Food Safety

Carbapenem resistance in the food chain. EFSA opinion

May 25, 2025

The recent scientific opinion by EFSA on bacteria resistant to carbapenems – a class of broad-spectrum antibiotics beta-lactams – highlights how this problem, traditionally confined to hospital environments, is also emerging in the agri-food chain.

This dangerous form of antibiotic resistance, in the broader global context of antimicrobial resistance, appears however underestimated in most EU Member States. EFSA (2025) recommends renewed commitment, at public and private level, in monitoring and prevention.

Table of Contents

Carbapenems, introduction

Carbapenems constitute a class of broad-spectrum antibiotics beta-lactams, considered last-line drugs in the treatment of serious infections caused by Gram-positive and Gram-negative bacteria.

As emphasised by Papp-Wallace et al. (2011), ‘carbapenems are highly effective due to their ability to inhibit bacterial cell wall synthesis and their stability against many beta-lactamases‘ (p. 4945), including ESBL (Extended-Spectrum Beta-Lactamases) type enzymes.

Their unique molecular structure confers resistance against most beta-lactamases produced by bacteria, making these antibiotics particularly valuable in the current scenario of increasing antibiotic resistance.

The contribution of the food chain to the spread of carbapenem resistance

Transmission routes: how foods can become vehicles of resistance

Although carbapenems are used almost exclusively in hospital settings, the presence of bacteria resistant to these antibiotics has been documented in the food chain. The main transmission mechanisms include:

direct contamination of foods of animal origin by resistant bacteria present in production animals;
horizontal transmission of resistance genes between bacteria present in foods;
cross-contamination during food processing and distribution phases.

Food products at risk and microorganisms involved

EFSA – in its recent scientific assessment on the topic – reports that ‘bacteria of the Enterobacteriaceae family producing Carbapenemases (CPE) have been detected in the agri-food chain in 14 of the 30 EU/EFTA Countries‘ (EFSA, 2025). These include Escherichia coli, Enterobacter cloacae, Klebsiella pneumoniae and Salmonella infantis, with E. coli distinguished by notable genetic variability, indicating significant clonal diversification.

The Authority emphasises that ‘most CPE detections come from animals intended for food production, particularly pigs, followed by cattle and poultry‘. The food products most affected include:

Fresh meat, especially pork and poultry;
Dairy products, to a lesser extent;
Fish and vegetable products, with emerging evidence of contamination.

Molecular mechanisms of spread

‘These resistance genes are often found on mobile genetic elements called plasmids, which can easily transfer between different bacteria‘ (EFSA, 2025). The plasmids most frequently associated with CPE belong to the groups IncHI2 (bla VIM-1, bla OXA-162), IncC (bla VIM-1, bla NDM-1), IncX3 (bla NDM-5, bla OXA-181), IncI and InCl (bla OXA-48). Their presence facilitates the spread of resistance not only between strains of the same species, but also between different bacterial species, amplifying the potential impact on public health.

EFSA 2025 assessment: comprehensive risk analysis in the European agri-food chain

Geographical distribution and trends

The latest EFSA assessment on carbapenem-resistant bacteria (CPE) updates the previous one, published in 2013 (EFSA, 2013), by analysing epidemiological data and scientific literature available until February 2025. The assessment highlights a growing spread of carbapenem-resistant bacteria (CPE) in Europe, with a particularly significant increase in recent years, especially in pigs.

Some countries have reported specific surges: for example, Italy in 2021 with bla OXA-181, and Spain and Portugal in 2023 with the simultaneous detection of various genes (bla OXA-48, bla OXA-181, bla OXA-244 and bla NDM-5). This non-uniform distribution suggests differences in farming practices, antibiotic use and surveillance systems between different Member States.

Knowledge gaps and detection methods

EFSA (2025) emphasises that ‘evidence documenting CPE transmission along the food chain or between animals and humans is still scarce and based mainly on indirect observations‘. The investigation revealed that ‘currently, in EU/EFTA countries different methodological approaches are used to identify and characterise CPE in foods‘ (EFSA, 2025, p. 67), with significant heterogeneity in isolation methods and molecular characterisation.

