Changes in antimicrobial resistance profiles of Escherichia coli and the metagenome on Dutch pig farms after antimicrobial usage interventions

The use of antimicrobials in livestock farming results in the development and spread of antimicrobial resistance (AMR). To reduce antimicrobial usage (AMU), veterinary stewardship programs are implemented which can include coaching of farmers to improve farm management practices. We studied the effect of reduced antimicrobial use on pig farms, by evaluating AMR profiles of 45 pig farms by both phenotypic and metagenomic approaches before and after implementation of an intervention program. The intervention followed a stepped-wedge design and the duration of the intervention ranged between 10 and 27 months. Both weaned piglet and fattener pig farms were included. This intervention study showed that over time, a decrease in the abundance of resistance genes of several classes of antimicrobials was observed as well as a reduction in overall resistance gene abundance in both weaned piglet and fattener pig farms. Time related changes in phenotypic AMR profiles of Escherichia. coli were less clear. Lowering AMU resulted in lower AMR for some antimicrobial classes even within a short time period. For example lower tetracycline use resulted in lower tetracycline resistance in E.coli and in fewer tetracycline genes in the metagenome. Lower Beta-lactam use resulted in lower ampicillin resistance in E. coli. A longer follow-up is needed to fully understand the effects of reduced AMU, but our study shows that the effects of veterinary antimicrobial stewardship programs in both fattener pig and weaned piglet farms are thus so far promising.