Antimicrobials destroy bacteria, viruses, fungi, algae, and other microbes. The cells of bacteria (prokaryotes), such as salmonella, differ from those of higher-level organisms (eukaryotes), such as fish. Antibiotics are chemicals designed to either kill or inhibit the growth of pathogenic bacteria while exploiting the differences between prokaryotes and eukaryotes in order to make them relatively harmless in higher-level organisms. Antibiotics are constructed to act in one of three ways: by disrupting cell membranes of bacteria (rendering them unable to regulate themselves), by impeding DNA or protein synthesis, or by hampering the activity of certain enzymes unique to bacteria.Todor’s Online Textbook of Bacteriology, Kenneth Todor, PhD., 2008 (last visited Oct 1, 2011)

Antibiotics are used in aquaculture to treat diseases caused by bacteria. Sometimes the antibiotics are used to treat diseases, but more commonly antibiotics are used to prevent diseases by treating the water or fish before disease occurs."Ecotoxicity of mixtures of antibiotics use in aquacultures". Environ. Toxicol. Chem. 25: 2208-2215. Christensen, A.M., Ingersley, F., and Baun, A. 2006. While this prophylactic method of preventing disease is profitable because it prevents loss and allows fish to grow more quickly, there are several downsides.

The overuse of antibiotics can create antibiotic-resistant bacteria. Antibiotic-resistant bacteria can spontaneously arise when selective pressure to survive results in changes to the DNA sequence of a bacterium allowing that bacterium to survive antibiotic treatments. Because some of the same antibiotics are used to treat fish that are used to treat human disease, pathogenic bacteria causing human disease can also become resistant to antibiotics as a result of treatment of fish with antibiotics.Antimicrobial agents in aquaculture: potential impact on health. APUA Newsletter. 18: 1-6. Angulo, F.J. 2000. For this reason, the overuse of antibiotics in treatment of fish aquaculture (among other agricultural uses) could create public health issues."Public health consequences of use of antimicrobial agents in food animals in the United States". Microb. Drug Resist 9: 373-379. Anderson, A.D., J.M. Nelson, S. Rossiter and F.J. Angulo. 2003.

Overview The issue has two sides. In some countries, clean water supplies for aquaculture are extremely limited.Tainted Seafood Reaching U.S., Food Safety Experts Say, Nicole Gilbert, News21, 2011 (last visited Oct. 2011). Untreated animal manure and human waste are used as feed in shrimp farms and tilapia farms in China and Thailand, in addition to the collection of waste products accumulating from inadequate sewage treatment. In order to prevent the spread of bacteria and disease in contaminated water, some foreign fish farms put U.S.-banned antibiotics into their fishmeal. However, because the more stringent growing regulations in the US increase the price of food, imports from nations without these regulations are increasing based on price and profit.SEAFOOD SAFETY, FDA Needs to Improve Oversight of Imported Seafood and Better Leverage Limited Resources, United States Government Accountability Office, April 14, 2011

Between 1995 and 2005, the first ten years of the NAFTA-WTO era in the US, seafood imports increased 65 percent and shrimp imports increased 95 percent.TRADE DEFICIT IN FOOD SAFETY, Proposed NAFTA Expansions Replicate Limits On U.S. Food Safety Policy That Are Contributing To Unsafe Food Imports, Public Citizen’s Global Trade Watch, 2007 Today, 80 percent of American seafood is imported, about half coming from aquaculture. China, Thailand and Vietnam together account for 44 percent of seafood imports into the United States.China 23%, Thailand 16%, and Vietnam 5%. SEAFOOD SAFETY, FDA Needs to Improve Oversight of Imported Seafood and Better Leverage Limited Resources, United States Government Accountability Office, April 14, 2011

The FDA has been testing for chemicals in aquaculture products for over two decades. In November 2005, the testing program for aquaculture drugs was revised to include antibiotics such as chloramphenicol, fluoroquinolones, nitrofurans, and quinolones, as well as antimicrobial compounds like malachite green that are not approved for use in aquaculture fish.USFDA, Industry Efforts Reduce Use of Unapproved Drugs. Global Aquaculture Advocate. July, August, 2006 Issue. p.38-39. Collette, B. From October 1, 2006, through May 31, 2007, FDA tested samples of catfish, basa, shrimp, dace, and eel from China, finding twenty-five percent of the samples to contain drug residues.Hearing on "Safety of Chinese Imports", statement of Murray M. Lumpkin, M.D., Deputy Commissioner for International and Special Program before the Senate Committee on Commerce, Science & Transportation, July 18, 2007 FDA has approved five different drugs for use in aquaculture as long as the seafood contains less than a mandated maximum residue limit: florfenicol, sulfamerazine, chorionic gonadotropin, oxytetracycline dihydrate, oxytetracycline hydrochloride, as well as a drug combination of sulfadimethoxine and ormetoprim. FDA has approved two drugs—formalin and hydrogen peroxide—for which it has not set a tolerance.

