Improved strategies and optimization of calibration models for real-time PCR absolute quantification

Water Research

Volumn 44, Issue 16, 2010, Pages 4726-4735

  Sivaganesan, Mano ^a   Haugland, Richard A ^b   Chern, Eunice C ^b   Shanks, Orin C ^a  

^a U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^b U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

Author keywords

Absolute quantification; Bayesian statistics; Real time quantitative PCR

Indexed keywords

DNA; MARKOV PROCESSES; MONTE CARLO METHODS; PARAMETER ESTIMATION; POLYMERASE CHAIN REACTION; POTABLE WATER; UNCERTAINTY ANALYSIS; WATER QUALITY;

ABSOLUTE QUANTIFICATION; BAYESIAN STATISTICS; CALIBRATION MODEL; DNA TARGETS; OPTIMISATIONS; REAL-TIME PCR; REAL-TIME QUANTITATIVE PCR; SINGLE CURVES; TARGET CONCENTRATIONS; UNCERTAINTY;

BAYESIAN NETWORKS;

DNA; DRINKING WATER;

BAYESIAN ANALYSIS; BIOASSAY; CALIBRATION; DNA; DRINKING WATER; EXPERIMENTAL DESIGN; MARKOV CHAIN; MODEL TEST; MONITORING; MONTE CARLO ANALYSIS; OPTIMIZATION; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; REAL TIME; RECREATIONAL FACILITY; STRATEGIC APPROACH; WATER QUALITY;

ACCURACY; ARTICLE; BAYESIAN LEARNING; CALIBRATION; MEASUREMENT; MODEL; MONTE CARLO METHOD; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; WATER QUALITY;

EID: 77957020519     PISSN: 00431354     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.watres.2010.07.066     Document Type: Article

References (36)

