Monitoring AMR in 𝙀𝙨𝙘𝙝𝙚𝙧𝙞𝙘𝙝𝙞𝙖 𝙘𝙤𝙡𝙞

Monitoring AMR in the commensal E. coli collected from the intestinal flora of healthy food-producing animals and derived food products provides information on the reservoirs of resistant bacteria and resistance determinants in healthy animal populations. Commensal E. coli is often used as an indicator species as E. coli is abundant in the intestinal content of healthy individuals, therefore, providing a representative overview of AMR in healthy food-producing animal populations. It also gives indirect information on the reservoirs of resistance genes that could potentially be transferred to other bacteria, including some pathogenic to humans and/or animals. Such monitoring has therefore relevance to both public and animal health.

The occurrence of resistance in indicator E. coli likely depends on several factors, including (1) the selective pressure exerted by the use of antimicrobials in food-producing animal populations; (2) the  clonal spread  of resistant bacteria; (3) the dissemination of genetic determinants of resitance, such as resistance plasmids; and (4) the effects of co-selection in bacteria exhibiting MDR ( EFSA, 2025 ). Using the same bacteria, such as commensal E. coli, as an indicator species to monitor AMR over time enables the assessment of changes and trends in AMR situation.

Positive associations between consumption of certain antimicrobials and resistance to those substances in bacteria from food-producing animals have been observed. The frequent occurrence of resistant isolates from animal origins to antimicrobials likely reflects the widespread past and present use of these antimicrobials in food-producing animal populations. The relative strength of these associations differed markedly depending on the antimicrobial class, the microorganisms and the agricultural sector ( JIACRA IV ). Difference between animal species may come from the quantity of antimicrobials used in the different animal populations and the mode of administration.

Among the AMR traits observed in E. coli, extended-spectrum β-lactamases (ESBL), AmpC β-lactamases, and carbapenemases (CPs) produced by the bacteria reduce the effectiveness of β-lactam antimicrobials, the most prescribed drug classes used in treatment of bacterial infections. Particularly, one of the β-lactam antimicrobials classes, the cephalosporins, is classified as highest priority critically important antimicrobial (hpCIA) in human medicine according to the World Health Organisation ( WHO ).

Initially ESBL- and AmpC- producing E. coli were associated with hospitals, but have now also been widely detected in food-producing animals, humans and the environment.  ESBL/AmpC-producing E. coli in animals is considered as potential source for human acquisition of such bacteria. Transmission from animals to humans may occur by direct contact or through the food chain.

 EFSA-ECDC AMR report, 2025  ;  EURL-AR protocols for the AMR monitoring  ;  Huijbers et al., 2016  ;  WHO 

It is mandatory to report on indicator E. coli that are isolated from food-producing animals and derived food. These data are then used by EFSA and European Center for Disease Prevention and Control (ECDC) to monitor and analyze the situation on AMR in Europe. Monitoring finding are presented in the annual   EU Summary Reports . The purpose of this monitoring is not only to keep track of AMR trends, but also to understand if strategies that have been put in place to reduce antimicrobial use and resistance are efficient.

Active monitoring programmes involve isolating indicator commensal E. coli isolates from representative caecal and meat samples of the four main food-producing animal populations in the EU. In even-numbered years, representative random sampling is carried out from broilers and fattening turkeys, whereas in odd-numbered years, sampling is performed in pigs and cattle (under 1 years of age).

The collected isolates undergo  antimicrobial susceptibility testing  (more details available in the  AMR story map ) using a harmonised panel of antimicrobials of relevance to human and veterinary medicine, as well as epidemiological purposes. Some of these are included in the list of high priority critically important antimicrobials for human medicine developed by the World Health Organisation (3rd- and 4th-generation cephalosporins, fluoroquinolones, aminoglycosides, macrolides, penicillins and polymyxins).( WHO )

Routine monitoring involves collecting representative E. coli isolates from the four main food-producing animal populations of interest which undergo antimicrobial susceptibility testing to a first panel of antimicrobials, including amikacin (since 2021), ampicillin, azithromycin, cefotaxime, ceftazidime, chloramphenicol, ciprofloxacin, colistin, gentamicin, meropenem, nalidixic acid, sulfamethoxazole, tetracycline, tigecycline and trimethoprim. All the isolates found resistant to cefotaxime or ceftazidime or meropenem in the first panel are further tested against a second panel of antimicrobials to determine if they exhibit phenotypic characteristics of extended-spectrum β-lactamase (ESBL)-, AmpC, and carbapenemase- producers according to the criteria proposed by EUCAST ( EUCAST, 2017 ).

Specific monitoring involves the use of a selective medium for the identification of E. coli isolates resistant to 3 ^rd -generation cephalosporins and/ or carbapenems. The identified isolates are then tested with the first panel of antimicrobials, as in the routine monitoring, and further tested with a second panel of antimicrobials, which includes cefoxitin, cefepime, temocillin as well as cefotaxime and ceftazidime alone and in combination with clavulanic acid for the detection of presumptive ESBL- and AmpC- producing isolates. Moreover, the second panel also contains imipenem, meropenem and ertapenem to detect presumptive carbapenemase producers.

