Sensitive detection of sample interference in environmental qPCR

Water Research

Volumn 46, Issue 10, 2012, Pages 3251-3260

  Green, Hyatt C ^a,b   Field, Katharine G ^a  

^a OREGON STATE UNIVERSITY   (United States)

^b U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

Author keywords

Bacteroides; Kinetic outlier detection; Microbial ecology; Microbial source tracking; QPCR; Water quality

Indexed keywords

ASSAYS; DATA HANDLING; ECOLOGY; EFFICIENCY; ENVIRONMENTAL REGULATIONS; ETHANOL; EXTRACTION; POLYMERASE CHAIN REACTION; POTABLE WATER; RECOVERY; STATISTICS; WATER QUALITY;

BACTEROIDES; E. COLI; HUMIC ACID; KINETIC OUTLIER DETECTION; MICROBIAL ECOLOGY; MICROBIAL SOURCE TRACKING; OUTLIER DETECTION; QPCR; QUANTITATIVE PCR; SENSITIVE DETECTION;

ESCHERICHIA COLI;

ALCOHOL; HUMIC ACID;

BACTERIUM; BIOASSAY; BIOMARKER; COLIFORM BACTERIUM; DETECTION METHOD; ENVIRONMENTAL RESEARCH; ETHANOL; FECAL COLIFORM; GENE EXPRESSION; HUMIC ACID; INHIBITOR; MICROBIAL ECOLOGY; NUCLEIC ACID; OUTLIER; POLYMERASE CHAIN REACTION; SAMPLING BIAS; WATER QUALITY;

ARTICLE; BACTERIUM MUTANT; BACTEROIDES; ESCHERICHIA COLI; GENE INSERTION; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SAMPLE; SENSITIVITY AND SPECIFICITY; WATER ANALYSIS; WATER CONTAMINATION; WATER QUALITY; WATER SAMPLING;

BACTEROIDES; ESCHERICHIA COLI;

EID: 84861199729     PISSN: 00431354     EISSN: 18792448     Source Type: Journal    
DOI: 10.1016/j.watres.2012.03.041     Document Type: Article

References (28)

