Prevalence of antimicrobial resistance genes in Escherichia coli isolated from pigs in England.

Escherichia coli are becoming increasingly antimicrobial resistant (AMR), affecting therapeutics available for treating infections. We combined genomics and epidemiology to assess the potential of E. coli from livestock as reservoirs for AMR for humans. WGS genotyping of >500 E. coli from 56 pig farms in England were performed. The majority of farms harboured multidrug resistant (MDR) E. coli, with fluoroquinolone resistant E. coli more likely to be MDR. Resistance to the critically important antibiotics carbapemen and colistin, were absent; although levels of extended-spectrum-cephalosporin resistance was similar to humans. E. coli were phylogenetically diverse, but presence of common AMR plasmids implicated possible circulation within and/or between animals and farms. Multivariable analysis suggested high antibiotic usage and finisher-only farms were twice as likely to have MDR E. coli, although feeding from ground or coarse feed decreased the odds. We believe our approach is applicable to other farming systems/countries for characterising MDR hazards.