Farm effluent from wastewater of diverse animal populations in Ireland (pigs, cattle and poultry) before and after treatment using integrated constructed wetlands (ICWs), contains critically important antimicrobial resistant organisms, including Enterobacteriaceae phenotypically classified as cefotaxime and/or fluoroquinolone resistant. This study uses whole genome sequencing to further characterise the Enterobacteriaceae isolated from farm waste and ICW treated farm water to A) validate obtained resistance phenotypes, B) identify plasmid replicon types, C) determine relatedness, and D) identify O and H phenotypes of E. coli isolates, in order to gain a better understanding of the mechanisms of dissemination of the most significant resistance determinants, namely cefotaxime and fluoroquinolone resistance encoding genes.The characterisation of these isolates, which included E. coli, Enterobacter, Citrobacter and Klebsiella, will assist the understanding of the significance of farm effluents as a source of antimicrobial resistance to the environment in Ireland.