Swine Growth Promotion with Antibiotics or Alternatives Increases Antibiotic Resistance Gene Mobility Potential in the Fecal Microbiome

The use of antimicrobials in animal production has been shown to contribute to the emergence of antimicrobial resistance. Currently, the use alternative growth promoters is increasing and more information is needed on their capability to select for antimicrobial resistance. We investigated the impact of different growth promoters on the pig fecal resistome and microbiome. The growth promoters were carbadox (antibiotic), copper sulfate and zinc oxide (metal) or mushroom powder (natural product). Six pens of seven weanling piglets per treatment were used in a 33-day growth trial. Fecal samples were taken from one median weight female and male pig per pen, samples from the same pen were pooled, and DNA was isolated. Relative antibiotic resistance gene (ARG) and mobile genetic element (MGE) abundances were measured using high-throughput qPCR array with 382 primers and the bacterial community composition was investigated by 16S rRNA gene sequencing. Only modest changes were observed in community structure and resistome in response to growth promoters, but more ARGs were co-occurring with MGEs in growth promoter group samples than in the control group samples. The taxonomic structure could not be linked to resistome structure in the growth promoter groups. These results suggest that horizontal gene transfer might be more important mechanism in the dissemination of antimicrobial resistance in response to growth promotion than the selection of resistant bacteria. Thus, ARG mobility should be taken into account when designing new antimicrobial use policies and antimicrobial resistance surveillances.