Molecular characterisation of multi-drug resistant Escherichia coli of bovine origin.

Antimicrobial resistance reported in bacteria of animal origin is considered a major challenge to veterinary public health. In this study, the genotypic and phenotypic characterisation of twelve Escherichia coli isolates of bovine origin is reported. Twelve bacterial isolates of animal origin were selected from a previous study based on their multidrug resistant (MDR) profile. Efflux pump activity was measured using ethidium bromide (EtBr) and the biofilm forming ability of the individual strains was assessed using a number of phenotypic assays. All isolates were resistant to tetracyclines and a number of isolates expressed resistance to fluoroquinolones which was also confirmed in silico by the presence of these resistance markers. Amino acid substitutions in the quinolone resistance-determining regions were identified in all isolates and the presence of several siderophores were also noted. Whole genomesequence (WGS) data showed different STs that were not associated with epidemic STs or virulent clonal complexes. Seven isolates formed biofilms in minimal media with some isolates showing better adaptation at 25 °C while others at 37 °C. The capacity to efflux EtBr was found to be high in 4 isolates and impaired in 4 others. The pathogenicity of three selected isolates was assessed in zebrafish embryo infection models, revealing isolates CFS0355 and CFS0356 as highly pathogenic. These results highlight the application of NGS technologies combined with phenotypic assays in providing a better understanding of E. coli of bovine origin and their adaptation to this niche environment.