Piglet gut and in-barn manure from farms on Raised Without Antibiotics program display a reduced antimicrobial resistance but an increased prevalence of pathogens

In response to new stringent regulations in Canada on the use of antibiotics in animal production, many farms implemented practices to produce animals that are Raised Without Antibiotics (RWA) from birth to slaughter. This study aimed to assess the impact of RWA production practices on reducing the actual total on-farm use of antibiotics, occurrence of pathogens, and the prevalence of antimicrobial resistance (AMR). A 28-month longitudinal surveillance monitoring of farms that adopted the RWA program and conventional farms using antibiotics as per the new regulations (non-RWA) was conducted by collecting fecal samples from 6-week old pigs and composite ma-nure from the barn over 6 time points and applying whole genome sequencing (WGS) to assess the prevalence of AMR genes as well as the abundance of pathogens. Analysis of in-barn drug records confirmed the decreased consumption of antibiotics in RWA barns compared to non-RWA barns. WGS analyses revealed that RWA barns had reduced frequency of AMR genes in piglet feces and in barn manure. However, metagenomic analyses showed that RWA barns had significant increase in the frequency of pathogenic Firmicutes in fecal samples and pathogenic Proteobacteria in barn manure samples.