Learning Objectives

1. Define aquaculture and name 3 countries leading the world in aquaculture production.

2. Identify 3 antimicrobial medicated feeds approved for aquaculture use in the United States.

3. List the criteria needed to establish a proper veterinarian-client-patient relationship.

4. Explain the environment impacts of antimicrobial resistance in aquaculture.

5. Describe a closed aquaculture system and how it helps to reduce environmental impacts of antimicrobial resistance.

6. Summarize what integrated aquaculture is and how it can be harmful to the environment and impact antimicrobial resistance.

7. Identify 3 alternatives to antibiotics in aquaculture.

Antimicrobial Resistance and Aquaculture

Aquaculture and Antimicrobial Resistance: What Every Veterinarian Should Know

Aquaculture is one of the fastest growing food production systems globally and it is thought that aquaculture will play a major role in providing food to a quickly expanding global population. According to the 2016 United Nations Food and Agriculture Organization report on The State of World Fisheries and Aquaculture, the United States ranks 17th in total aquaculture production behind China, Indonesia, India, Vietnam, Philippines, Bangladesh, the Republic of Korea, Norway, Chile, Egypt, Japan, Myanmar, Thailand, Brazil, Malaysia, and the Democratic People's Republic of Korea.

In the United States, sales of domestic marine aquaculture have grown on average 13 percent per year from 2007-2011 led by increases in oyster and salmon production. 

 By definition, aquaculture is the production of finfish or shellfish that spend at least part of their life cycle in a confined production facility (e.g. net, pond, tank, etc.). Although most veterinarians in the US have had little training in aquaculture and fish health, with the growth of the industry as well as how it is regulated, an increase in veterinary involvement in aquaculture is inevitable.  In this module we will summarize what every veterinarian should know about the rapidly expanding field of aquaculture, how the new veterinary feed directive (VFD) rules apply to aquaculture, and what you can do to help minimize the impacts of antimicrobial resistance (AMR) in aquaculture.

  Image result for aquaculture .gov

Net pen aquaculture in deep coastal waters

The Global Aquaculture Industry & AMR

Making generalizations about aquaculture is a major challenge, primarily because of the diversity of species cultivated (>500 species), the variety of production systems employed, and the variation in how aquaculture is regulated around the world. It is fair to say that we know very little about the use of antibiotics in aquaculture globally and what impact this use may have on the development of AMR. What we do know about these topics is largely derived from aquaculture conducted in Europe, North America, and Japan. In these regions, increased regulatory efforts and consumer interest appear to be driving the industry to foster responsible and sustainable aquaculture practices, including the judicious use of antibiotics. For example, Norway is greatly reducing antimicrobial use by 99% from 1987 to 2013 through the development of stricter regulatory oversight, more responsible health management, and the advent of efficacious vaccines. However, most seafood produced (> 90%) through aquaculture is produced in developing countries, most of which lack appropriate regulations and/or enforcement on the use of antibiotics. Data in the use antimicrobials and their impact on the development of AMR in these countries is scarce. 


Proportion of global aquaculture production by volume by country. Data from FAO (2015).

Antimicrobial use in Aquaculture in the US

The overwhelming majority of antimicrobials used in aquaculture are administered via feed. In the US, there are currently only 3 antibiotics that can be used for aquaculture.  Use of these antibiotics via feed requires a veterinary feed directive (VFD) order, and these forms can be obtained from the manufacturer, the AVMA or the FDA.

Antimicrobial Medicated Feeds Approved for US Aquaculture

  • Aquaflor© (Florfenicol).  First VFD approved drug.  2015 VFD approved.
  • Terramycin© (oxytetracycline).  2017 VFD approved.
  • Romet© (Ormetoprim sulfadimethozine).  2017 VFD approved.

In order to write a VFD, a licensed veterinarian needs to maintain a Veterinarian-Client-Patient Relationship (VCPR) with the client. A VCPR requires each of the following:

1.  Knowledge of the fish health by recent examination of the first or a farm visit

2.  Responsible clinical assessment of fish health

3.  Must be available for follow-up

4.  Must give oversight for use of the medication

5.  Must maintain records

Use of these antimicrobials must be limited to therapeutic purposes only; these antimicrobials are not to be used for growth-promotion, prophylactic, or metaphylactic purposes. The producer must follow the dose, duration of treatment, withdrawal time and expiration date. The VFD must be issued in writing, and both the veterinarian and the producer must keep a copy for at least 2 years.  You give a copy to the producer and distributor once you and the client have agreed on a treatment plan.

