Comparison of quantitative PCR assays for Escherichia coli targeting ribosomal RNA and single copy genes

Letters in Applied Microbiology

Volumn 52, Issue 3, 2011, Pages 298-306

  Chern, E C ^a   Siefring, S ^a   Paar, J ^a   Doolittle, M ^b   Haugland, R A ^a  

^a U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^b New England Regional Laboratory ^*  (United States)

Author keywords

Escherichia coli; QPCR; RRNA; uidA

Indexed keywords

ASSAYS; DNA SEQUENCES; GENES; POLYMERASE CHAIN REACTION; RNA; WATER POLLUTION;

COPY GENES; E. COLI; MULTI COPIES; PCR ASSAY; QPCR; QUANTITATIVE PCR; RIBOSOMAL RNA; RRNA; UIDUM; WATER SAMPLES;

ESCHERICHIA COLI;

BACTERIAL DNA; RIBOSOME RNA;

BIOASSAY; BIOINDICATOR; COLIFORM BACTERIUM; COMPARATIVE STUDY; MITOCHONDRIAL DNA; POLLUTION MONITORING; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; SAMPLING; WASTEWATER;

ARTICLE; BACTERIAL CELL; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM DETECTION; CONTROLLED STUDY; DNA EXTRACTION; ESCHERICHIA; ESCHERICHIA COLI; ESCHERICHIA FERGUSONII; FILTRATION; GENE SEQUENCE; GENE TARGETING; GENETIC ANALYSIS; INTERMETHOD COMPARISON; LIMIT OF DETECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; POLLUTION; REAL TIME POLYMERASE CHAIN REACTION; TAXONOMY; WASTE WATER;

ESCHERICHIA COLI;

EID: 79551651305     PISSN: 02668254     EISSN: 1472765X     Source Type: Journal    
DOI: 10.1111/j.1472-765X.2010.03001.x     Document Type: Article

References (27)

