Development of a qPCR assay for the detection of naturalized wastewater E. coli strains

We recently demonstrated the presence of naturalized populations of Escherichia coli in municipal sewage. We wanted to develop a quantitative polymerase chain reaction (qPCR) assay targeting the uspC-IS30-flhDC marker of naturalized wastewater E. coli and assess the prevalence of these naturalized strains in wastewater. The limit of detection for the qPCR assay was 3.0 × 10^-8 ng of plasmid DNA template with 100% specificity. This strain was detected throughout the wastewater treatment process, including treated effluents. We evaluated the potential of this marker for detecting municipal sewage/wastewater contamination in water by comparing it to other human and animal markers of fecal pollution. Strong correlations were observed between the uspC-IS30-flhDC marker and the human fecal markers Bacteroides HF183 and HumM2, but not animal fecal markers, in surface and stormwater samples. The uspC-IS30-flhDC marker appears to be a potential E. coli-based marker for human wastewater contamination.