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A Customized DNA Microarray for Microbial Source Tracking in Environmental Systems
Citation:
Li, X., V. Harwood, B. Nayak, C. Staley, M. Sadowsky, AND J. Weidhass. A Customized DNA Microarray for Microbial Source Tracking in Environmental Systems. Presented at 2016 Recreational Waters Conference, New Orleans, LA, April 12 - 15, 2016.
Impact/Purpose:
To inform the public.
Description:
It is estimated that more than 160, 000 miles of rivers and streams in the United States are impaired due to the presence of waterborne pathogens. These pathogens typically originate from human and other animal fecal pollution sources; therefore, a rapid microbial source tracking (MST) method is needed to facilitate water quality assessment and impaired water remediation. We report a novel qualitative DNA microarray technology consisting of 453 probes for the detection of general fecal and host-associated bacteria, viruses, antibiotic resistance, and other environmentally relevant genetic indicators. A novel data normalization and reduction approach is also presented to help alleviate false positives often associated with high-density microarray applications. To evaluate the performance of the approach, DNA and cDNA was isolated from swine, cattle, duck, goose and gull fecal reference samples, as well as soiled poultry liter and raw municipal sewage. Based on nonmetric multidimensional scaling analysis of results, findings suggest that the novel microarray approach may be useful for pathogen detection and identification of fecal contamination in recreational waters. The ability to simultaneously detect a large collection of environmentally important genetic indicators in a single test has the potential to provide water quality managers with a wide range of information in a short period of time. Future research is warranted to measure microarray performance in different geographic regions and water types.