1. American Public Health Association (APHA) 1995. Standard Methods for Examination of Water and Wastewater, 19th edn. Washington, DC: American Public Health Association (APHA).
2. Bej, A.K., DiCesare, J.L., Haff, L. and Atlas, R.M. (1991) Detection of Escherichia coli and Shigella spp. in water by using the polymerase chain reaction and gene probes for uid. Appl Environ Microbiol 57, 1013-1017.
3. Berlyn, M.A. (1998) Linkage map of Escherichia coli K-12, Edition 10: the traditional map. Microbiol Mol Biol Rev 62, 814-948.
4. Bernasconi, C., Volponi, G., Picozzi, C. and Foschino, R. (2007) Use of the tna Operon as a new molecular target for Escherichia coli detection. Appl Environ Microbiol 73, 6321-6325.
5. Cabelli, V.J., Dufour, A.P., McCabe, L.J. and Levin, M.A. (1982) Swimming-associated gastroenteritis and water quality. Am J Epidemiol 115, 606-616.
6. Chern, E.C., Brenner, K., Wymer, L. and Haugland, R.A. (2009) Comparison of fecal indicator bacteria densities in marine recreational waters by QPCR. Water Qual Expo Health 1, 203-214.
7. Feng, P., Lum, R. and Chang, G.W. (1991) Identification of uidA gene sequences in β- glucuronidase - negative Escherichia coli. Appl Environ Microbiol 57, 320-323.
8. Frahm, E. and Obst, U. (2003) Application of the fluorogenic probe technique (Taqman PCR) to the detection of Enteroccoccus spp. and Escherichia coli in water samples. J Microbiol Methods 52, 123-131.
9. Haugland, R.A. and Heckman, J.L. (1998) Identification of putative sequence specific PCR primers for detection of the toxigenic fungal species Stachybotrys chartarum. Mol Cell Probes 12, 387-396.
10. Haugland, R.A., Siefring, S., Wymer, L., Brenner, K. and Dufour, A. (2005) Comparison of Enterococcus measurements in freshwater at two recreational beaches by quantitative polymerase chain reaction and membrane filter culture analysis. Water Res 39, 559-568.
11. Huys, G., Cnockaert, M., Janda, J.M. and Swings, J. (2003) Escherichia albertii sp. nov., a diarrhoeagenic species isolated from stool specimens of Bangladeshi children. Int J Syst Evol Microbiol 53, 807-810.
12. Iqbal, S., Robinson, J., Deere, D., Saunders, J.R., Edwards, C. and Porter, J. (1997) Efficiency of the polymerase chain reaction amplification of the uid gene for detection of Escherichia coli in contaminated water. Lett Appl Microbiol 24, 498-502.
13. Juck, D., Ingram, J., Prevost, M., Coallier, J. and Greer, C. (1996) Nested PCR protocol for the rapid detection of Escherichia coli in potable water. Can J Microbiol 42, 862-866.
14. Ludwig, W. and Schleifer, K.H. (2000) How quantitative is quantitative PCR with respect to cell counts? Syst Appl Microbiol 23, 556-562.
15. Mahapatra, A., Mahapatra, S. and Mahapatra, A. (2005) Escherichia fergusonii: an emerging pathogen in South Orissa. Indian J Med Microbiol 23, 204.
16. Maheux, A.F., Picard, F.J., Boissinot, M., Bissonnette, L., Paradis, S. and Bergeron, M.G. (2009) Analytical comparison of nine PCR primer sets designed to detect the presence of Escherichia coli/Shigella in water samples. Water Res 43, 3019-3028.
17. McDaniels, A.E., Rice, E.W., Reyes, A.L., Johnson, C.H., Haugland, R.A. and Stelma, G.N. Jr (1996) Confirmational identification of Escherichia coli, a comparison of genotypic and phenotypic assays for glutamate decarboxylase and beta-D-glucuronidase. Appl Environ Microbiol 63, 3350-3354.
18. Menon, P., Billen, G. and Servais, P. (2003) Mortality rates of autochthonous and fecal bacteria in natural aquatic ecosystems. Water Res 37, 4151-4158.
19. Rice, E.W., Allen, M.J. and Edberg, S.C. (1990) Efficacy of β- glucuronidase assay for identification of Escherichia coli by the defined - substrate technology. Appl Environ Microbiol 56, 1203-1205.
20. Sandhya, S., Chen, W. and Mulchandani, A. (2008) Molecular beacons: a real-time polymerase chain reaction assay for detecting Escherichia coli from fresh produce and water. Anal Chim Acta 614, 208-212.
21. Silkie, S.S. and Nelson, K.L. (2009) Concentrations of host-specific and generic fecal markers measured by quantitative PCR in raw sewage and fresh animal feces. Water Res 43, 4860-4871.
22. Silkie, S.S., Tolcher, M.P. and Nelson, K.L. (2008) Reagent decontamination to eliminate false-positives in Escherichia coli qPCR. J Microbiol Methods 72, 275-282.
23. U.S. Environmental Protection Agency. (1986) Ambient Water Quality Criteria for Bacteria - 1986. EPA 440/5-84/002. Washington, DC: Criteria and Standards Division, U.S. Environmental Protection Agency.
24. U.S. Environmental Protection Agency. (2002) Method 1603: Escherichia coli (E. coli) in Water by Membrane Filtration using Modified Membrane-Thermotolerant Escherichia coli Agar (Modified mTEC). Publication EPA-821-R-02-023. Washington, D.C: US EPA Office of Water, Office of Science and Technology.
25. US Environmental Protection Agency. (2003) Bacterial Water Quality Standards for Recreational Waters (Freshwater and Marine Waters). EPA-823-R-03-008. Washington, DC: Office of Water, US Environmental Protection Agency.
26. Wade, T.J., Calderon, R.L., Sams, E., Beach, M., Brenner, K.P., Williams, A.H. and Dufour, A.P. (2006) Rapidly measured indicators of recreational water quality are predictive of swimming-associated gastrointestinal illness. Environ Health Perspect 114, 24-28.
27. Wade, T.J., Calderon, R.L., Brenner, K.P., Sams, E., Beach, M., Haugland, R., Wymer, L. and Dufour, A.P. (2008) High sensitivity of children to swimming-associated gastrointestinal illness: results using a rapid assay of recreational water quality. Epidemiology 19, 375-383.