UK pig farms show positive association between level of antimicrobial drug use and prevalence of antibiotic resistant Escherichia coli

ObjectivesTo compare patterns of resistance (phenotypic and genotypic), plus strain persistence, among E. coli on a low- versus a higher-antimicrobial-usage pig farm.MethodsPooled faeces were collected on several occasions over two years on each farm, both being part of the same production pyramid. Quantitative culture was performed on Chromagar ECC, with and without added ciprofloxacin or cefotaxime. Species-confirmed isolates were screened for phenotypic resistance to 14 antimicrobial drugs, and whole-genome sequencing allowed analysis for multi-locus sequence typing, phylogeny based on single nucleotide polymorphisms, and antimicrobial resistance determinants.ResultsFrom a total of 180 pools, ciprofloxacin and cefotaxime resistant E. coli were commonly present but at very low frequencies on both farms, despite rare or zero recent use of either drug class. Comparing isolates from weaner and grower/finisher pigs between farms, resistance to at least one of the screened antimicrobials was significantly (P < 0.0001) more frequent from the higher-usage farm. The same contrast was observed for multi-resistant isolates. Genotype analysis also showed a higher prevalence of AMR determinants from the higher antimicrobial-usage farm. Sequence analyses of ciprofloxacin-resistant E. coli indicated that AMR determinants per isolate were more diverse from the higher-usage farm, but also that some closely-related strains existed on both farms, and at multiple times.ConclusionsThere was a clear correlation between the level of antimicrobial drug use and the frequency of AMR and multi-drug resistance in the two farms studied. The presence of a reservoir of strains resistant to critically important antibiotic classes on both farms, in the absence of direct selective pressure, is also notable