents. In: Kurst C.J., Knudsen G.R., McInnerney M.J., Stetzenbach L.D., and Walter M.V. (Eds). Manual of Environmental Microbiology (1997), American Society for Microbiology, Washington, D.C
31. Monday S.R., Whittam T.S., and Feng P.C.H. Genetic and evolutionary analysis of mutations in the gusA gene that cause the absence of β-glucuronidase activity in Escherichia coli O157:H7. J. Infect. Dis. 184 (2001) 918-921
32. Moreira D. Efficient removal of PCR inhibitors using agarose-embedded DNA preparations. Nucleic Acids Res. 26 (1998) 3309-3310
33. Noble R.T., and Weisberg S.B. A review of technologies for rapid detection of bacteria in recreational waters. J. Water Health 3 (2005) 381-392
34. Noble R.T., Griffith J.F., Blackwood A.D., Fuhrman J.A., Gregory J.B., Hernandez X., Liang X., Bera A.A., and Schiff K. Multitiered approach using quantitative PCR to track sources of fecal pollution affecting Santa Monica Bay, California. Appl. Environ. Microbiol. 72 (2006) 1604-1612
35. Pommepuy M., Butin M., Derrien A., Gourmelon M., Colwell R.R., and Cormier M. Retention of enteropathogenicity by viable but nonculturable Escherichia coli exposed to seawater and sunlight. Appl. Environ. Microbiol. 62 (1996) 4621-4626
36. Roszak D.B., and Colwell R.R. Survival strategies of bacteria in the natural environment. Microbiol. Rev. 51 (1987) 365-379
37. Schets F.M., and Havelaar A.H. Comparison of indole production and β-glucuronidase activity for the detection of Escherichia coli in a membrane filter method. Lett. Appl. Microbiol. 13 (1991) 272-274
38. Schets F.M., Nobel P.J., Strating S., Mooijman K.A., Engels G.B., and Brouwer A. EU drinking water directive reference methods for enumeration of total coliforms and Escherichia coli compared with alternative methods. Lett. Appl. Microbiol. 34 (2002) 227-231
39. Toranzos G.A., and McFeters G.A. Detection of indicator microorganisms in environmental freshwaters and drinking waters. In: Kurst C.J., Knudsen G.R., McInnerney M.J., Stetzenbach L.D., and Walter M.V. (Eds). Manual of Environmental Microbiology (1997), American Society for Microbiology, Washington, D. C
40. Tsen H.Y., Lin C.K., and Chi W.R. Development and use of 16S rRNA gene targeted PCR primers for the identification of Escherichia coli cells in water. J. Appl. Microbiol. 85 (1998) 554-560