Antimicrobial Resistance

Primary reference(s)

FAO, 2011. Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance. CAC/GL 77-2011. Food and Agriculture Organization of the United Nations and World Health Organization (FAO). Accessed 26 October 2020.

Additional scientific description

Antimicrobial resistance (AMR) occurs when microorganisms (bacteria, fungi, viruses, protozoa) evolve to survive and/or proliferate in concentrations of antimicrobial that would otherwise be microbiocidal (kill) or microbiostatic (inhibit the growth) to the organism or other organisms of the same or similar species. This can occur naturally through adaption to the environment but has been exacerbated by inappropriate and excessive use of antimicrobial agents (FAO, 2016).

Microorganisms in food are potential food safety hazards. The relationship between the use of antimicrobial agents in food production (terrestrial and aquatic food-producing animals and crop plants) and the emergence of resistant microorganisms in the food chain is a concern as food can become contaminated with antimicrobial resistant organisms and/or antimicrobial resistance genes. When humans ingest antimicrobial resistant microorganisms in food or water, some of these may cause illness, and in cases where antimicrobial treatment in needed this becomes a challenge. This has been the subject of numerous national and international consultations (FAO and WHO, 2018a).

Data to support risk assessment and risk management, while improving, remains an important challenge in the context of antimicrobial resistance. For example, 118 countries reported quantitative data on antimicrobial use in animals in 2017, an increase from 89 reporting in 2015. However, few countries collect data on antimicrobial use in plant production. Also, according to the World Health Organization (WHO) there are few countries worldwide that have adequate surveillance across the food chain (WHO, 2015a).

In summary antimicrobial-resistant bacteria, antimicrobial residues and antimicrobial resistance genes could be transmitted from animal, clinical, and environmental sources to foods, feeds of animals and plants. There are around 700,000 human deaths each year related to antimicrobial resistance (CDC, 2021).

Notes: In some cases, the terms antibiotic resistance and antimicrobial resistance are used interchangeably which is incorrect. Antibiotic resistance has a narrower definition referring only to resistance to antibiotics which target bacteria while antimicrobial resistance relates to resistance or a broader range of microbes (bacteria, viruses, fungi, protozoa) and to a broader range of agents (antibiotics, antivirals, antifungals, antiprotozoals) (WHO, 2020a,b).

Antimicrobial resistance should be differentiated from antimicrobial residues which are trace amounts of the chemical substances present in foods and in the environment after antimicrobial use or disposal. Antimicrobial residues pose a food safety risk and may contribute to the development of antimicrobial resistance in the environment (CDC, 2021).

Metrics and numeric limits

The Food and Agriculture Organization of the United Nations (FAO) and WHO have published maximum residue limits in foodstuffs (FAO and WHO, 2018b,c).

Examples of drivers, outcomes and risk management

Much attention has been focused on human exposure to antimicrobial resistant pathogens in hospitals and similar settings and the implications for public health. However, the presence of antimicrobial resistant microorganisms in food production systems means that the food consumed can also be a source of exposure. Development and transmission of antimicrobial resistance through the food chain is complex with multiple contributing factors, hence addressing it using a coordinated, ‘one health’ response provides the most effective approach.

Excessive and inappropriate use of antimicrobial agents in a range of sectors (human health, animal health, crop production), together with other aspects, such as lack of proper waste management or appropriate waste treatment, are key drivers in the exacerbation of antimicrobial resistance. The availability and use of antimicrobial drugs for human health as well as in terrestrial and aquatic animals and in crop production is essential to both health and productivity. The increase in antimicrobial resistance is a major global threat of increasing concern to human, animal and plant health. It also has implications for both food safety and food security and the economic wellbeing of millions of farming households (FAO and WHO, 2018a).