Although the guidelines created for VFD’s which were initiated at the beginning of 2017 indicate that extra-label use (ELDU) is strictly prohibited, because the indications for use of these antimicrobials in finfish are extremely limited, the FDA is currently using enforcement discretion for therapeutic ELDU (except for florfenicol, which should never be used off-label due to increased potential risk to the consumer), as outlined in the FDA Compliance Policy Guide Sec. 615.115 “Extralabel Use of Medicated Feeds for Minor Species”. This being said, a definitive diagnosis should be achieved prior to treatment if possible and a complete evaluation of the production system should be conducted to identifying underlying factors that may be contributing to the bacterial infection present. Most bacterial infections in finfish can be avoided with proper attention to water quality, stress, and husbandry. For more on this, please reach out to a veterinarian with advanced knowledge of fish health. For more on what is considered acceptable ELDU in aquaculture, please contact the FDA.

Additional Background

It’s a Global Industry

Only about 5-7% of the USA’s seafood comes from domestic aquaculture (NOAA, 2014; Done et al., 2015). Greater that 90% of global seafood is produced in Asia (Done et al., 2015; Watts et al., 2017).  China produces about 70% of the world’s aquaculture food.  Furthermore, an estimated 90% of shrimp eaten in the U.S. comes from other countries (Gale, 2016).  Currently 84% of seafood consumed in the United States is imported, and about 50% comes from aquaculture (GAO, 2011).  The U.S. inspection system is meant to ensure that imported seafood meets certain regulatory standards, but compliance is difficult. 

The reliance on antibiotics for aquaculture also differs widely between nations.  Done et al. (2015) cites an example of salmon production in which Chile used about 0.5 kg of antibiotic for each Kg of salmon produced, whereas Norway used only 0.002 kg.  No veterinary oversight of antibiotics is required in India, China or many other nations.  Regulation in China has been described as “lax” (Done et al., 2015).  Aquaculture outside the US uses many antibiotics (aminoglycosides, macrolides, penicillins, quinolones, sulfonamides, tetracyclines) that are critically important in human medicine.  In this way, aquaculture may be fostering the same resistance genes that are problematic in land-based food animal production.  Fish disease rates increase when stocking densities are too high and water quality becomes poor, leading to antibiotic usage to ameliorate the problem (Watts, 2017).  This is chain of events is analogous to how antibiotics are commonly used in some livestock operations in an attempt to replace the need for good management. 

It is worth noting that antibiotics used in aquatic systems are usually slow to bio-degrade, so residual concentrations can remain in the seafood that is consumed by people.  Some studies have found antibiotic residues in as much as 52% of aquatic products (Wang et al., 2017).  The FDA increased its surveillance efforts of imported seafood from China after a 2006 survey showed that about a fourth of their samples had residues of unapproved and unsafe additives (Gale, 2016).

Integrated fish/duck tilapia pond in Panama


It is difficult for the consumer to determine where their seafood originated.  Gale et al. (2016) gives an interesting account of how antibiotics are used liberally in Asia and how “shell” companies are quickly started and dissolved to misrepresent the country of origin to avoid tariffs and other importation. They describe how Chinese shrimp were imported as having come from Malaysia, and then mysteriously showed up as coming from Ecuador.   Given the global nature of the seafood business, the critical control point would appear to be better regulation and testing of imported seafood, however traceability may be difficult. 

Environmental impacts

Since aquaculture antibiotics are administered in the feed, the doses used can be higher than what is commonly used for livestock. About 70-80% of antibiotics fed to fish are excreted into the water where they can facilitate the transfer of AMR in the water and sediment ecosystems by potentially promoting horizontal transfer of resistance genes (Watts, 2017).  Closed aquaculture systems are used where effluent is treated and recycled. This greatly reduces the release of antibiotics and waste into the environment.

