Florfenicol administration in piglets co-selects for multiple antimicrobial resistance genes

Antimicrobial use in food-producing animals such as pigs is a significant issue due to its association with antimicrobial resistance. Florfenicol is a broad-spectrum phenicol antibiotic used in swine for various indications; however, its effect on the swine microbiome and resistome is largely unknown. This study investigated these effects in piglets treated intramuscularly with florfenicol at 1 and 7 days of age. Fecal samples were collected from treated (<i>n</i> = 30) and untreated (<i>n</i> = 30) pigs at nine different time points up until 140 days of age, and the fecal metagenomes were sequenced. The fecal microbiomes of the two groups of piglets were most dissimilar in the immediate period following florfenicol administration. These differences were driven in part by an increase in the relative abundance of <i>Clostridium scindens</i>, <i>Enterococcus faecalis</i>, and <i>Escherichia</i> spp. in the florfenicol-treated piglets and <i>Fusobacterium</i> spp., <i>Pauljensenia hyovaginalis</i>, and <i>Ruminococcus gnavus</i> in the control piglets. In addition to selecting for florfenicol resistance genes (<i>floR</i>, <i>fexA</i>, and <i>fexB</i>), florfenicol also selected for genes conferring resistance to the aminoglycosides, beta-lactams, or sulfonamides up until weaning at 21 days of age. Florfenicol-resistant <i>Escherichia coli</i> isolated from these piglets were found to carry a plasmid with <i>floR</i>, along with <i>tet</i>(A), <i>aph(6)-Id</i>, <i>aph(3″)-Ib</i>, <i>sul2</i>, and <i>bla</i>_TEM-1/<i>bla</i>_CMY-2. A plasmid carrying <i>fexB</i> and <i>poxtA</i> (phenicols and oxazolidinones) was identified in florfenicol-resistant <i>Enterococcus avium</i>, <i>Enterococcus faecium</i>, and <i>E. faecalis</i> isolates from the treated piglets. This study highlights the potential for co-selection and perturbation of the fecal microbial community in pre-weaned piglets administered florfenicol.IMPORTANCEAntimicrobial use remains a serious challenge in food-animal production due to its linkage with antimicrobial resistance. Antimicrobial resistance can reduce the efficacy of veterinary treatment and can potentially be transferred to humans through the food chain or direct contact with animals and their environment. In this study, early-life florfenicol treatment in piglets altered the composition of the fecal microbiome and selected for many unrelated antimicrobial resistance genes up until weaning at 21 days of age. Part of this co-selection process appeared to involve an <i>Escherichia coli</i> plasmid carrying a florfenicol resistance gene along with genes conferring resistance to at least four other antimicrobial classes. In addition, florfenicol selected for certain genes that provide resistance to multiple antimicrobial classes, including the oxazolidinones. These results highlight that florfenicol can co-select for multiple antimicrobial resistance genes, and their presence on mobile genetic elements suggests the potential for transfer to other bacteria.