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Prevalence and trend analysis of antimicrobial resistance in clinical Escherichia coli isolates collected from diseased pigs in USA between 2006-2016.

Antimicrobial resistance (AMR) is an emerging threat to both human and animal health. Antimicrobial use and resistance in food animal production including swine has received increased scrutiny as a source of resistant foodborne pathogens. Continuous surveillance of AMR in bacterial isolates of swine origin can guide in conservation of antimicrobials used in both human and swine medicine. The objective of this study was to evaluate the prevalence and trends of the phenotypic AMR in Escherichia coli of swine origin isolated from clinical samples at the Minnesota Veterinary Diagnostic laboratory between 2006-2016. The prevalence of resistance to ampicillin, tetracyclines and sulphadimethoxine remained greater than 50% throughout the period. There was a drastic change in enrofloxacin resistance, increasing from less than 1% to more than 20% between 2006-2016 (annual relative increase of 57% between 2006-13 and 16% between 2013-16). The prevalence of resistance to other antimicrobials remained constant (ceftiofur, oxytetracycline, chlortetracycline) or changed significantly (annual relative changes of less than 10%) for at least some time-period between 2006-16 (ampicillin, florfenicol, gentamicin, neomycin, sulphadimethoxine, trimethoprim-sulphamethoxazole, spectinomycin). Rarefaction analysis revealed an increase in the number of unique combinations of AMRs per year. Network analysis was performed by estimating and plotting partial correlations between minimum inhibitory concentrations of various antimicrobials. An increase in strength of these networks was observed, particularly in networks created for years later than 2010 which can be indicative of increased multiple antimicrobial resistance in these isolates. These results provide valuable insight into the trends in AMR in E. coli of swine origin in USA and act as supplementary information to existing active AMR surveillance systems.