Aquaculture Magazine

June/July 2016

Antimicrobials in Aquaculture – Research Opportunities

By C. Greg Lutz

The use of antibiotics and other compounds in aquaculture has been under scrutiny for several decades now, and is a common topic when the industry is subject to broad-brush criticism in the media.

By Greg Lutz*

Antibiotic use has been widespread and indiscriminate for many decades, not only in aquaculture but in human populations and farmed animals throughout the planet. This has led to the development of antibiotic resistance in many pathogenic microorganisms. Once they arise, resistance genes can be transferred between bacterial communities, especially in aquatic environments. Unfortunately, many microbes appear to be developing resistance much more rapidly than we are developing new compounds to combat them.

Several years ago, Hansa Done and Rolf Halden, researchers at Arizona State University, conducted a comprehensive study on the use of antibiotics in aquaculture industries across the globe. They looked for the presence of 47 different antibiotics in samples of aquacultured species ranging from swai to salmon, and found traces of 5 of the compounds. Although all the levels detected were below FDA limits, the results were published in the Journal of Hazardous Materials and served as the basis for news stories and a press release by the University which stated that “massive aquaculture operations threaten the health of seas, due to large volumes of fish waste emitted, containing excess nutrients,” and “large amounts of pathogens…”

In spite of such sensationalism having nothing to do with the topic of the research in question (with the implication that wild fish apparently emit little or no waste), the use of antibiotics in aquaculture should be of special concern to all of us because the transfer of genetic resistance from one bacteria to another appears to occur more commonly in aquatic environments. Around the same time that the Done and Halden study was promoted (late 2014), President Barack Obama established a federal task force to address problems surrounding the development of resistant strains of microbes, which at that time were implicated in the deaths of some 23,000 Americans each year. In the interim, more and more reports are coming to light of multi-drug resistant “super-bugs” that pose serious threats to human health.

On May 2, 2016 the U.S. Department of Agriculture (USDA) announced the availability of $6 million to fund research to address antimicrobial resistance (AMR) in a number of areas of food production, including aquaculture. This funding is available through the Agriculture and Food Research Initiative (AFRI), authorized by the 2014 Farm Bill, and administered by USDA’s National Institute of Food and Agriculture (NIFA).

“Through our Antimicrobial Resistance Action Plan, USDA is leading the way to better understand how antibiotic resistance develops find alternatives to antibiotics, and educate people practices that reduce the need for antibiotics,” said Agriculture Secretary Tom Vilsack. “The research projects funded through this announcement will help us succeed in our efforts to preserve the effectiveness of antibiotics and protect public health.”

This funding announcement is one of many ways that USDA supports the Combating Antimicrobial Resistant Bacteria (CARB) National Action Plan and work of the Task Force for Combating Antibiotic Resistance, which USDA co-chairs. Specifically, this program priority promotes the development of sustainable and integrated food safety strategies that reduce public health risks along the entire food chain, from producer to consumer.

Applications must address one or more of the following:

• Develop novel systems approaches to investigate the ecology of microbial resistance microbes and gene reservoirs in the environment in animals, in crops, in food products, or in farm-raised aquaculture products.

Develop, evaluate, and implement effective and sustainable resources and strategies, to include alternative practices, techniques, technologies or tools that mitigate emergence, spread or persistence of antimicrobial resistant pathogens within the agricultural ecosystem, in animals, in crops, and in food.

• Identify critical control points for mitigating antimicrobial resistance in the pre- and post-harvest food production environment.

• Design innovative training, education, and outreach resources (including web-based resources) that can be adapted by users across the food chain, including policy makers, producers, processors, retailers and consumers.

• Design and conduct studies that evaluate the impact and efficacy of proposed research, education and extension/outreach interventions on antimicrobial resistance across the food chain, from primary producers to primary consumers.

Agriculture or aquaculture crops and species must be used for at least 50% of any proposed research, as outlined in the Program Area Priority Section of the Request for Applications. Applications are due by August 3, 2016. See the request for applications ( for more information.

C. Greg Lutz, has a PhD in Wildlife and Fisheries Science from the Louisiana State University. His interests include recirculating system technology and population dynamics, quantitative genetics and multivariate analyses and the use of web based technology for result-demonstration methods.


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