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Advancements in mitigating interference in quantitative polymerase chain reaction (qPCR) for microbial water quality monitoring
Citation:
Nappier, S., A. Ichida, K. Jaglo, Rich Haugland, AND K. Jones. Advancements in mitigating interference in quantitative polymerase chain reaction (qPCR) for microbial water quality monitoring. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, Netherlands, 671:732-740, (2019). https://doi.org/10.1016/j.scitotenv.2019.03.242
Impact/Purpose:
In the 2012 Recreational Water Quality Criteria (RWQC), the United States Environmental Protection Agency (EPA) proposed qPCR Method 1611 as a supplemental indicator to detect and quantify Enterococcus spp. in ambient water on a site-specific basis (U.S. EPA, 2012a). The qPCR methodology offers the advantage of providing rapid detection results (2-6 hours), allowing beach managers to make same-day decisions to protect families and their children. In contrast, water quality results for traditional culturable indicator methods are not available until 24-48 hours after sampling (Haugland et al., 2016).
Description:
The United States Environmental Protection Agency's (EPA)1 2012 Recreational Water Quality Criteria included an Enterococcus spp. quantitative polymerase chain reaction (qPCR) method as a supplemental indicator-method. In 2012, performance of qPCR for beach monitoring remained limited, specifically with addressing interference. A systematic literature search of peer-reviewed publications was conducted to identify where Enterococcus spp. and E. coli qPCR methods have been applied in ambient waters. In the present study, we evaluated interference rates, contributing factors resulting in increased interference in these methods, and method improvements that reduced interference. Information on qPCR methods of interest and interference controls were reported in 16 papers for Enterococcus spp. and 13 papers for E. coli. Of the Enterococcus spp. qPCR methods assessed in this effort, the lowest frequencies of interference were reported in samples using Method 1609. Low frequencies of sample interference were also reported EPA's modified E. coli qPCR method, which incorporates the same reagents and interference controls as Method 1609. The literature indicates that more work is needed to demonstrate the utility of E. coli qPCR for widespread beach monitoring purposes, whereas more broad use of Method 1609 for Enterococcus spp. is appropriate when the required and suggested controls are employed.
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DOI: Advancements in mitigating interference in quantitative polymerase chain reaction (qPCR) for microbial water quality monitoring