Since 2021, the European Member States (MSs) may decide to use  whole genome sequencing (WGS)  as an alternative method to broth microdilution as a susceptibility test against the second panel of antimicrobials, when carrying out the specific monitoring of ESBL- or AmpC- or CP-producing E. coli and when further testing E.coli isolates showing resistance to cefotaxime, ceftazidime and meropenem (the list of genes is available  here ).

Occurrence of resistance: Within the framework of the hamonised monitoring of AMR in food-producing animals and food, the occurrence of AMR is defined as the proportion of bacterial isolates tested for a given antimicrobial and found to present any degree of acquired reduced phenotypic susceptibility – i.e. to exhibit microbiological resistance. This contrasts with clinical resistance, characterised by treatment failure.  Epidemiological cut-off values (ECOFFs)  are used as interpretative criteria of microbiological resistance.

Key outcome indicators (KOIs) are measures used to assess the overall AMR in indicator E. coli while considering the different sizes of the animal populations monitored from which E. coli is isolated. KOIs have been developed by  EFSA, ECDC and European Medicines Agency (EMA)  to support European Union MSs in their progress to reduce the use of antimicrobials and AMR in food-producing animals.

The KOIs, by accounting for the relative differences in the sizes of animal populations provide an overall view of the AMR situation in the most important production animals (chickens, turkeys, pigs and calves) ( EFSA, 2023  ;  EFSA 2024 ;  EFSA 2025 ). 

Key outcome indicators for complete susceptibility (KOI _CS ) and for the prevalence of ESBL, AmpC- and CP-producers (KOI _ESC ) are used in the EU MSs to evaluate general trends regarding the occurrence of antimicrobial resistance. These indicators account for differences in the relative size of food animal populations in a country.

A completely susceptible indicator E. coli isolate is defined as being non-resistant to all tested antimicrobial substances included in the harmonised set of substances tested. KOI _CS   is the proportion of fully susceptible indicator E. coli isolates (from routine monitoring), weighted by the size of the populations of the production animals monitored (chickens, turkeys, pigs and calves).

The underlying assumption is that E. coli isolates will be fully susceptible if they are rarely, if ever, exposed to antimicrobials. Within the  Jiacra  initiative, the KOI _CS   has been used to indirectly assess the development of AMR in relation to the total use of antimicrobials in food-producing animals. The results show that a reduction in the total use of antimicrobials in food-producing animals would result in a noticeable improvement (or increase) of the KOI _CS . In other words, reducing AMC overall can help lower AMR. This also highlights the importance of measures that promote human and animal health, such as vaccination and better hygiene, thereby reducing the need for antimicrobials.

See the  EFSA AMR dashboard on KOI _CS   for more detailed information and results.

The KOI _ESC   is used to assess the level of ESBL-, AmpC, and CP-producing E. coli in food-producing animals.

Extended-spectrum β-lactamases (ESBL), AmpC β-lactamases, and carbapenemases (CPs) are a threat to public health as they reduce the effectiveness of β-lactam antimicrobials to treat infections caused by bacteria carrying these enzymes. ESBL- and AmpC- producing E. coli are widely presentin food-producing animals and the environment, while the number of CP-producing E. coli isolates is slowly increasing in food producing animals (Lee, 2020).

KOI _ESC  measures the prevalence of ESBL- and/or AmpC-producing E. coli weighted by the size of the populations of the food-producing animals (chickens, turkeys, pigs, calves). A decrease in this KOI would be preferred as it corresponds to a reduced detection of ESBL-, AmpC-, and CP- producing isolates.

As for the KOI _CS,   the KOI _ESC   has been calculated from data reported for two consecutive years as data from different animal populations were reported in alternating years (chicken and turkeys one year and pigs and bovines the following year). The KOI _ESC  is calculated from E. coli isolates that were identified within the framework of specific monitoring of presumptive ESBL-/AmpC-producers (see ' Monitoring AMR ' for further information).

See the  EFSA AMR dashboard on KOI _ESC   for more detailed information and results.

 EFSA-ECDC AMR report, 2025  ;  EURL-AR protocols 

• Resistance to ampicillin, sulfamethoxazole, trimethoprim or tetracycline was common and the median   levels of resistance to those substances were high or very high in all animal populations in 2022-2023. Resistance to quinolones was common in broilers and fattening turkeys for which median levels of resistance were very high and high, respectively. Resistance to other antimicrobials was less common. 

• Resistance to meropenem was detected in one isolate from turkeys in 2022 but not in any isolates in 2023. The isolate was reported by Italy and was confirmed to carry the bla _OXA-181  gene. 

• Large differences in the levels of AMR were recorded among countries. Lower levels were typically reported in Northern Europe. 

