Getting to the Source: A Solution to Solving Bacteria Contamination in Waterways

Unhealthy levels of bacteria, specifically Escherichia coli (E. coli), in waterways is a leading concern for South Carolina, with millions of dollars spent in planning, monitoring, and addressing these failures to meet water quality standards in rivers and lakes. A bacteria monitoring result, such as an E. coli sample, only informs a watershed manager that there is or is not an indication of bacteria contamination in a waterway. These results neither inform the watershed manager of actual presence of contamination, nor the source of the fecal waste. The possible sources are many, including all species of wildlife, domestic pets, sewage, livestock, and waterfowl.

Knowing the relative source of bacteria, from those we can identify, will help the resource manager determine the most effective next steps for a targeted approach to protect drinking water sources and recreational waterways. The use of qPCR has been shown to effectively reduce sampling frequencies and to direct efforts to effectively mitigate the source of bacteria contamination. 

Technical Service
Microbial source tracking is an emerging technology to identify the species of bacteria in a water sample using DNA. Specifically, Clemson University offers this technical service using qPCR, or quantitative polymerase chain reaction. Species currently available for detection are swine, bovine, human, and dog. This list could expand to include other mammals, should the project scope demand it and resources are available. 

wild hogs caught on camera

qPCR is a genetic method that quantifies targeted DNA sequences using a fluorescently tagged probe created to seek that matching sequence. The amount of fluorescence resulting is directly proportional to the amount of amplified DNA. The method is not geographic dependent, meaning no library of information and DNA sequences needs to first be developed for species specific to an area. This makes for a more rapid and cost-effective assessment, typically, and is often referred to as real-time PCR. The Clemson University qPCR service will provide results within seven business days. 

This service is being performed in partnership with the Clemson University Molecular Plant Pathogen Detection Lab. This laboratory, equipment, and staff, are certified annually by the USDA to perform qPCR to detect plant pathogens and assess honeybees as European or Africanized. This service presents an opportunity to utilize available equipment and professional laboratory staff to provide an additional service to meet the needs of South Carolina's resource managers, protect water resources, and provide tools towards more informed watershed management. As a land grant university, Clemson seeks to provide resources that improve the lives of South Carolinians, bringing research and science to application in service to the public. 

Information Sheet

Information sheet image

Click here to open. 

Interested in Submitting Samples?

Cost per sample: $350 in SC; $400 for out of state.
Contact Katie Callahan at 864-646-2158 or to get started or for more information.

Sample Preservation Guidance

Resource for this pilot program - click to download: