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Inter-laboratory Comparison of Real-time PCR Methods for Quantification of General Fecal Indicator Bacteria
SHANKS, O. C., M. SIVAGANESAN, R. T. Noble, R. N. Bushon, J. Kinzelman, C. Sinigalliano, J. Griffith, V. J. Harwood, AND R. A. HAUGLAND. Inter-laboratory Comparison of Real-time PCR Methods for Quantification of General Fecal Indicator Bacteria. Presented at IWA 15th International Conference on Diffuse Pollution and Eutrophication, Rotorua, NEW ZEALAND, September 18 - 23, 2011.
The application of quantitative real-time PCR (qPCR) technologies for the rapid identification of fecal bacteria in environmental waters is being considered for use as a national water quality metric in the United States. The transition from research tool to a standardized protocol requires information on the reproducibility and sources of variation associated with qPCR methodology across laboratories. This study examines inter-laboratory variability in the measurement of enterococci and Bacteroidales concentrations from standardized, spiked, and environmental sources of DNA using the Entero1a and GenBac3 qPCR methods, respectively. Comparisons are based on data generated from eight different research facilities. Special attention is placed on reference DNA sources, influence of the DNA isolation/purification step, and effect of simplex and multiplex approaches. Results suggest that a crude lysate is sufficient for DNA isolation unless environmental samples contain substances that can inhibit qPCR amplification. No appreciable difference was observed between simplex and multiplex approaches. In addition, inter-laboratory variability levels remained low (< 10% coefficient of variation) regardless of qPCR method.
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Record Details:Record Type: DOCUMENT (PRESENTATION/POSTER)
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