Abstract
The use of antimicrobials in animal production has been shown to increase the abundance of antibiotic resistance genes (ARGs) in microbiomes and it is recommended by international health organizations that the use of antimicrobial growth promoters would be restricted. Consequently, the use alternative growth promoters is increasing, however, their influence on the collection of ARGs (the resistome) in the animal microbiome is understudied. 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 growth trial and after 33 days, 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. The community composition was investigated by 16S rRNA gene sequencing and relative ARG and mobile genetic element (MGE) abundances were measured using qPCR array with 382 primers. Only modest shifts 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. The ARG–MGE co-occurrence patterns suggest that replacing the use of antibiotics with alternative growth promoters might be an insufficient antibiotic resistance mitigation strategy and active selection against ARGs will require a more comprehensive approach.
Importance Due to increasing antimicrobial drug resistance of pathogenic bacteria, international organizations are advising livestock and poultry industries to limit the use of antimicrobials in growth promotion. Together with growing consumer concerns towards antimicrobials, the markets are favorable to alternative growth promoters. Since the interest towards enhancing animal productivity and health through microbiomes is also increasing, it is important to study the linkages between the resistome and bacterial community structure to avoid enriching ARGs in animal microbiomes. Our study explores the influences of different growth promoters on the bacterial community and resistome compositions and we show that resistance gene mobility should be taken into account when considering the changes in agricultural antibiotic use policies.