Evaluation of Host Associated Genetic Markers for Rapid PCR Based Identification of Fecal Contamination Sources in Water

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Abstract
The water quality of many waterways in the state of Alabama, and in the nation as a whole, is deteriorating due to point and nonpoint source pollution from human and animal waste. Accurate identification of contamination sources is essential if we are to develop cost-effective pollution control strategies. The direct detection of host specific genetic markers by Polymerase Chain Reactions (PCR) has been widely used in identifying sources of fecal contamination in environmental waters. In this study, we conducted experiments to validate genetic markers associated with deer/elk, Canada goose, dog, and cattle for Microbial Source Tracking (MST) in Alabama. End point PCR was performed on 10 raw sewage samples and 133 fecal samples from nine animal species. Our results showed that CowM 3 , GFD (goose), and deer/elk associated markers have acceptable specificity and sensitivity, making them suitable for MST studies. However, the dog marker and one of the cattle markers (CowM 2) exhibited cross reactions with other fecal samples. The performance of these host associated markers in environmental water was evaluated using both end point and quantitative PCR (qPCR). Human, goose, and dog markers were detected in several water samples by end point PCR; the human marker and CowM 2 marker were also detected by qPCR. Samples collected after a significant rainfall event showed the highest frequency of genetic marker detection. Both human and Canada geese contributed to fecal pollution in samples from Parkerson Mill Creek.

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