title: Detection limits and cost comparisons of human- and gull-associated conventional and quantitative PCR assays in artificial and environmental waters.
abstract: Some molecular methods for tracking fecal pollution in environmental waters have both PCR and quantitative PCR (qPCR) assays available for use. To assist managers in deciding whether to implement newer qPCR techniques in routine monitoring programs, we compared detection limits (LODs) and costs of PCR and qPCR assays with identical targets that are relevant to beach water quality assessment. For human-associated assays targeting Bacteroidales HF183 genetic marker, qPCR LODs were 70 times lower and there was no effect of target matrix (artificial freshwater, environmental creek water, and environmental marine water) on PCR or qPCR LODs. The PCR startup and annual costs were the lowest, while the per reaction cost was 62% lower than the Taqman based qPCR and 180% higher than the SYBR based qPCR. For gull-associated assays, there was no significant difference between PCR and qPCR LODs, target matrix did not effect PCR or qPCR LODs, and PCR startup, annual, and per reaction costs were lower. Upgrading to qPCR involves greater startup and annual costs, but this increase may be justified in the case of the human-associated assays with lower detection limits and reduced cost per sample.
authors.affiliation: Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA. Electronic address: triedel@utexas.edu.
authors.forename: Timothy E
authors.initials: TE
authors.lastname: Riedel
authors.affiliation: Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA; Institute of the Environment and Sustainability, University of California Los, Angeles, Los Angeles, CA 90095, USA.
authors.forename: Amity G
authors.initials: AG
authors.lastname: Zimmer-Faust
authors.affiliation: Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Thulsiraj
authors.affiliation: Source Molecular Corporation, Miami, FL 33155, USA.
authors.forename: Tania
authors.initials: T
authors.lastname: Madi
authors.affiliation: Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA.
authors.forename: Kaitlyn T
authors.initials: KT
authors.lastname: Hanley
authors.affiliation: Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA.
authors.forename: Darcy L
authors.initials: DL
authors.lastname: Ebentier
authors.affiliation: U.S. Geological Survey, Great Lakes Science Center, Lake Michigan Ecological Research Station, Porter, IN 46304, USA.
authors.forename: Muruleedhara
authors.initials: M
authors.lastname: Byappanahalli
authors.affiliation: Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA.
authors.forename: Blythe
authors.initials: B
authors.lastname: Layton
authors.affiliation: Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA.
authors.forename: Meredith
authors.initials: M
authors.lastname: Raith
authors.affiliation: Environmental and Water Studies, Department of Civil and Environmental, Engineering, Stanford University, Stanford, CA 94305, USA.
authors.forename: Alexandria B
authors.initials: AB
authors.lastname: Boehm
authors.affiliation: Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA.
authors.forename: John F
authors.initials: JF
authors.lastname: Griffith
authors.affiliation: Bren School of Environmental Science & Management, and Earth Research Institute, University of California, Santa Barbara, CA 93106, USA.
authors.forename: Patricia A
authors.initials: PA
authors.lastname: Holden
authors.affiliation: U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, OH 45268, USA.
authors.forename: Orin C
authors.initials: OC
authors.lastname: Shanks
authors.affiliation: Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA.
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Weisberg
authors.affiliation: Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Jay
mesh_terms: D000818:Animals; D041963:Bacteroidetes / Q000302:isolation & purification; D001681:Biological Assay / Q000191:economics / Q000379:methods; D046091:Charadriiformes; D003365:Costs and Cost Analysis; D004269:DNA, Bacterial / Q000302:isolation & purification*; D023381:Endpoint Determination / Q000191:economics / Q000379:methods; D004787:Environmental Pollution / Q000032:analysis; D005243:Feces / Q000737:chemistry; D005819:Genetic Markers; D006801:Humans; D057230:Limit of Detection; D016014:Linear Models; D016015:Logistic Models; D016133:Polymerase Chain Reaction / Q000191:economics* / Q000379:methods*; D014867:Water / Q000737:chemistry*; D014871:Water Microbiology / Q000592:standards; D060753:Water Quality / Q000592:standards
chemical_list: D004269:DNA, Bacterial; D005819:Genetic Markers; D014867:Water
keywords: Cost analysis; Endpoint; Gull; HF183; LOD; qPCR