Only 10 countries out of 30 have specific emergency plans to address CPE, which also include epidemiological investigations, such as trace-back, to trace contamination sources. Overall, available data remain limited, especially regarding bacteria and food matrices not systematically monitored.

Public health risk assessment

The EFSA assessment integrates information collected at national level from EU Member States and EFTA countries, with technical and analytical support from the European Centre for Disease Prevention and Control (ECDC). The document, it should be noted:

does not quantify the risk to human health arising from the presence of CPE in foods, but
highlights the potential of these bacteria to contribute to the global problem of antibiotic resistance, with significant implications for the treatment of human infections especially.

Solutions and mitigation strategies: EFSA recommendations

Expansion of surveillance programmes

The EFSA assessment concludes with the recommendation to ‘expand the scope of monitoring activities for carbapenemase-producing bacteria (CPE) including food matrices previously excluded from systematic programmes, such as fish products, vegetables and other foods of plant origin‘ (EFSA, 2025).

The extension of surveillance is justified by growing evidence that resistant microorganisms can colonise environments and substrates different from traditional zootechnical ones.

Furthermore, it is suggested to include in monitoring also less investigated bacterial species, such as Klebsiella spp., which are emerging as important reservoirs of resistance genes.

Standardisation of analytical methods

Monitoring and prevention of the spread of carbapenem-resistant bacteria (CPE) depends primarily on improving analytical methods. This involves:

‘the need to refine diagnostic methods in terms of sensitivity and specificity, in order to ensure more effective identification of resistant strains‘ (EFSA, 2025);
the standardisation of analytical methods, at least at European level, to obtain comparable data representative of the real spread of the phenomenon.

Implementation of advanced traceability systems

In parallel to improving diagnostic techniques, EFSA recommends implementing more effective traceability investigations (trace-back) and deepening molecular typing of isolated strains, to better understand transmission dynamics within the agri-food chain. Such studies should also assess possible spread mediated by operators, contact surfaces, production environments and feed.

‘One Health’ approach: an integrated strategy

‘Only through coordinated action between the public health, veterinary and environmental sectors‘ – the One Health approach – ‘will it be possible to effectively contain the spread of carbapenem resistance‘ (EFSA, 2025). This strategy requires:

intersectoral coordination between public health, veterinary and environmental authorities;
harmonisation of monitoring plans and diagnostic methodologies;
data sharing between different sectors and Member States;
adoption of preventive measures throughout the food chain, from primary production to consumption

Conclusions and prospects

The presence of carbapenemase-producing bacteria in the food chain represents an emerging challenge for food safety and public health in Europe. The phenomenon, although not yet fully characterised, requires urgent attention from all actors involved in the food chain and health sector.

EFSA recommendations offer a framework for developing effective monitoring and control strategies. However, the success of such strategies will depend on the ability to implement a truly integrated approach, which considers antimicrobial resistance as a complex and multidimensional phenomenon, influenced by human, animal and environmental factors.

Future research will need to fill current knowledge gaps, particularly regarding transmission mechanisms of resistance genes along the food chain and quantitative risk assessment for consumers. Only through coordinated commitment at European and global level will it be possible to effectively address this emerging threat to public health.

Dario Dongo and Ylenia Desirée Patti Giammello

References

European Food Safety Authority. (2013). Scientific opinion on the public health risks of bacterial strains producing carbapenemases in food and food-producing animals. EFSA Journal, 11(12), 3501. https://doi.org/10.2903/j.efsa.2013.3501
European Food Safety Authority. (2025). Scientific opinion on the occurrence and spread of carbapenemase-producing Enterobacteriaceae (CPE) in the food chain. EFSA Journal, 23(4), 9336. https://doi.org/10.2903/j.efsa.2025.9336
Papp-Wallace, K. M., Endimiani, A., Taracila, M. A., & Bonomo, R. A. (2011). Carbapenems: Past, present, and future. Antimicrobial Agents and Chemotherapy, 55(11), 4943–4960. https://doi.org/10.1128/AAC.00296-11