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bioRxiv · 10.1101/2024.06.03.597168

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

Holman, D. B.·James-Gzyl, K. E.·Kommadath, A.
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Abstract

Florfenicol is a broad-spectrum phenicol antibiotic used in swine for various indications. However, information regarding its effect on the pig gut microbiome and resistome is lacking. Therefore, this study investigated those effects by treating piglets with an intramuscular injection of florfenicol at 1 and 7 days of age. Fecal samples were collected from treated (n =30) and untreated (n = 30) pigs at nine different time points up until 140 days of age and their microbiomes were profiled using both 16S rRNA gene and shotgun metagenomic sequencing. The gut 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 enrichment in Clostridium scindens, Enterococcus faecalis, and Escherichia spp. in the florfenicol-treated piglets and Fusobacterium spp., Pauljensenia hyovaginalis, and Ruminococcus gnavus in the control piglets. In addition to florfenicol resistance genes including floR, fexA, and fexB, florfenicol also selected for genes conferring resistance to the aminoglycosides, beta-lactams, peptides, or sulfonamides up until weaning at 21 days of age. Florfenicol-resistant Escherichia coli isolated from these piglets were found to carry a plasmid with a floR, along tet(A), aph(6)-Id, aph(3)-Ib, sul2, and blaTEM-1/ blaCMY-2. A plasmid carrying fexB and poxtA was identified in florfenicol-resistant Enterococcus avium, Enterococcus faecium, and E. faecalis isolates from the treated piglets. This study highlights the potential for co-selection and perturbation of the gut microbial community in pre-weaned piglets administered florfenicol. ImportanceAntimicrobial use and resistance remain a serious challenge in food-animal production systems. Understanding how specific antimicrobials affect the gut microbiome and resistome is an important step in reducing antimicrobial use and resistance. Florfenicol is an antimicrobial used in swine production, yet very little is known about its effect on the pig gut microbiome and resistome. In this study, we administered florfenicol to piglets at 1 and 7 days of age and characterized their fecal metagenomes through to 140 days of age. Florfenicol altered 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 Escherichia coli plasmid carrying a florfenicol resistance gene along with genes conferring resistance to at least four other antimicrobial classes. These results demonstrate the potential for certain antimicrobials to co-select for multiple, unrelated antimicrobial resistance genes in pigs.

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Holman, D. B., James-Gzyl, K. E., Kommadath, A.. 2024-06-04. Florfenicol administration in piglets co-selects for multiple antimicrobial resistance genes. https://doi.org/10.1101/2024.06.03.597168

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