Genotypic characterization of ESBL/AmpC-producing E. coli from the German National Zoonoses Monitoring from 2016-2023 within the food production chain

The AMR monitoring was conducted following technical specifications given by Commission Implementing Decision (CID) 2013/652/EU and CID 2020/1729/EU and complemented by additional national programs using the same methods. Isolates were obtained from different matrices from broilers (N = 1650), fattening turkeys (N = 1303), fattening ducks (n=55), fattening pigs (N = 992) and cattle (N = 1206), and at different levels of the food production chain (primary production, slaughterhouse and retail) as well as from wild animals, small ruminants, freshwater fish and plant-based food were included (N = 119). Between 2016 and 2020 presumed ESBL/AmpC-producing isolates were examined using real-time PCR and genotype was determined by PCR  sequencing. Since 2021, presumed ESBL/AmpC-producing isolates were characterized by whole genome sequencing.
The variability of ESBL genes is fairly low with 23±3 different detected genes and gene
combinations each year. The majority of isolates harbored one ESBL/AmpC gene, only few carried two or more genes. In cattle and pigs, the majority of isolates (75.8 %) produce CTX-M-1 or CTX-M-15, whereas in poultry, a more even distribution of CTX-M-1, CTX-M-15, CMY-2, TEM-52 and SHV-12 was observed. In isolates from caecum content of pigs and calves, there were no major variations of genes over the years. In contrast significant changes were observed in isolates from poultry. ESBL/AmpC genes found in isolates from wild animals, small ruminants, freshwater fish and plant-based food were to the same as those found in pigs and cattle. In conclusion, there are changes in the specific ESBL gene patters observed in some food production chains. It is important to observe them closely to assess their potential role as sources of human exposure. In addition, further research is needed to understand the factors triggering the changes observed in distribution patterns in poultry.