The FDA now enforces regulations in the US requiring testing of certain imported products for antimicrobial agents under Import Alert 16–131.FDA Import Alert 16-131, https://www.accessdata.fda.gov/cms_ia/importalert_33.html The Import Alert provides that the use of antimicrobials during the various stages of aquaculture, including malachite green, nitrofurans, fluoroquinolones, and gentian violet, may contribute to an increase of antimicrobial resistance in human pathogens and that prolonged exposure to nitrofurans, malachite green, and gentian violet has been shown to have a carcinogenic affect. In a consumer brochure, the FDA describes the reasoning for enforcement under the import alert:

After FDA repeatedly found that farm-raised seafood from China was contaminated, the agency announced on June 28, 2007, a broader import control of all farm-raised catfish, basa, shrimp, dace(related to carp), and eel from China. During targeted sampling, from October 2006 through May 2007, FDA repeatedly found that farm-raised seafood from China was contaminated with antimicrobial agents that are not approved for use in the United States. More specifically, the antimicrobials nitrofuran, malachite green, gentian violet, and fluoroquinolones, were detected.How FDA Regulates Seafood, FDA, 2007. ()

Due to limitations on funding and resources, U.S. Government Accountability Office states that only 1% of seafood, compared with 2% of all imports, is inspected and only 0.1% of all seafood is tested for antibiotic residue.

Example antimicrobials

Copper alloys

Recently, copper alloys have become important netting materials in aquaculture (the farming of aquatic organisms including fish farming). Various other materials including nylon, polyester, polypropylene, polyethylene, plastic-coated welded wire, rubber, patented twine products (Spectra, Dyneema), and galvanized steel are also used for netting in aquaculture fish enclosures around the world.Offshore Aquaculture in the United States: Economic considerations, implications, and opportunities, U.S. Department of Commerce, National Oceanic & Atmospheric Administration, July 2008, p. 53Southern Regional Aquaculture Center at http://aquanic.org/publicat/usda_rac/efs/srac/162fs.pdf All of these materials are selected for a variety of reasons, including design feasibility, material strength, cost, and corrosion resistance.

What sets copper alloys apart from the other materials used in fish farming is that copper alloys are antimicrobial (For information about the antimicrobial properties of copper and its alloys, see Antimicrobial properties of copper and Antimicrobial copper alloy touch surfaces). In the marine environment, the antimicrobial/algaecidal properties of copper alloys prevent biofouling, which can briefly be described as the undesirable accumulation, adhesion, and growth of microorganisms, plants, algae, tube worms, barnacles, mollusks, and other organisms on man-made marine structures.Marine Fouling and its Prevention, Wood Hole Oceanographic Institution, 1952, United States Naval Institute, Annapolis, Maryland, USA By inhibiting microbial growth, copper alloy aquaculture pens avoid the need for costly net changes that are necessary with other materials. The resistance of organism growth on copper alloy nets also provides a cleaner and healthier environment for farmed fish to grow and thrive. In addition to their antifouling benefits, copper alloys have strong structural and corrosion-resistant properties in marine environments. Brass alloy netting cages are also currently being deployed in commercial-scale aquaculture operations in Asia, South America, and the USA. See antimicrobial properties of brass

Methylene blue Methylene blue is used in aquaculture and by tropical fish hobbyists as a treatment for fungal infections. It can also be effective in treating fish infected with ich, the parasitic protozoa Ichthyophthirius multifiliis. It is usually used to protect newly laid fish eggs from being infected by fungus or bacteria. This is useful when the hobbyist wants to artificially hatch the fish eggs. Methylene Blue is also very effective when used as part of a "medicated fish bath" for treatment of ammonia, nitrite, and cyanide poisoning as well as for topical and internal treatment of injured or sick fish as a "first response". Aquarium Chemical Treatments

Ozone Ozone is added to seawater and used for the surface disinfection of haddock and Atlantic halibut eggs against nodavirus. Nodavirus is a lethal and vertically transmitted virus which causes severe mortality in fish. Haddock eggs should not be treated with high ozone level as eggs so treated did not hatch and died after 3–4 days.

Some problematic antimicrobials

Malachite green In 1983, the FDA banned the use of malachite green in aquaculture. Toxicity studies have shown that this chemical can have serious toxic side effects. Malachite green is not actually an antibiotic, but has antibiotic properties. Malachite green is somewhat stable within the environment and, therefore, is detectable in fish that were treated with the chemical at some point even after treatment has discontinued."Quantitative and confirmatory analyses of malachite green and leucomalachite gree residues in fish and shrimp". USFDA Laboratory Information Bulletin. LIB No. 4363 Vol 21 (11). Andersen, W. C., S. B. Turnipseed and J. E. Roybal 2005. After more stringent testing and inspection by the governments of Western Countries, the use of malachite green began to wane and other drugs began to become more prevalent.

Chloramphenicol While the U.S. has tested farm-raised shrimp for chloramphenicol since 1994, over the last decade the FDA developed a more sensitive testing methodology and changed the levels of detection for chloramphenicol in response to increasing discovery of traces of chloramphenicol in imports.Keyes, C.W. 2006. "Safety in Seafood, Regulatory Interplay Combines Testing, Enforcement". Global Aquaculture Advocate. April/May p. 20-23. In response to the US discovery of chloramphenicol in imported shrimp and subsequent increased testing sensitivity, the use of this compound in aquaculture began to decrease.Collette, B. 2006 USFDA, "Industry Efforts Reduce Use of Unapproved Drugs". Global Aquaculture Advocate. July/August. p.38-39.

Gentian violet