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Antimicrobial Resistance

Antimicrobial Resistance

Antimicrobials are substances used to kill micro-organisms or to stop them growing and multiplying. They are commonly used to treat infectious diseases in human and veterinary medicine for instance in the form of antibiotics. Antimicrobial treatments also have uses in plants and foods for instance in the form of biocides to fight against pathogenic microbes, some of them responsible for food-borne diseases such as Salmonella, Campylobacter and Listeria.

Antimicrobial resistance refers to the ability of microbes to withstand antimicrobial treatments. It is an issue of concern for scientists and policy-makers since the overuse or misuse of antibiotic treatments has been linked to the emergence and spread of microbes which are resistant to them, rendering such treatments ineffective against them. This can pose a serious risk to public health - a well known example being the Methicillin-resistant Staphylococcus aureus (MRSA) bacterium, some strains of which have been reported to be resistant to several antimicrobial classes.

In the field of food safety, policy makers need to identify any potential risks to consumers and to establish the best control options to reduce the risk associated with the development of antimicrobial resistance. Scientists and risk assessors are examining the different factors which may lead to antimicrobial resistance emerging or spreading via the food chain, providing appropriate scientific advice to decision-makers.

EU framework

In 2001 the European Commission launched an EU strategy to combat the threat of antimicrobial resistance to human, animal and plant health. It included the phasing out of antibiotics for non-medical use in animals, and covered a range of actions at EU and national level in the areas of data collection, surveillance, research and awareness-raising. A subsequent Council Recommendation on the prudent use of antibiotics adopted in 2002 outlined measures in human medicine that Member States could take to reduce antimicrobial resistance.

A number of risk management measures are in place in the food safety area. EU legislation on animal nutrition bans the use of antibiotics used for growth promotion in animal feed since January 2006.

EU legislation on zoonoses - animal diseases or infections transmissible to humans such as Salmonella - obliges Member States to monitor trends in antimicrobial resistance in zoonoses and other agents that present a threat to the public health.

At international level, countries cooperate through an Intergovernmental Task Force on Antimicrobial Resistance of the Codex Alimentarius Commission where the European Commission represents the EU.

The European Centre for Disease Prevention and Control organises the annual European Antibiotic Awareness Day, in close cooperation with the World Health Organization.

EFSA’s role and activities

EFSA provides scientific advice to risk managers on the risks to human and animal health of the possible emergence, spread and transfer to humans of antimicrobial resistance via the food chain. As this issue cuts across various sectors of the food chain, EFSA takes an integrated approach involving a number of EFSA Panels and Units.

While EFSA’s scientific advice includes appropriate recommendations on the monitoring of antimicrobial resistance in the food chain, the Community Reference Laboratory for Antimicrobial Resistance has the job of supporting the Commission on the development and quality assurance of methods to test for antimicrobial resistance.

Food ad animals as vehicles for transmitting antimicrobial resistance

In July 2008 the BIOHAZ Panel issued an opinion on food-borne antimicrobial resistance as a biological hazard, examining how food may become a vehicle for transmitting antimicrobial resistant bacteria to humans. It looked at food contaminated by bacteria present in live animals, fresh produce from land recently irrigated with contaminated water, and food contaminated during handling and preparation. The opinion made recommendations for preventing and controlling transmission, highlighting good hygiene practices at all stages of the food chain as a critical prevention and control factor.

In November 2009 EFSA, the European Centre for Disease Prevention and Control, the European Medicines Agency and the European Commission’s Scientific Committee on Emerging and Newly Identified Health Risks published a joint scientific opinion on antimicrobial resistance focused on infections transmitted to humans from animals and food. The report concludes that bacterial resistance to antimicrobials has increased in recent years worldwide, making it more difficult to treat some human and animal infections. There is specific concern in human medicine about bacterial resistance to antibiotics used in the treatment of Salmonella and Campylobacter infections - the two most reported zoonotic infections in Europe. Even though the use of antibiotics is considered the main factor in the development of bacterial resistance, the report concludes that the use of biocides (including disinfectants, antiseptics and preservatives) may also contribute to bacterial resistance.

Monitoring antimicrobial resistance in the food chain

EFSA’s Zoonoses Data Collection Unit, supported by a Task Force of Member State experts, analyses data on antimicrobial resistance in Salmonella and Campylobacter isolated from animals and food of animal origin, as submitted annually by Member States under EU zoonoses legislation.

The Zoonoses Data Collection Unit produces the Annual Community Summary reports on trends and sources of zoonoses, zoonotic agents and antimicrobial resistance in the EU, in cooperation with the ECDC. EFSA’s BIOHAZ and AHAW Panels review the annual reports and make recommendations on prevention and reduction measures. The latest such opinion identified antimicrobial resistance as a public health concern and made recommendations including mandatory monitoring of the use of antimicrobials in food producing animals.

It also collects data on antimicrobial resistance in microbes other than the zoonotic ones if they present a risk to humans - such as E.coli and enterococci. It has developed guidance for harmonised monitoring and reporting of antimicrobial resistance in animals and food across the EU.

