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Monitoring and surveillance of antimicrobial resistance in bacterial pathogens from aquaculture

Regional Guidelines for the Monitoring and Surveillance of Antimicrobial Resistance, Use and Residues in Food and Agriculture – Volume 3









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Last updated 29/02/2024, see Corrigendum


FAO, NParks and SFA, 2023. Monitoring and surveillance of antimicrobial resistance in bacterial pathogens from aquaculture – Regional Guidelines for the Monitoring and Surveillance of Antimicrobial Resistance, Use and Residues in Food and Agriculture. Volume 3. Bangkok.



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    Improving biosecurity through prudent and responsible use of veterinary medicines in aquatic food production 2012
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    The current trend towards increasing intensification and diversification of global aquaculture has lead to its dramatic growth, thus making aquaculture an important food-producing sector that provides an essential source of aquatic protein for a growing human population. For both developed and developing countries, the sector is recognized as creator of jobs and an important source of foreign export earnings. The expansion of commercial aquaculture, as is the case in commercial livestock and pou ltry production, has necessitated the routine use of veterinary medicines to prevent and treat disease outbreaks due to pathogens, assure healthy stocks and maximize production. The expanded and occasionally irresponsible global movements of live aquatic animals have been accompanied by the transboundary spread of a wide variety of pathogens that have sometimes caused serious damage to aquatic food productivity and resulted in serious pathogens becoming endemic in culture systems and the natura l aquatic environment. The use of appropriate antimicrobial treatments is one of the most effective management responses to emergencies associated with infectious disease epizootics. However, their inappropriate use can lead to problems related to increased frequency of bacterial resistance and the potential transfer of resistance genes in bacteria from the aquatic environment to other bacteria. Injudicious use of antimicrobials has also resulted in the occurrence of their residues in aquacultur e products, and as a consequence, bans by importing countries and associated economic impacts, including market loss have occurred. Since disease emergencies can happen even in well-managed aquaculture operations, careful planning on the use antimicrobials is essential in order to maximize their efficacy and minimize the selection pressure for increased frequencies of resistant variants. The prudent and responsible use of veterinary medicines is an essential component of successful commercial aq uaculture production systems. The FAO/AAHRI Expert Workshop on Improving Biosecurity through Prudent and Responsible Use of Veterinary Medicines in Aquatic Food Production was convened in Bangkok, Thailand from 15 to 18 December 2009, in order to understand the current status of the use of antimicrobials in aquaculture and to discuss the concerns and impacts of their irresponsible use on human health, the aquatic environment and trade. Such discussions became the basis for drafting recommenda tions targeted to the state and private sectors and for developing guiding principles on the responsible use of antimicrobials in aquaculture that will be part of the FAO Code of Conduct for Responsible Fisheries Technical Guidelines on Prudent and Responsible Use of Veterinary Medicines in Aquaculture. Since aquaculture is expected to continue to increase its contribution to the world¿s production of aquatic food, offer opportunities to alleviate poverty, increase employment and community de velopment and reduce overexploitation of natural aquatic resources, appropriate guidance to aquaculture stakeholders on the responsible use of veterinary medicines has become essential. Safe and effective veterinary medicines need to be available for efficient aquaculture production, and their use should be in line with established principles on prudent use to safeguard public and animal health. The use of such medicines should be part of national and on-farm biosecurity plans and in accordance with an overall national policy for sustainable aquaculture. This publication is presented in two parts: Part 1 contains 15 technical background papers presented during the expert workshop, contributed by 28 specialists and which served as a basis for the expert workshop deliberations; Part 2 contains the highlights of the expert workshop.
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    This West Balkans Regional Aquatic Animal Disease Diagnostic Manual is a handbook whose main purpose is to facilitate the daily duties at aquaculture farms and provide a useful reference that will answer the majority of practical questions posed by official veterinarians, veterinary inspectors and fish health experts in five Western Balkan countries (Bosnia and Herzegovina, the Republic of Croatia, The former Yugoslav Republic of Macedonia, Montenegro and the Republic of Serbia). It is developed through the Food and Agriculture Organization of the United Nations (FAO) Technical Cooperation Programme Project TCP/RER/3402 “Assistance to Western Balkan Countries for Improving Compliance to International Standards on Aquatic Animal Health”, a regional project that is based on a consultative and consensusbuilding process. This is a diagnostic guide for the surveillance, clinical inspection and sampling at aquaculture facilities with the aim to detect the diseases listed by the Word Organiza tion for Animal Health (OIE) and the European Union (EU) according to their guidelines and standards, as well as other diseases of economic importance. Both standards include monitoring for diseases, the obligatory notification of clinical signs in registered farms and sampling by official veterinarians, activities that unconditionally require knowledge on diseases, farm production, normal appearance of the farmed species, and recognition of any changes that could lead to the suspicion of diseas e occurrence. Thus, this manual provides essential information on how to perform clinical inspections of fish and mollusc farms, how to recognize unusual behaviour of fish; how to select the most appropriate specimens for laboratory examination; and how to collect, pack and ship samples to the diagnostic laboratory. The laboratory procedures employed to identify the various disease agents are described, and information on the viral, bacterial and parasitic diseases of fish and molluscs in the We stern Balkans is provided. The information presented should assist countries to maintain and improve their national aquatic animal health status, harmonize standards regionally, and better comply with the health standard requirements of regional and international trading partners.
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    Antimicrobials (AM) play a critical role in the treatment of human and animal (aquatic and terrestrial) diseases, which has led to their widespread application and use. Antimicrobial resistance (AMR) is the ability of microorganisms (e.g. bacteria, viruses and some parasites) to stop an antibiotic, such as an antimicrobial, antiviral or antimalarial, from working against them. Globally, about 700 000 deaths per year arise from resistant infections as a result of the fact that antimicrobial drugs have become less effective at killing resistant pathogens. Antimicrobial chemicals that are present in environmental compartments can trigger the development of AMR. These chemicals can also cause antibiotic-resistant bacteria (ARB) to further spread antibiotic resistance genes (ARG) because they may have an evolutionary advantage over non-resistant bacteria. This paper will provide alternative screening methods useful for environmental samples and surveillance approaches in planning such screening efforts. Based on case studies, this paper aims to summarize the current understanding of the occurrence of ARG in the environment, and the antimicrobial movement from agricultural areas to the environment.

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