1. Abolmaaty A., Gu W., Witkowsky R., Levin R.E. The use of activated charcoal for the removal of PCR inhibitors from oyster samples. Journal of Microbiological Methods 2007, 68:349-352.
2. Baar C., d'Abbadie M., Vaisman A., Arana M.E., Hofreiter M., Woodgate R., et al. Molecular breeding of polymerases for resistance to environmental inhibitors. Nucleic Acids Research 2011, 39:e51.
3. Bar T., Kubista M., Tichopad A. Validation of kinetics similarity in qPCR. Nucleic Acids Research 2011, 19:1-12. [Epub, Available Oct].
4. Bernhard A.E., Field K.G. A PCR assay to discriminate human and ruminant feces based on host differences in Bacteroides-Prevotella 16S ribosomal DNA. Applied and Environmental Microbiology 2000, 66:4571-4574.
5. Boehm A.B., Yamahara K.M., Love D.C., Peterson B.M., McNeill K., Nelson K.L. Covariation and photoinactivation of traditional and novel indicator organisms and human viruses at a sewage-impacted marine beach. Environmental Science & Technology 2009, 43:8046-8052.
6. Braid M.D., Daniels L.M., Kitts C.L. Removal of PCR inhibitors from soil DNA by chemical flocculation. Journal of Microbiological Methods 2003, 52:389-393.
7. Cook K.L., Britt J.S. Optimization of methods for detecting Mycobacterium avium subsp. paratuberculosis in environmental samples using quantitative, real-time PCR. Journal of Microbiological Methods 2007, 69:154-160.
8. Folkesson A., Haagensen J.A.J., Zampaloni C., Sternberg C., Molin S. Biofilm induced tolerance towards antimicrobial peptides. PLoS ONE 2008, 3:e1891.
9. Green H.C., Shanks O.C., Sivaganesan M., Haugland R., Field K.G. Differential decay of human fecal Bacteroides in marine and fresh water. Environmental Microbiology 2011, 13:3235-3249.
10. Hugget J.F., Novak T., Garson J.A., Green C., Morris-Jones S.D., Miller R.F., Zumla A. Differential susceptibility of PCR reactions to inhibitors: an important and unrecognised phenomenon. BMC Research Notes 2008, 1.
11. Kreader C.A. Relief of amplification inhibition in PCR with bovine serum albumin or T4 Gene 32 protein. Applied and Environmental Microbiology 1996, 62:1102-1106.
12. Newton R.J., VandeWalle J.L., Borchardt M.A., Gorelick M.H., McLellan S.L. Lachnospiraceae and Bacteroidales alternative fecal indicators reveal chronic human sewage contamination in an urban harbor. Applied and Environmental Microbiology 2011, 77:6972-6981.
13. Peed L.A., Nietch C.T., Kelty C.A., Meckes M., Mooney T., Sivaganesan M., Shanks O.C. Combining land use information and small stream sampling with PCR-based methods for better characterization of diffuse sources of human fecal pollution. Environmental Science & Technology 2011, 45:5652-5659.
14. Pontiroli A., Travis E.R., Sweeney F.P., Porter D., Gaze W.H., Mason S., et al. Pathogen quantitation in complex matrices: a multi-operator comparison of DNA extraction methods with a novel assessment of PCR inhibition. PLoS ONE 2011, 6:e17916.
15. R: a Language and Environment for Statistical Computing 2010, R Development Core Team, R Foundation for Statistical Computing, Vienna, Austria.
16. 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.
17. Ramakers C., Ruijter J.M., Deprez R.H.L., Moorman A.F.M. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neuroscience Letters 2003, 339:62-66.
18. Ritz C., Spiess A. qpcR: an R package for sigmoidal model selection in quantitative real-time polymerase chain reaction analysis. Bioinformatics 2008, 24:1549-1551.
19. Sauer E.P., VandeWalle J.L., Bootsma M.J., McLellan S.L. Detection of human specific Bacteroides genetic marker provides evidence of widespread sewage contamination of stormwater in the urban environment. Water Research 2011, 45:4081-4091.
20. Schriewer A., Miller W.A., Byrne B.A., Miller M.A., Oates S., Conrad P.A., et al. Presence of Bacteroidales as a predictor of pathogens in surface waters of the Central California Coast. Applied and Environmental Microbiology 2010, 76:5802-5814.
21. Schriewer A., Wehlmann A., Wuertz S. Improving qPCR efficiency in environmental samples by selective removal of humic acids with DAX-8. Journal of Microbiological Methods 2011, 85:16-21.
22. Shanks O.C., Nietch C., Simonich M., Younger M., Reynolds D., Field K.G. Basin-wide analysis of the dynamics of fecal contamination and fecal source identification in Tillamook Bay, Oregon. Applied and Environmental Microbiology 2006, 72:5537-5546.
23. 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.
24. Tichopad A., Bar T., Pecen L., Kitchen R.R., Kubista M., Pfaffl M.W. Quality control for quantitative PCR based on amplification compatibility test. Methods 2010, 50:308-312.
25. Tsai Y.L., Olson B.H. Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Applied and Environmental Microbiology 1992, 58:2292-2295.
26. 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.
27. Wade T.J., Calderon R.L., Brenner K.P., Sams E., Beach M., Haugland R., et al. High sensitivity of children to swimming-associated gastrointestinal illness: results using a rapid assay of recreational water quality. Epidemiology 2008, 19:375-383.
28. Wade T.J., Sams E., Brenner K.P., Haugland R., Chern E., Beach M., et al. Rapidly measured indicators of recreational water quality and swimming-associated illness at marine beaches: a prospective cohort study. Environmental Health 2010, 9.