EPA Science Inventory

Detection limits and cost comparisons of human- and gull-associated conventional and quantitative PCR assays in artificial and environmental waters

Citation:

Riedel, T., A. Zimmer-Faust, V. Thulsiraj, T. Madi, K. Hanley, D. Ebentier, M. Byappanahalli, B. Layton, M. Raith, A. Boehm, J. Griffith, P. Holden, O. Shanks, S. Weisberg, AND J. Jay. Detection limits and cost comparisons of human- and gull-associated conventional and quantitative PCR assays in artificial and environmental waters. JOURNAL OF ENVIRONMENTAL MANAGEMENT. Elsevier Science Ltd, New York, NY, 136:112-120, (2014).

Description:

Modern techniques for tracking fecal pollution in environmental waters require investing in DNA-based methods to determine the presence of specific fecal sources. To help water quality managers decide whether to employ routine polymerase chain reaction (PCR) or quantitative PCR (qPCR), this study compared the limit of detection (LOD) and costs associated with the human-associated Bacteroidales HF183 Endpoint, HF183 Taqman, HF183 SYBR assays and gull-associated Catellicoccus marimammalium Gull2 Endpoint and Gull2 Taqman assays. LODs were determined using dilutions of sewage or gull feces spiked in three water types (artificial freshwater, environmental creek water, environmental marine water) and logistic modeling of the results. The HF183 Endpoint LOD is 70 times higher than that of HF183 Taqman and HF183 SYBR. The Gull2 Endpoint LOD is not statistically distinguishable from Gull2 Taqman. There was no systematic difference with assay performance based on the water types tested. Initial capital, annual maintenance, and the per reaction consumable costs of the Gull2 Endpoint assay are $15134, $0, and $1.12, respectively, while the Gull2 Taqman assay costs are $29900, $716, and $1.38. Upgrading to qPCR involves greater costs in equipment, maintenance, and consumables, but this increase may be justified with reduced analysis time and, in some cases, lower detection limits.

Purpose/Objective:

To inform the public on matters relating to new methods to distinguish human and bird fecal contamination in environmental waters

URLs/Downloads:

http://dx.doi.org/10.1016/j.jenvman.2014.01.029   Exit

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Record Details:

Record Type: DOCUMENT (JOURNAL/PEER REVIEWED JOURNAL)
Start Date: 04/01/2014
Completion Date: 04/01/2014
Record Last Revised: 03/11/2014
Record Created: 03/10/2014
Record Released: 03/10/2014
OMB Category: Other
Record ID: 270476

Organization:

U.S. ENVIRONMENTAL PROTECTION AGENCY

OFFICE OF RESEARCH AND DEVELOPMENT

NATIONAL RISK MANAGEMENT RESEARCH LABORATORY

WATER SUPPLY AND WATER RESOURCES DIVISION

MICROBIAL CONTAMINANTS CONTROL BRANCH