Environmental Pathogen Studies

USDA/Agriculture and Food Research Initiative (AFRI)


Project Title: A systems approach to identifying and filling gaps in and between knowledge and practice in production and distribution of local and regional foods for a more secure food supply chain

In Alabama and nationwide, the popularity and demand for locally grown food is soaring, as consumers increasingly insist on knowing where their food comes from and who grew it. That is excellent news for small-scale local producers and processors, and for rural economies in general, but Bratcher notes that those consumers have high expectations.

an innovative project based at Auburn University aimed at ensuring the quality and safety of locally and regionally produced meat. This USDA/AFRI-funded project is led by a multidisciplinary team of professors and extension specialists at AU and Tuskegee University who specialize in animal sciences, agriculture economics, food safety, supply chain analysis, marketing, sociology, business, and environmental sciences. This project is supported by the Agriculture and Food Research Initiative competitive grant no. 2013-06767 of the USDA National Institute of Food and Agriculture.

AU Animal Sciences Department assistant professor, Christy Bratcher and the multidisciplinary team have been awarded a five-year, $4.8 million grant from USDA’s National Institute of Food and Agriculture (NIFA) to help ensure the safety of locally produced foods. “We’re going to look at current production practices and find out how close farmers’ perceptions of what they’re doing to supply safe food actually come to reality and then develop approaches these and other small, local farms and processors can use to improve their production practices and reduce the risks of food contamination,” Bratcher says.

Dr. Bratcher (left) and graduate research assistant Christine swabbing hay feeder for bacterial analysis

The project goal is to identify consumer perceptions about locally/regionally produced foods and compare that to the perceptions of the farmers/producers. The information will then be evaluated to develop guidelines and practices aimed toward improving food safety and build teaching modules to deliver the information to farm operators. The first phase of the project consists of on-farm data collection – bacterial sampling of troughs, barns and equipment as well as microbial sampling of streams located on or near each farm to evaluate water quality.

Dr. Luxin Wang swabbing cattle hides for bacterial analysis

AU Water Resource Center staff who coordinate the Alabama Water Watch Program are conducting the on-farm evaluation of water quality portion of the project. Bacteriological monitoring of streams flowing through farms is being conducted using the Coliscan Easygel ® method (the same method that AWW trains and certifies citizen monitor in). Through this monitoring effort, combined with the additional on-farm bacteriological monitoring, the research team plans to evaluate and track paths of bacterial contamination throughout the supply chain and develop production and processing recommendations that result in a healthier food supply.

AL WRRI Bacteriological Study

Alabama Water Resources Research Institute (AL WRRI) Bacterial Contamination Study
Click here for the PROJECT FINAL REPORT

AWW staffer, Eric Reutebuch, sampling a stream for bacteria

AU researchers and outreach specialists are partnering with citizen volunteer monitoring groups on two major lakes in Alabama to evaluate water quality at public use areas and investigate better ways to protect the public’s health. Luxin Wang, microbiological researcher at AU, and Eric Reutebuch, director of the Alabama Water Watch Program, received a one-year grant from the Alabama Water Resources Research Institute to sample public swimming areas at lakes Martin and Logan Martin alongside AWW-certified bacteriological monitors.

The health and well-being of Alabama’s citizens relative to recreational water usage depends on credible and timely monitoring of public swimming areas and other recreational waters to assess these areas for contamination with pathogens and other pollutants. Escherichia coli bacteria are commonly used as indicator organisms for the presence of fecal contamination and its associated pathogens in inland waters, while Enterococci are used in marine waters (USEPA, 2012). The State (Alabama Department of Environmental Management) routinely monitors swim areas along Alabama’s coast – the Coastal Alabama Beach Monitoring Program involves the routine collection of water samples from 25 high-use and/or potentially high-risk public recreational sites from Perdido Bay to Dauphin Island, for details see http://adem.alabama.gov/programs/coastal).

Inland swimming and recreational-use areas are not routinely monitored by the State. With increasing pressures on these inland waters from urban development, industrial needs, agricultural needs and others, there is increasing risk to the public health from contaminated waters (Natural Resources Defense Council, 2013).


LMLPA volunteer monitor Wayne Wilcox using AWW protocol
to test for bacterial contamination in lake Logan Martin
at the beach area of Lakeside Park in Pell City, AL
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The objectives of this project are to:

  • sample multiple public swimming/recreational-use areas for bacterial contamination on two major reservoirs, one in the Tallapoosa Basin (Lake Martin) and one in the Coosa Basin (Lake Logan Martin) throughout the outdoor recreational season;
  • sample swim beach sediments to test for the presence of E. coli, and to test for other fecal bacteria (Salmonella);
  • conduct additional side-by-side AWW volunteer monitor bacteriological testing  and agency testing, and;
  • test for sourcing of E. coli using selective antibiotic disks on bacterial media cultures.

Expected project benefits and information include the following:

  • development of recommendations for swim beach/recreation area monitoring protocols that are most protective of human health will be developed;
  • dissemination of project results, conclusions and recommendations to AWW volunteer monitors throughout the state and to state agencies involved in monitoring public waters, and;
  • improved monitoring of public swimming and recreational-use areas in inland waters based on the results and recommendations of this project.

Update: Read the article in Lake Magazine on the project’s preliminary results:

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