Standardized data quality acceptance criteria for a rapid Escherichia coli qPCR method (Draft Method C) for water quality monitoring at recreational beaches. (1st June 2019)

• Record Type: Journal Article
• Authors: Sivaganesan, Mano; Aw, Tiong Gim; Briggs, Shannon; Dreelin, Erin; Aslan, Asli; Dorevitch, Samuel; Shrestha, Abhilasha; Isaacs, Natasha; Kinzelman, Julie; Kleinheinz, Greg; Noble, Rachel; Rediske, Rick; Scull, Brian; Rosenberg, Susan; Weberman, Barbara; Sivy, Tami; Southwell, Ben; Siefring, Shawn; Oshima, Kevin; Haugland, Richard
• Is Part Of: Water research. Volume 156(2019)
• Page Start: 456
• Page End: 464
• Publication Date: 2019-06-01
• Subjects: qPCR -- E. coli -- EPA method C -- Data quality criteria -- Water quality criteria; Water -- Pollution -- Research -- Periodicals; 363.7394
• DOI: 10.1016/j.watres.2019.03.011
• Languages: English
• ISSNs: 0043-1354

Abstract

Abstract: There is growing interest in the application of rapid quantitative polymerase chain reaction (qPCR) and other PCR-based methods for recreational water quality monitoring and management programs. This interest has strengthened given the publication of U.S. Environmental Protection Agency (EPA)-validated qPCR methods for enterococci fecal indicator bacteria (FIB) and has extended to similar methods for Escherichia coli ( E. coli ) FIB. Implementation of qPCR-based methods in monitoring programs can be facilitated by confidence in the quality of the data produced by these methods. Data quality can be determined through the establishment of a series of specifications that should reflect good laboratory practice. Ideally, these specifications will also account for the typical variability of data coming from multiple users of the method. This study developed proposed standardized data quality acceptance criteria that were established for important calibration model parameters and/or controls from a new qPCR method for E. coli (EPA Draft Method C) based upon data that was generated by 21 laboratories. Each laboratory followed a standardized protocol utilizing the same prescribed reagents and reference and control materials. After removal of outliers, statistical modeling based on a hierarchical Bayesian method was used to establish metrics for assay standard curve slope, intercept and lower limit of quantification that included between-laboratory, replicate testing within laboratory, and random error variability. A nested analysis of variance (ANOVA) was used to establish metrics for calibrator/positive control, negative control, and replicate sample analysis data. These data acceptance criteria should help those who may evaluate the technical quality of future findings from the method, as well as those who might use the method in the future. Furthermore, these benchmarks and the approaches described for determining them may be helpful to method users seeking to establish comparable laboratory-specific criteria if changes in the reference and/or control materials must be made. Graphical abstract: Image 1 Highlights: Data QA criteria were established for an EPA E. coli qPCR method (Draft Method C). QA parameters were slope, intercept for standard curve, LLOQ, Ct values of controls. Data QA was based on use of prescribed reference and control materials by 21 labs. The study also provides guidance for labs to establish QA with their own materials. Polymerase reagent lots should be checked for E. coli signal before use in Method C.