Risk Factors for Antimicrobial Resistance in Turkey Farms: A Cross-Sectional Study in Three European Countries

Abstract

Food-producing animals are an important reservoir and potential source of transmission ofantimicrobial resistance (AMR) to humans. However, research on AMR in turkey farms is limited.This study aimed to identify risk factors for AMR in turkey farms in three European countries(Germany, France, and Spain). Between 2014 and 2016, faecal samples, antimicrobial usage (AMU),and biosecurity information were collected from 60 farms. The level of AMR in faecal sampleswas quantified in three ways: By measuring the abundance of AMR genes through (i) shotgunmetagenomics sequencing (n= 60), (ii) quantitative real-time polymerase chain reaction (qPCR)targetingermB,tetW,sul2, andaph3′-III; (n= 304), and (iii) by identifying the phenotypic prevalenceof AMR inEscherichia coliisolates by minimum inhibitory concentrations (MIC) (n= 600). Theassociation between AMU or biosecurity and AMR was explored. Significant positive associationswere detected between AMU and both genotypic and phenotypic AMR for specific antimicrobialclasses. Beta-lactam and colistin resistance (metagenomics sequencing); ampicillin and ciprofloxacinresistance (MIC) were associated with AMU. However, no robust AMU-AMR association wasdetected by analyzing qPCR targets. In addition, no evidence was found that lower biosecurityincreases AMR abundance. Using multiple complementary AMR detection methods added insightsinto AMU-AMR associations at turkey farms.