Report on AMR in zoonotic and indicator bacteria from humans, animals and food in the EU

On 29 March 2022, the European Centre for Disease Prevention and Control (ECDC) and the European Food Safety Authority (EFSA) published their joint annual summary report regarding data on antimicrobial resistance (AMR) in zoonotic and indicator bacteria from humans, animals and food In EU member states.

Monitoring and reporting of AMR in 2019 to 2020 included data regarding Salmonella, Campylobacter and indicator Escherichia coli (E. coli) isolates, as well as data obtained from the specific monitoring of presumptive ESBL-/AmpC-/carbapenemase-producing E. coli isolates. Additionally, some member states reported voluntary data on the occurrence of methicillin-resistant Staphylococcus aureus in animals and food, with some countries also providing data on antimicrobial susceptibility.

The report provides an overview of the main findings of the 2019 to 2020 harmonised AMR monitoring in the main food-producing animal populations monitored, in carcase or meat samples, and in humans. Where available, monitoring data obtained from pigs, calves, broilers, laying hens and turkeys, as well as from carcase or meat samples and humans, were combined and compared at the EU level, with particular emphasis on multidrug resistance, complete susceptibility and combined resistance patterns to critically important antimicrobials, as well as Salmonella and E. coli isolates possessing ESBL-/AmpC-/carbapenemase phenotypes.

The key outcome indicators for AMR in food-producing animals, such as complete susceptibility to the harmonised panel of antimicrobials in E. coli and the prevalence of ESBL-/AmpC-producing E. coli have been specifically analysed over the period 2014 to 2020.

The report found the antibiotic resistance in Salmonella and Campylobacter bacteria is still high, with campylobacteriosis being the most reported zoonosis in the EU in 2020 and the most frequently reported cause of foodborne illness. Campylobacter bacteria from humans and poultry continues to show very high resistance to ciprofloxacin, a fluoroquinolone antibiotic, that is commonly used to treat some types of bacterial human infection.

Increasing trends of resistance against the fluoroquinolone class of antibiotics has been observed in humans and broilers for Campylobacter jejuni (C. jejuni). In Salmonella Enteritidis (S. Enteritidis), the most common type of Salmonella in humans, increasing trends of resistance to the quinolone and fluoroquinolone class of antibiotics were observed. In animals, resistance to these antibiotics in C. jejuni and S. Enteritidis were generally moderate to high.

However, despite the increasing trends of resistance against certain antibiotics, simultaneous resistance to two critically important antibiotics remains low for E. coli, Salmonella and Campylobacter in bacteria from both humans and food-producing animals.

A decline in resistance to tetracyclines and ampicillin in Salmonella from humans was observed in nine and ten countries, respectively, over the period 2016 to 2020, and this was particularly evident in Salmonella Typhimurium. Despite the decline, resistance to these antibiotics still remains high in bacteria from both humans and animals.

Furthermore, in more than half of EU countries, a statistically significant decreasing trend in the prevalence of extended-spectrum β-lactamase (ESBL)-producing E. coli was observed in food-producing animals. This is an important finding as particular strains of ESBL-producing E. coli are responsible for serious infections in humans.

Carbapenem resistance remains extremely rare in E. coli and Salmonella from food-producing animals. Carbapenems are a class of last resort antibiotics and any findings showing resistance to these in zoonotic bacteria are concerning.

Although findings and trends are consistent with data reported in previous years, the COVID-19 pandemic had an impact on the amount of data reported, particularly with regards to public health.

Sources: ECDC, 29 March 2022 and EFSA, 29 March 2022