Comparison of Enterococcus quantitative polymerase chain reaction analysis results from Midwest U.S. river samples using EPA Method 1611 and Method 1609 PCR reagents

•The U.S. EPA will offer two qPCR methods for beach water monitoring for enterococci.•River water analyses with qPCR reagents from the two methods were compared.•The newer reagent had less inhibition and allowed analyses of more DNA extract.•Enterococci densities were estimated as calibrator sequence equivalents (CSE).•CSE estimates from diluted DNA extracts were indistinguishable with these reagents.

Enterococci target sequence density estimates from analyses of diluted river water DNA extracts by EPA Methods 1611 and 1609 and estimates with lower detection limits from undiluted DNA extracts by Method 1609 were indistinguishable. These methods should be equally suitable for comparison with U.S. EPA 2012 Recreational Water Quality Criteria values.