Antimicrobial resistance genes aph(3’)-III, ermB, sul2 and tetW abundance in animal faeces, products, production environments and human faeces in Europe

Objectives: We present a comparison of antimicrobial resistance genes (ARGs) abundance across animals, related environments and humans in nine European countries. Variation sources in ARG abundance were investigated, and the relationship between farm ARG levels and antimicrobial use (AMU) was determined. The correlation between relative ARG abundance assessed by qPCR and metagenomics were evaluated. 
Methods: A cross-sectional study was conducted in nine European countries comprising 9632 samples. qPCR was used to quantify ARG abundances (aph(3’)-III, ermB, sul2, tetW) and 16S rRNA. ANOVA was used in the abundance comparison. Random-effects meta-analysis was used to determine the relationship between AMU and relative ARG abundance in pigs and poultry. Spearman's rank correlation was assessed. 
Results: Between animal species, production environment and humans, we found high ARG abundance variation, which was contributed mostly by the variation between countries or farms. On-farm macrolide use and relative ermB abundance showed a significant positive association (FDR p < 0.1) in pigs and poultry. ARG abundance tended to decrease in pig and poultry production chains. A high relative ARG abundance was observed in occupationally exposed humans. qPCR results correlated well with metagenomics data for the ARGs studied (Spearman’s ρ > 0.7). 
Conclusion: This study shows qPCR analysis is a valuable tool to assess ARG abundance in a large collection of livestock associated samples. The ARG abundance varied across sample types and decreased along the animal production chain. ARG abundance in human faeces was related to occupational AMR exposure. The relationship between AMU and ARGs was confirmed.