The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2020/2021

Abstract

Antimicrobial resistance (AMR) data on zoonotic and indicator bacteria from humans, animals and food are collected annually by the EU Member States (MSs) and reporting countries, jointly analysed by EFSA and ECDC and presented in a yearly EU Summary Report. This report provides an overview of the main findings of the 2020–2021 harmonised AMR monitoring in Salmonella spp., Campylobacter jejuni and C. coli in humans and food‐producing animals (broilers, laying hens and turkeys, fattening pigs and bovines under 1 year of age) and relevant meat thereof. For animals and meat thereof, indicator E. coli data on the occurrence of AMR and presumptive Extended spectrum β‐lactamases (ESBL)‐/AmpC β‐lactamases (AmpC)‐/carbapenemases (CP)‐producers, as well as the occurrence of methicillin‐resistant Staphylococcus aureus are also analysed. In 2021, MSs submitted for the first time AMR data on E. coli isolates from meat sampled at border control posts. Where available, monitoring data from humans, food‐producing animals and meat thereof were combined and compared at the EU level, with emphasis on multidrug resistance, complete susceptibility and combined resistance patterns to selected and critically important antimicrobials, as well as Salmonella and E. coli isolates exhibiting ESBL‐/AmpC‐/carbapenemase phenotypes. Resistance was frequently found to commonly used antimicrobials in Salmonella spp. and Campylobacter isolates from humans and animals. Combined resistance to critically important antimicrobials was mainly observed at low levels except in some Salmonella serotypes and in C. coli in some countries. The reporting of a number of CP‐producing E. coli isolates (harbouring bla OXA‐48 , bla OXA‐181 , and bla NDM‐5 genes) in pigs, bovines and meat thereof by a limited number of MSs (4) in 2021, requests a thorough follow‐up. The temporal trend analyses in both key outcome indicators (rate of complete susceptibility and prevalence of ESBL‐/AmpC‐ producers) showed that encouraging progress have been registered in reducing AMR in food‐producing animals in several EU MSs over the last years.

Prevalence, antibiotic resistance, and genomic characterisation of Campylobacter spp. in retail chicken in Hanoi, Vietnam

“…jejuni isolates were susceptible to the remaining three antimicrobials (streptomycin, gentamicin, and erythromycin) and none were multidrug resistant, a resistance pattern commonly reported for C. jejuni in the European Union and the United Kingdom [10] and Vietnam [21, 23]. For C.…”

“…coli [9]. There has been an increase in the prevalence of antimicrobial resistance in Campylobacter isolates over time and resistances to fluoroquinolones and macrolides are of particular concern, given their use for treatment of human infections [10, 11].…”

Cross-Cutting Approach for the Characterization of Microbial Emerging Hazards in Agriculture Settings from Circular Economy-Driven Wastewater Streams

“…The profiling of microbial communities, antimicrobial residues, and AMR genes allows the traceability of the considered biowastes and supports the monitoring of AMR in zoonotic and indicator bacteria from humans, animals, and food . This could have implications in the discrimination between sludges originating from municipal WWTPs and those from the food industry, today framed within the same legislative biowastes category, even with different risk profiles.…”

“…The profiling of microbial communities, antimicrobial residues, and AMR genes allows the traceability of the considered biowastes and supports the monitoring of AMR in zoonotic and indicator bacteria from humans, animals, and food. 52 This could have implications in the discrimination between sludges originating from municipal WWTPs and those from the food industry, today framed within the same legislative biowastes category, even with different risk profiles. Lastly, the relevance of generating FAIR (Findability, Accessibility, Interoperability, and Reuse of digital assets) data should be not overlooked: the metagenomic sequences are stored in public repositories, thus supporting the epidemiological investigation of foodborne outbreaks or other adverse effects in the environment and food production systems.…”

Multi‐country outbreak of Salmonella Senftenberg ST14 infections, possibly linked to cherry‐like tomatoes

“…Resistance of Salmonella strains from humans and animals to antibiotics is reported annually in the European Union summary report. In 2020, quinolone resistance was reported as high to very high among Salmonella isolates recovered from poultry and moderate in human cases from 2021 [7].…”