Integrated aquaculture

Watts et al. (2017) and Gale et al. (2016) provide a good discussion of integrated aquaculture as practiced in Africa and Asia.  In such a system, finfish or shellfish are raised with pigs, cattle or poultry that are near or above a pond such that the fish can eat the manure and left-over feed.  The fish get the antibiotics from the livestock as well as any that is given to them directly.  The impact on resistant bacteria can be multiplicative due to exposure of the fish to foodborne pathogens from the livestock. Considerable antimicrobials and AMR bacteria can accumulate in the pond water.  Pond water is often eventually released into rivers, distributing the antibiotics and resistant bacteria through the aquatic environment.


Integrated aquaculture with pig farming

Alternative to antibiotics

Land-based animal agriculture and aquaculture share a common problem in that antibiotics are often used to substitute for good sanitation and management (Singer et al., 2016). Methods to reduce antibiotic use include lower stocking density, vaccination, improved diagnostics and medical management.  Alternatives to antibiotics can include vegetable extracts, immune stimulation products, phage therapy, and quorum sensing disruption agents. (Watts et al., 2016; Caruso et al., 2016).  Treatment of effluent waste water is also used to reduce the number of antibiotics released into the environment.  The effectiveness of this intervention is dependent on the type of waste treatment system.  


Treatment of effluent waste water

As is the case with land-based animal agriculture, disease prevention can greatly reduce the need for antibiotics. A management system where vaccines, sanitation, and reducing farm density are good practices to keep fish healthy and reducing the amount of antibiotics used (Guy et al., 2017).

Why does it matter? 

While the transfer of AMR genes can be difficult to trace, the potential flow of such genes from agricultural production environments to the consumer is important to limit.  A recent British review estimated that 700,000 people die each year from AMR infections, which is projected to rise to 10 million by 2050 with 100 trillion U.S. dollars in economic impact (O’Neill et al., 2017).  Like other food industries that use antibiotics, the aquaculture industry must develop and use technologies to reduce its reliance on antibiotics. 


Andrew C. Singer, Helen Shaw, Vicki Rhodes and Alwyn Hart.  Review of Antimicrobial Resistance in the Environment and Its Relevance to Environmental Regulators.  2016.  Frontiers in Microbiology.  November 2016, Volume 7, Article 1728.

Caruso, G.  Antibiotic Resistance in Fish Farming Environments: A GlobalConcern.  2016.  Journal of Fisheries 10(4):9-13.

Done, Hansa Y., Arjun K. Venkatesan and Rolf U. Halden.  2015. Does the Recent Growth of Aquaculture Create Antibiotic Resistance Threats Different from those Associated with Land Animal Production in Agriculture?  The AAPS Journal, Vol. 17, No. 3, May 2015.

Gale, Jason, Mulvany, Lydia, and Reel, Monte.  How Antibiotic-Tainted Seafood from China Ends Up on Your Table.  Bloomberg Buisnessweek. Dec 15, 2016. 

Gaunt, Patricia. 2017 NIAA Annual Conference, U.S. Animal Agriculture's Future Role In World Food Production - Obstacles & Opportunities, April 4 - 6, Columbus, OH, USA.

Government Accountability Office (GAO)  SEAFOOD SAFETY, FDA Needs to Improve Oversight of Imported Seafood and Better Leverage Limited Resources,  April 14, 2011.

Guy, Allison.  With Record Antibiotic Use, Concerns Mount that Chile’s Salmon Farms Are Brewing Superbugs. August 1, 2016.  Oceana – Protecting the World’s Oceans.

NOAA. 2017. U.S. Seafood Facts. National Oceanic and Atmospheric Administration.

O’Neill, J. Antimicrobial Resistance: Tackling a Crisis for the Health and Wealth of Nations. The Review on Antimicrobial Resistance. Available online: (accessed on 25 May 2017).

Wang, H.; Ren, L.; Yu, X.; Hu, J.; Chen, Y.; He, G.; Jiang, Q. Antibiotic residues in meat, milk and aquatic products in Shanghai and human exposure assessment. Food Control 2017, 80, 217–225.

Watts, Joy E. M., Harold J. Schreier, Lauma Lanska  and Michelle S. Hale. 2017. The Rising Tide of Antimicrobial Resistance in Aquaculture: Sources, Sinks and Solutions 2017. Mar. Drugs 2017, 15, 158.

Useful links

U.S. Fish and Wildlife Services 

International Association for Aquatic Animal Medicine

World Aquatic Veterinary Medical Association

FDA – Aquaculture