Risks of MRSA from animals and foods

MRSA has been reported to occur in food-producing animals, and several Member States are currently undertaking studies to understand better the impact of these findings. EFSA’s Task Force on Zoonoses Data Collection recommended carrying out an EU-level baseline survey on the prevalence of MRSA in breeding pigs, to help quantify the spread of MRSA in farm animals throughout the EU.
MRSA has been reported to occur in food-producing animals, and several Member States are currently undertaking studies to understand better the impact of these findings. EFSA’s Task Force on Zoonoses Data Collection recommended carrying out an EU-level baseline survey on the prevalence of MRSA in breeding pigs, to help quantify the spread of MRSA in farm animals throughout the EU. In November 2009 the analysis of the survey was published.

The survey was carried out in 24 Member States in 2008, 17 of which found some type of MRSA in their holdings with breeding pigs and 7 none at all. On average, different types of MRSA have been found in 1 out of 4 holdings across the EU. However, the survey also revealed that figures vary greatly between Member States. EFSA recommends further monitoring of pigs and other food producing animals as well as further research on the causes and implications of these findings in order to propose options on possible control measures.

In 2009 the BIOHAZ Panel carried out a self-tasked  assessment of the public health significance of MRSA in animals and foods . It examined the human health risk of MRSA associated with food-producing animals, the importance of food and food-producing or domestic animals for the risk of human infection, and which animal species and derived foods may present the highest risks. The opinion also examined possible control options to minimise the risk of transmission of MRSA to humans. The Panel noted that a specific MRSA type (CC398) has emerged in food-producing animals, most often associated with asymptomatic carriage in intensively reared animals. The opinion concluded that where MRSA prevalence in food-producing animals is high, people in contact with live animals, especially farmers, veterinarians and their families, are at greater risk than the general population. The Panel found that food may be contaminated by CC398, but it has not been associated with foodborne intoxications and there is currently no evidence for increased risk of infection following contact or consumption of this food. The Panel made several recommendations, including systematic surveillance and monitoring of MRSA in intensively reared animals.


Use of antimicrobial decontamination treatments

In some countries food producers may use antimicrobial decontamination treatments on animal carcasses to kill microbes responsible for food-borne diseases such as Salmonella or Campylobacter. This is not allowed to substitute good hygiene practices in the EU, and may only be considered if the substance concerned is shown to be safe and effective.

EFSA’s BIOHAZ and former AFC Panels have provided scientific advice to the Commission on the safety and efficacy of such practices. In 2008 the BIOHAZ Panel examined the possible development of antimicrobial resistance linked to four substances used to treat poultry carcasses. It found there are no published data indicating that the four substances will lead to increased bacterial tolerance to the specific substances or to increased resistance to therapeutic antibiotics and other antimicrobial agents.

To follow up this work, the BIOHAZ Panel will update its technical guidance including for monitoring and collecting data on antimicrobial resistance linked to decontamination treatments to further support the Commission, working closely with the Community Reference Laboratory for Antimicrobial Resistance.

Micro-organisms added to animal feed

Micro-organisms may be used in animal feed for instance to help prevent health problems or improve performance in terms of food-production. EU legislation on feed additives requires that these must be free of antibiotic activity and tested for resistance to antibiotics used in human and veterinary medicine.

The FEEDAP Panel is responsible for assessing the safety of animal feed additives, including the risks related to antibiotic resistance where micro-organisms are involved. To ensure EFSA’s assessments remain in line with the latest scientific approaches, in June 2008 the Panel updated the criteria applied to bacteria for use in animal feed to determine the risks in terms of antimicrobial resistance.

Use of antibiotic resistance marker genes in GM plants

Marker genes encoding resistance to specific antibiotics may be used in genetic modification to help identify GM cells among the untransformed cells.

In June 2009 EFSA published a consolidated overview on the use of antibiotic resistant marker genes in GM plants, including a joint scientific opinion by the GMO and BIOHAZ Panels. The Panels concluded that, according to information currently available, adverse effects on human health and the environment resulting from the transfer of the two antibiotic resistance marker genes, nptII and aadA, from GM plants to bacteria, associated with use of GM plants, are unlikely. Uncertainties in this opinion are due to limitations related, among others, to sampling and detection, as well as challenges in estimating exposure levels and the inability to assign transferable resistance genes to a defined source. Two members of the BIOHAZ Panel expressed minority opinions concerning the possibility of adverse effects of antibiotic resistance marker genes on human health and the environment.

In another opinion, the GMO Panel reviewed its previous assessments of individual GM plants containing ARMG taking into account the findings and conclusions of the joint opinion of the GMO and BIOHAZ Panels. The GMO Panel concluded that its previous risk assessments on the use of the nptII marker gene in GM plants are consistent with the risk assessment strategy described in the joint opinion and that no new scientific evidence has become available that would prompt it to change its previous opinions on these GM plants.

Following the adoption of the joint opinion of the GMO and BIOHAZ Panels, EFSA asked the panels to consider whether the minority opinions required any clarification of the joint opinion or additional scientific work. The Panel chairs responded that the minority opinions had been extensively considered during the preparation of the joint opinion and no further clarification or scientific work were needed at this time.

For more information


Scientific Documents  
Joint Opinion on antimicrobial resistance (AMR) focused on zoonotic infections

Published: 16 November 2009  Adopted: 28 October 2009

Technical Guidance: Microbial Studies

Published: 21 October 2008  Adopted: 21 October 2008