Quantitative real-time PCR does not reliably detect single fecal indicator bacteria in drinking water

The microbial quality of drinking and environmental water is usually determined by culture-based detection of fecal indicator bacteria according to ISO reference methods 16649-1 and 7899-2, respectively. Because of an increasing demand for rapid, culture-independent methods, we tested three quantitative polymerase chain reaction (qPCR) approaches for the simultaneous detection of both, Escherichia coli and Enterococcus spp., using either 16S rRNA or 16S rDNA as a target molecule. Filter sterilized drinking water was artificially contaminated with bacteria from either high or low nutrient culture conditions and directly analyzed after membrane filtration without any other enrichment. Depending on the culture condition used, qPCR analyses revealed a lower limit of detection of 1-10 E. coli/100 ml and 10-100 E. faecalis/100 ml, respectively. In addition, the microbial quality of different surface water samples was monitored. The analyses revealed a clear correlation between viable cell counts and qPCR data. However, the safe and reliable detection of 1 CFU/100 ml failed.