Abstract/Summary

Enterobacterales from livestock are potentially important reservoirs for antimicrobial resistance (AMR) to pass through the food chain to humans, thereby increasing the AMR burden and affecting our ability to tackle infections. In this study 168 isolates from four Enterobacterales genera, primarily Escherichia coli, were purified from livestock (cattle, pigs, and sheep) faeces from 14 farms in the United Kingdom. Their genomes were resolved using long and short read sequencing to analyse AMR genes and their genetic context, as well as to explore the relationship between AMR burden and on-farm antimicrobial usage (AMU), in the three months prior to sampling. Although E. coli isolates were genomically diverse, phylogenetic analysis using a core-genome SNP tree indicated pig isolates to generally be distinct from sheep, with cattle isolates being intermediates. Approximately 28% of isolates harboured AMR genes, with the greatest proportion detected in pigs, followed by cattle then sheep; pig isolates also harboured the highest number of AMR genes per isolate. Although 90% of sequenced isolates harboured diverse plasmids, only 11% of plasmids (n=58/522) identified contained AMR genes, with 91% of AMR plasmids being from pig, 9% from cattle and none from sheep isolates; these results indicated pigs were a principle reservoir of AMR genes harboured by plasmids likely involved in their horizontal transfer. Significant associations were observed between AMU (mg/kg) and AMR. As both the total and the numbers of different antimicrobial classes used on-farm increased, the risk of multi-drug resistance (MDR) in isolates rose. However, even when AMU on pig farms was comparatively low, pig isolates had increased likelihood of being MDR; harbouring relatively more resistances than other livestock species. Therefore, our results show that AMR prevalence in livestock is not only impacted by recent AMU on-farm but also livestock related factors, which can influence the AMR burden in these reservoirs and its plasmid mediated transmission