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.

Tilapia culture is an important source of income and nutrition to many rural families. Since 2000, the production of tilapia increased and reached domestic and global markets. Major farmed species is Nile tilapia (Oreochromis niloticus), in earthen ponds and cage cultures. Intensification contributed to global tilapia disease outbreaks, with bacterial infections causing mortalities and morbidities, threatening sustainable production. At tilapia farms, high nutrient concentrations, water temperature and fish densities enhance bacterial growth including virulent bacterial clones and potential zoonotic bacteria. Global warming favours this. This review respectively provides a comprehensive overview of the most common and emerging bacterial pathogens, diseases, clinical presentations and diagnostics of tilapia, including bacteria and diseases with zoonotic potential. First, common bacterial disease outbreaks, including streptococcosis, motileAeromonassepticaemia, francisellosis, columnaris disease and vibriosis are described. Then, information on emerging bacterial infections of concern for tilapia, like edwardsiellosis throughEdwardsiella ictaluriandE.tarda, as well asAeromonas schubertiiis provided. Reports of infectious bacterial tilapia disease outbreaks from other bacteria, includingLactococcus garvieae,Aerococcus viridans,Pseudomonasspp.,Mycobacterium marinumandChlamydiaspp., and others are reviewed. Furthermore, bacteria with zoonotic potential, likeStreptococcus agalactiaeST283,S.iniae,Aeromonassp.,E.tarda,Vibrio vulnificuspathovar (pv)piscisandM.marinumare included in the review, to provide the most current overview of the disease risks affecting production and post‐harvest stages. Additionally, the status and risks of antimicrobial resistance in bacteria from tilapia and other cultured fish through imprudent use of antibiotics, and its future at a global level are provided.

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.

Since the establishment of a Global Action Plan (GAP) on Antimicrobial Resistance (AMR) (68th World Health Assembly, Geneva, Switzerland, 2015), most members of the World Health Organisation (WHO) have developed and implemented a National Action Plan (NAP) based on a “One Health” approach to AMR. Aquaculture, significant among the food producing sectors, has often been overlooked in AMR governance. We did a systematic review of 95 country NAPs and assessed the inclusion of aquaculture. We also reviewed the scientific literature from 1996 until April 2021 to retrieve data characterising AMR in aquaculture during the last 25 years. In our analysis, 37% of countries did not mention an aquaculture component within their AMR NAP. The South‐East Asia Region had the highest implementation rate of AMR‐aquaculture programmes. Our literature review indicated that most AMR‐aquaculture related studies have taken place in the People's Republic of China, followed by the United States of America and India. Beta‐lactamases, tetracyclines, sulfonamides, macrolides, and fluoroquinolones were the most represented classes of antibiotics, with Vibrio spp. and Aeromonas spp. as the most investigated antimicrobial‐resistant bacteria. This review highlighted the gaps in AMR‐aquaculture governance and the progress made across WHO members. Countries are encouraged to (i) fulfil their commitments by developing and/or fully implementing the AMR NAP, (ii) further engage in the research, monitoring, and surveillance of antimicrobial usage and AMR within the aquaculture sector, and (iii) collaborate at national and international level for a concerted “One Health” approach.