• Complete susceptibility (CS) was more common in isolates from fattening pigs and cattle under 1 year of age than in those from broilers and fattening turkeys. Conversely, multidrug resistance (MDR) was more frequent in isolates from broilers and turkeys than in those from pigs and cattle under 1 year of age. Marked differences in the levels of CS and MDR were observed among countries. The antimicrobials most often represented in the MDR patterns were tetracycline, ampicillin, sulfamethoxazole, trimethoprim and additionally, quinolones in broilers and turkeys. 

• The Key Outcome Indicator of complete susceptibility (KOI _CS ), accounting for the varying sizes of the different food-producing animal populations in a country, varied widely between countries, ranging from <10% to >80%. The highest KOI _CS  were usually observed in Northern Europe. 

• Resistance to highest priority critically important antimicrobials (hpCIA) in human medicine was uncommon for colistin, azithromycin and third-generation cephalosporins (cefotaxime or ceftazidime), and median levels of resistance ranged between rare and low in all animal populations. Median levels of resistance to ciprofloxacin were low for pigs and cattle under 1 year of age but very high for broilers and high for fattening turkeys. Combined resistance to third-generation cephalosporins and fluoroquinolones was generally uncommon in all animal populations. 

• Statistically significant decreasing temporal trends in resistance to ampicillin, ciprofloxacin, cefotaxime, tetracycline and colistin, as well as increasing trends in CS and KOI _CS  reveal progress towards lower levels of resistance in several reporting countries. Improvement in the situation has been most pronounced in broilers and fattening turkeys over the recent years. 

 EFSA-ECDC AMR report, 2025 ;   EFSA dashboard on antimicrobial resistance 

 _{Note: In accordance with the Agreement on the withdrawal of the United Kingdom of Great Britain and Northern Ireland from the European Union and the European Atomic Energy Community, and in particular Article 5(4) of the Windsor Framework (see Joint Declaration No 1/2023 of the Union and the United Kingdom in the Joint Committee established by the Agreement on the withdrawal of the United Kingdom of Great Britain and Northern Ireland from the European Union and the European Atomic Energy Community of 24 March 2023,  OJ L 102, 17.4.2023, p.87 ) in conjunction with section 24 of Annex 2 to that Framework, for the purposes of this Regulation, references to Member States should include the United Kingdom in respect of Northern Ireland.} 

Antimicrobials have been widely used to treat bacterial infections in humans and animals. Over-use and misuse of antimicrobials can make bacteria resistant (see the  infographic  from RONAFA on spread of AMR).

Resistant bacteria can then:

• Spread afterwards and be transferred between the environment, animals, and humans.
• Be present in the food derived from animals , such as meat, unpasteurized milk or eggs.

Monitoring antimicrobial resistance is a world challenge and the use of antimicrobials for animals' and humans’ infections is part of the problem.

Prevention of E. coli transmission, especially MDR isolates, is an important factor in reducing the spread of AMR. Control measures that are put in place to achieve this span across all stages of the food chain, from agricultural production and processing to manufacturing and preparation of foods in both commercial and household settings.

Safe hygienic practices during slaughter reduce contamination of carcasses by faeces, and hygienic handling of foods at farms, abattoirs, and food production can minimise microbiological contamination. Basic good food hygiene practices in the household can also prevent transmission of E. coli.

Concrete measures to reduce the need to use antimicrobial agents in food-producing animals in Europe have been proposed ( EMA and EFSA, 2017 ).

Reducing the use of antimicrobials in food-producing animals, replacing them where possible and re-thinking the livestock production system is essential for the future of animal and public health ( EMA and EFSA dynamic infographic ).

• REDUCE THE USE OF ANTIMICROBIALS
  • Set targets for reducing the use of critically important antimicrobials that are crucial for the treatment of serious human diseases.
  • Increasing responsibility of veterinarians regarding their prescribing decisions, which should be based on regular farm visits, clinical examination of animals and laboratory tests.
  • Use antimicrobials only when needed. In particular, antimicrobials should not be used to prevent diseases in healthy animals.
• REPLACE ANTIMICROBIALS WITH ALTERNATIVE TREATMENTS
  • Consider alternatives to antimicrobials that have been shown to improve animal health and that could reduce the need for antimicrobials (i.e.  probiotics ,  prebiotics ,  bacteriophages , or  organic acids ).
  • Research new alternatives to antimicrobials or to reduce their need
  • Develop a EU legal framework to promote the development and possible authorisation of products that can be used as alternatives to antimicrobials.

• RETHINK THE LIVESTOCK PRODUCTION SYSTEM
  • Improve prevention and control of zoonotic diseases in animals
  • Explore alternative farming systems leading to a reduced use of antimicrobials
  • Invest on education and awareness of antimicrobial resistance at all levels of society and especially to veterinarians and farmers.

EFSA and the European Medicines Agency coordinate these actions in an integrated strategy, monitor the antimicrobial resistance but governments, industries, health care providers, scientist, and consumers also have a role to play.