1. Applied Biosystems Essentials of real time PCR. Applied Biosystems 2006.
2. Bae S., Wuertz S. Rapid decay of host-specific fecal Bacteroidales cells in seawater as measured by quantitative PCR with propidium monoazide. Water Research 2009, 43:4850-4859.
3. Bell A., Layton A.C., McKay L., Williams D., Gentry R., Sayler G.S. Factors influencing the persistence of fecal Bacteroides in stream water. Journal of Environmental Quality 2009, 38(3):1224-1232.
4. Caldwell J.M., Raley M.E., Levine J.F. Mitochondrial multiplex real-time PCR as a source tracking method in fecal-contaminated effluents. Environmental Science and Technology 2007, 41:3277-3283.
5. Chern E.C., Brenner K.P., Wymer L., Haugland R. Comparison fecal indicator bacteria densities in marine recreational waters by qPCR. Water Quality, Exposure and Health 2009, 1:203-214.
6. Dick L.K., Simonich M.T., Field K.G. Microplate subtractive hybridization to enrich for Bacteroidales genetic markers for fecal source identification. Applied and Environmental Microbiology 2005, 71(6):3179-3183.
7. Haugland R.A., Siefring S.C., Wymer L.J., Brenner K.P., Dufour A.P. Comparison of Enterococcus measurements in freshwater at two recreational beaches by quantitative polymerase chain reaction and membrane filter culture analysis. Water Research 2005, 39:559-568.
8. Ibekwe A.W., Watt P.M., Grieve C.M., Sharma V.K., Lyons S.R. Multiplex fluoregenic real-time PCR for detection and quantification of Escherichia coli O157:H7 in dairy wastewater wetlands. Applied and Environmental Microbiology 2002, 68(10):4853-4862.
9. Kildare B.J., Leutenegger C.M., McSwain B.S., Bambic D.G., Rajal V.B., Wuertz S. 16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales: a Bayesian approach. Water Research 2007, 41:3701-3715.
10. Kirs M., Smith D.C. Multiplex quantitative real-time reverse transcriptase PCR for F+-specific RNA coliphages: a method for use in microbial source tracking. Applied and Environmental Microbiology 2007, 73(3):808-814.
11. Layton A., McKay L., Williams D., Garrett V., Gentry R., Sayler G. Development of Bacteroides 16S rRNA gene TaqMan-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water. Applied and Environmental Microbiology 2006, 72(6):4214-4224.
12. Leach M.D., Broschat S.L., Call D.R. A discrete, stochastic model and correction method for bacterial source tracking. Environmental Science and Technology 2008, 42:524-529.
13. Lunn D.J., Thomas A., Best N., Spiegelhalter D. WinBUGS-A Bayesian modeling framework: concepts, structure, and extensibility. Statistics and Computing 2000, 10:325-337.
14. Martin B., Jofre A., Garriga M., Pla M., Aymerich T. Rapid quantitative detection of Lactobacillus sakei in meat and fermented sausages by real-time PCR. Applied and Environmental Microbiology 2006, 72(9):6040-6048.
15. McQuaig S.M., Scott T.M., Harwood V.J., Farrah S.R., Lukasik J. Detection of human-derived fecal pollution in environmental waters by use of a PCR-based human polyomavirus assay. Applied and Environmental Microbiology 2006, 72:7567-7574.
16. Mumy K.L., Findaly R.H. Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative-competitive PCR. Journal of Microbiological Methods 2004, 57:259-268.
17. Okabe S., Okayama N., Savichtcheva O., Ito T. Quantification of host-specific Bacteroides-Prevotella 16S rRNA genetic markers for assessment of fecal pollution in freshwater. Applied Microbiology and Biotechnology 2007, 74:890-901.
18. Okabe S., Shimazu Y. Persistences of host-specific Bacteroides-Prevotella 16S rRNA genetic markers in environmental waters: effects of temperature and salinity. Applied Microbiology and Biotechnology 2007, 76:935-944.
19. Pfaffl M.W. A-Z of Quantitative PCR 2004, 87-112. International University Line, La Jolla. S.A. Bustin (Ed.).
20. Pfaffl M.W., Hageleit M. Validities of mRNA quantification using recombinant RNA and recombinant DNA external calibration curves in real-time PCR. Biotechnology Letters 2001, 23:275-282.
21. Rajal V.B., McSwain B.S., Thompson D.E., Leutenegger C.M., Kildare B.J., Wuertz S. Validation of hollow fiber ultrafiltration and real-time PCR using bacteriophage PP7 as surrogate for the quantification of viruses from water samples. Water Research 2007, 41:1411-1422.
22. Rasmussen R. Rapid Cycle Real-time PCR: Methods and Applications 2001, 21-34. Springer Press, Heidelberg. S. Meuer, C. Wittwer, K. Nakagawara (Eds.).
23. Reischer G.H., Kasper D.C., Steinborn R., Mach R.L., Farnleitner A.H. Quantitative PCR method for sensitive detection of ruminant fecal pollution in freshwater and evaluation of this method in Alpine Karstic regions. Applied and Environmental Microbiology 2006, 72(8):5610-5614.
24. Rinttila T., Kassinen A., Malinen E., Krogius L., Palva A. Development of an extensive set of 16S-rDNA-targeted primers for quantification of pathogenic and indegenous bacteria in faecal samples by real-time PCR. Journal of Applied Microbiology 2004, 97:1166-1177.
25. Rutledge R.G., Cote C. Mathematics of quantitative kinetic PCR and the application of standard curves. Nucleic Acids Research 2003, 31(16):e93.
26. Seurinck S., Defoirdt T., Verstraete W., Siciliano S. Detection and quantification of human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater. Environmental Microbiology 2005, 7(2):249-259.
27. Shanks O.C., Atikovic E., Blackwood A.D., Lu J., Noble R.T., Santo Domingo J., Siefring S., Sivaganesan M., Haugland R.P. Quantitative PCR for detection and enumeration of genetic markers of bovine fecal pollution. Applied and Environmental Microbiology 2008, 74(3):745-752.
28. Shanks O.C., Kelty C.A., Sivaganesan M., Varma M., Haugland R.A. Quantitative PCR for genetic markers of human fecal pollution. Applied and Environmental Microbiology 2009, 75:5507-5513.
29. Shanks O.C., White K., Kelty C.A., Hayes S., Sivaganesan M., Jenkins M., Varma M., Haugland R.A. Performance assessment of cattle-associated PCR and quantitative real-time PCR assays targeting Bacteroidales genes. Applied and Environmental Microbiology 2010, 76(5):1359-1366.
30. Silkie S.S., Nelson K.L. Concentrations of host-specific and generic fecal markers measured by quantitative PCR in raw sewage and fresh animal feces. Water Research 2009, 43:4860-4871.
31. Sivaganesan M., Seifring S., Varma M., Haugland R.A., Shanks O.C. A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards. BMC Bioinformatics 2008, 9:120.
32. Stoeckel D.M., Stelzer E.A., Dick L.K. Evaluation of two spike-and-recovery controls for assessment of extraction efficiency in microbial source tracking studies. Water Research 2009, 43:4820-4827.
33. Volkmann H., Schwartz T., Kirchen S., Stofer C., Obst U. Evaluation of inhibition and cross-reaction effects on real-time PCR applied to the total DNA of wastewater samples for the quantification of bacterial antibiotic resistance genes and taxon-specific targets. Molecular and Cellular Probes 2007, 21(2):125-133.
34. Wade T.J., Calderon R.L., Brenner K.P., Sams E., Beach M., Haugland R., Wymer L., Dufour A.P. High sensitivity of children to swimming-associated gastrointestinal illness: results using a rapid assay of recreational water quality. Epidemiology 2008, 19(3):375-383.
35. Wade T.J., Calderon R.L., Sams E., Beach M., Brenner K.P., Williams A.H., Dufour A.P. Rapidly measured indicators of recreational water quality are predictive of swimming-associated gastrointestinal illness. Environmental Health Perspectives 2006, 114:24-28.
36. Walters S.P., Yamahara K.M., Boehm A.B. Persistence of nucleic acid markers of health-relevant organisms in seawater microcosms: implications for their use in assessing risk in recreational waters. Water Research 2009, 43:4929-4939.