With the rapid growth of the aquaculture production since the 1980s, there has been a concomitant increase in disease outbreaks. The injudicious and/or incorrect use of antimicrobial agents against diseases of farmed aquatic species poses a considerable threat to the development and growth of a successful and sustainable aquaculture industry. An increase in antimicrobial resistance (AMR) is an important consequence, resulting to the difficulty in treating common bacterial diseases in populations of aquatic organisms, combined with the presence of antibiotic residues in food fish and their products, leading to import refusals and negative impacts on international trade. To reduce the frequency of AMR, good aquaculture and effective biosecurity practices should include the prudent and responsible use of antibiotics and also consider the use of alternatives to antibiotics, in addition to disease prevention management. This article reviews the literature discussing the scope of the problem pertaining to antibiotic use, the emergence of AMR in aquaculture and to consider and discuss viable alternatives (e.g., vaccination, bacteriophages, quorum quenching, probiotics and prebiotics, chicken egg yolk antibody and medicinal plant derivative). We also discuss lessons learnt, from specific case studies such as the vaccination of farmed salmon in Norway and the use of ‘specific pathogen‐free’ seed—as primary and essential part of a biosecurity strategy.

The challenges and problems of managing good biosecurity are wide‐ranging and multifactorial with many compounding factors to pre‐dispose farmed stocks to an increased risk of infection with consequential stock losses. Many challenges are anthropogenic in origin and may be the result of the physical location (site) and/or the poor design of the production facility (i.e., water re‐use; lack of zoning based on biosecurity risk, etc.) as well as from inappropriate decisions and practices made once the site is in production (i.e., pushing the system for increased biomass production). There is a need for better regulation and health legislation across aquaculture—an industry that embraces the culture of >500 species. In the absence of regulatory frameworks and culture guidelines, it is difficult for farmers to apply certain measures such as maximum stocking densities and maximum allowed biomass, conduct disease surveillance and regular health checks, and report diseases to relevant authorities for advice. In this review, we have identified several issues which are continuing to challenge the design and implementation of efficient and effective biosecurity strategies and protocols at all levels, requiring attention over the coming decade. They are, not in any order of priority: (a) healthy seed, (b) emergency preparedness and response, (c) diagnostics, (d) microbial management at the production level, (e) disease and pathogen surveillance, (f) trade in aquatic species, (g) policies and regulatory framework, (h) welfare, (i) research and technology development, (j) antimicrobial resistance, (k) non‐conventional ways of pathogen transfer, and (l) Progressive Management Pathway.