Closely Related Escherichia coli Strains with Multiple Resistances Found on Co-Managed Pig Farms Despite Marked Differences in Farm Antimicrobial Drug Usage

Bacterial resistance on farms can be driven by antimicrobial use. Less is known about inter-farm transfer of resistance genes and their persistence under low antimicrobial pressure. Over two years and nine visits, we examined the shedding of resistant indicator bacteria (Escherichia coli) on one lower- and one higher-antimicrobial-usage pig farm. There was a unidirectional transfer of some less healthy pigs from the former to the latter. Faecal pools (180) were cultured on Chromagar ECC, with and without added cefotaxime or ciprofloxacin. Presumptive E. coli were phenotyped, and many ciprofloxacin-resistant isolates were whole-genome sequenced. Comparing farms, there was more (p < 0.0001) phenotypic resistance to the antimicrobial panel from the higher-usage unit, and markedly more (about ten-fold) multi-resistance. Significantly elevated individual drug resistances on this unit correlated with recently used antimicrobials. Ciprofloxacin and/or cefotaxime-resistant isolates were often present, although in low proportions. Neither of these antimicrobial classes had been administered recently, except for one fluoroquinolone course late in the study. AMR genes were more diverse from the higher-usage farm, but some resistant and multi-resistant isolates were closely related between farms. Thus, we demonstrated the maintenance of resistance genes in strains present on farms, even where selective pressure was low.