Escherichia coli from six European countries reveals differences in profile and distribution of critical antimicrobial resistance determinants within One Health compartments, 2013 to 2020

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Abstract
Background: Antimicrobial resistance (AMR) is a global threat. Monitoring using an integrated One Health approach is essential to detect changes in AMR occurrence. Aim: We aimed to detect AMR genes in pathogenic and commensal Escherichia coli collected 2013–2020 within monitoring programmes and research from food animals, food (fresh retail raw meat) and humans in six European countries, to compare vertical and horizontal transmission. Methods: We whole genome sequenced (WGS) 3,745 E. coli isolates, detected AMR genes using ResFinder and performed phylogenetic analysis to determine isolate relatedness and transmission. A BLASTn-based bioinformatic method compared draft IncI1 genomes to conserved plasmid references from Europe. Results: Resistance genes to medically important antimicrobials (MIA) such as extended-spectrum cephalosporins (ESC) were widespread but predicted resistance to MIAs authorised for human use (carbapenem, tigecycline) was detected only in two human and three cattle isolates. Phylogenetic analysis clustered E. coli according to phylogroups; commensal animal isolates showed greater diversity than those from human patients. Only 18 vertical animal-food and human-animal transmission events of E. coli clones were detected. However, IncI1 plasmids from different sources and/or countries carrying resistance to ESCs were conserved and widely distributed, although these variants were rarely detected in human pathogens. Conclusion: Using WGS we demonstrated AMR is driven vertically and horizontally. Human clinical isolates were more closely related, but their IncI1 plasmids were more diverse, while animal or food isolates were less similar with more conserved IncI1 plasmids. These differences likely arose from variations in selective pressure, influencing AMR evolution and transmission.

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