Evaluation of Host Associated Genetic Markers
for Rapid PCR Based Identification of Fecal
Contamination Sources in Water
Volume 1 - Issue 2
Jia Xue* and Yucheng Feng
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- Electrical Engineer Specializing in Automation and Telemechanics, Republic of Kazakhstan
*Corresponding author:
Jia Xue Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, Alabama, USA
Received: August 14, 2018; Published: August 28, 2018
DOI: 10.32474/OAJESS.2018.01.000107
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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 CowM3, 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 (CowM2) 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 CowM2 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.
Abbreviations: PCR: Polymerase Chain Reactions; MST: Microbial Source Tracking; qPCR: quantitative PCR; ADEM: Alabama
Department of Environmental Management’s; FIB: Fecal Indicator Bacteria; NTC: No Template Controls; AE: Amplification Efficiencies
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