Validation of qPCR method for enterococci quantification at Toronto beaches: Application for rapid recreational water monitoring

Rapid quantitative PCR-based methods for enterococci monitoring can allow public health authorities to make more timely beach posting decisions. However, qPCR methods must be assessed for proposed sites as locale-specific factors may affect DNA recovery or qPCR inhibition. We assessed the feasibility of the USEPA 1609.1 qPCR-based (Enterococcus) method at two urban Toronto beaches and three recreational areas at nearby river mouths in parallel with culture-based methods on the same water samples. A strong positive correlation was observed between the Enterococcus qPCR method and culturing-based quantification methods for E. coli and enterococci at both beaches and two river mouth areas. One river, known to be highly sewage-impacted, did not yield DNA suitable for qPCR analyses. qPCR results from biological replicates were strongly correlated and showed coefficients of variation as low as or lower than culture-based methods. With respect to Beach Action Value exceedances, the USEPA 1609.1 qPCR method provided an 80–90% level of agreement with E. coli enumeration results and >90% with enterococci enumeration. Results indicated that if recreational water locations and sampling conditions met the requirements of the USEPA 1609.1 qPCR method, the method can meet or exceed all quality control requirements and provide water quality results within 3.5 h for diverse recreational water settings around the City of Toronto.