Owing to the inter-related multiple dimensions of antimicrobial resistance, the food safety aspects cannot be addressed in isolation. A holistic approach, which takes into account animal and plant production, the environment and food processing should be considered. This can be done using a One Health approach. For example, animal diseases can have major impacts on food production, food security and farming livelihoods. Antimicrobial agents have an important role in treating such diseases, but their misuse in agriculture contributes to the spread of antimicrobial resistance and undermines the effectiveness of veterinary medicines. Similarly, antimicrobials are vital to treat and control plant diseases. Contamination of soils with these products following crop application leads to enrichment of antimicrobial-resistant bacteria and genes in the environment. However, the extent to which the treatment of crops with antimicrobial agents (or copper formulations) promotes antimicrobial resistance in bacteria found on the edible parts of crops is uncertain. Other inputs to plant production, such as water and manure, can also be a source from which plants become contaminated with antimicrobial-resistant organisms or genes. Contamination at the primary production level can lead to exposure to antimicrobial-resistant organisms/genes via the food consumed. Thus, addressing antimicrobial resistance as a food safety hazard is complex and requires an integrated approach (FAO, no date a).

A global Action Plan on antimicrobial resistance adopted in 2016 (WHO, 2015b) has served as a major driver for increased risk management. This was followed by a political declaration of the high level meeting of the United Nations General Assembly on antimicrobial resistance (WHO, 2016) which has been important to gain political commitment to address the risks posed.

At the next level the Codex Alimentarius has developed several texts directly related to antimicrobial resistance (FAO and WHO, 2005, 2011) and is in the process of updating its Code of Practice and developing new Guidelines for surveillance of antimicrobial resistance which are expected to be completed by 2021 (FAO and WHO, no date).

The World Organization for Animal Health (OIE) has developed standards specifically related to the management of antimicrobial resistance in the animal sector (OIE, no date).

On a more practical level the FAO is working closely with the WHO and OIE, and together they share responsibility for addressing and coordinating global activities addressing antimicrobial resistance at the animal-human-ecosystems interface (FAO, 2020).

In this context, the implementation of good practices is key to reducing the risk of developing and transmitting antimicrobial resistance through the food chain. Practical guidance has been and continues to be developed for the different sectors. Examples follow for animal production and health, plant production and health, environment, and food safety.

Animal production and health: While the prudent use of antibiotics is important to treat animal diseases, its overuse and misuse can contribute to antimicrobial resistance and with two-thirds of the estimated future growth of usage of antimicrobials estimated to be within the animal production sector, efforts to reduce use and the related consequences need to be addressed. Addressing antimicrobial resistance effectively requires the livestock sectors to join others in committing to implement practices to minimise the need for and use of antimicrobials. Key actions required include: tracking and monitoring of animal disease to allow a rapid response; applying good husbandry practices; improving animal welfare during all phases including production, transport and slaughter; using animals of locally adapted breeds which are more resistant to diseases and stress or animals bred for disease resistance (resistant animals will require fewer treatments with antimicrobials); ensuring good hygiene, biosecurity measures, and general conditions on farms to prevent the need for any medicines in the first place; applying rigorous disease control measures (e.g., vaccination); using feed ingredients/additives that enhance the efficiency of feed conversion to substitute antibiotics as growth promoters; avoiding feed ingredients with antinutritional properties (such as lectins, and protease inhibitors); and applying good practices for waste management. For further information on management options see FAO (no date a).

Plant production and health: The most effective approach to limit the use of antimicrobials in plant production is through use of the well-established procedures of ‘integrated pest management’ – a systems approach designed to minimise economic losses for crops, as well as to minimise risks to people and the environment through the use of pesticides. Key components of integrated pest management for preventing and managing plant diseases are: accurate and timely diagnosis and monitoring; use of disease-resistant crop varieties; exclusionary practices (biosecurity) that prevent the introduction of pathogens into a crop; careful site selection and soil improvement to maximise plant health and minimise environmental factors that favour pathogens; crop rotation and other cultural practices to prevent pathogen build-up; use of biological and biorational products; and judicious use of antimicrobials (FAO and WHO, 2019). For further information on management options see FAO (no date b).

Environment: Taking action to manage antimicrobial resistance in the environment is now recognised as very important to manage the development of spread of antimicrobial resistance, including through the food chain. However it is only recently that there have been concrete efforts to address this, with the need for policies to tackle this aspect being a key action required. For further information see FAO, WHO and OIE (2020).

Food safety: Good hygiene practices throughout the food chain are key to minimising the transfer of microorganisms through food (FAO and WHO, 2003). Monitoring of residues of veterinary drugs or pesticides in foods is also an important element of the risk management approach. But critical to all of these approaches is the capacity to both implement the relevant measures and have the necessary oversight mechanisms to inspect and enforce their implementation.