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Low Frequencies of Interference to EPA Quantitative Polymerase Chain Reaction (qPCR) Methods for Microbial Water Quality Monitoring in U.S. Rivers and Streams and Coastal Waters
Haugland, Rich, S. Siefring, E. Anneken, M. Varma, S. Keely, R. Mitchell, AND S. Lehmann. Low Frequencies of Interference to EPA Quantitative Polymerase Chain Reaction (qPCR) Methods for Microbial Water Quality Monitoring in U.S. Rivers and Streams and Coastal Waters. 2018 UNC Water Microbiology Conference, Chapel Hill, NC, May 22 - 24, 2018.
2018 UNC Water Microbiology Conference oral presentation.
In collaboration with U.S States and Tribes, the United States Environmental Protection Agency (EPA) conducts periodic and rotating, statistically based surveys of U.S. rivers and streams (National Rivers and Streams Assessment, NRSA), estuarine and Great Lakes nearshore coastal waters (National Coastal Condition Assessment, NCCA), as well as lakes and ponds and wetlands from the lower contiguous 48 states. These studies, collectively referred to as the National Aquatic Resources Surveys (NARS), are performed to provide the public and decision makers with nationally consistent and representative information on the condition of all the nation’s waters. Among the numerous parameters investigated in these surveys, EPA has determined enterococci fecal indicator bacteria genetic marker concentrations from NRSA and NCCA samples since 2008-2009 for comparisons with national recreational water quality criteria established by the EPA. This report compares QPCR interference rates from EPA Method A for enterococci, determined from the 2008-2009 NRSA samples, with rates obtained from the 2013-2014 NRSA and 2015 NCCA samples using more recently introduced EPA Method 1609.1 for enterococci and draft Method C for E. coli. Interfering samples were identified based on results of similar controls provided in each of these methods. These national surveys indicate lower rates of sample interference with the two more recent EPA methods (1.8% for Method 1609.1 and 2.0% for Method C compared to 7.5% for Method A) in rivers and streams. Even lower interference rates were obtained with Method 1609.1 and Method C in coastal waters. These observations from single samples collected from thousands of sites nationwide are consistent with published results from a smaller number of more extensively sampled sites, suggesting that current EPA qPCR methods are sufficiently robust to be used for monitoring a wide variety of different surface waters in the U.S.