Temporal dynamics of the resistome in gilts raised in an organic operation in which semen used for artificial insemination is the primary source of antimicrobial exposure.

Natural bacterial contaminants in boar semen make it necessary to use preservative-level antibiotics in semen extenders to ensure long-term sperm viability and artificial insemination (AI) success. While concerns exist about the role of semen extender antibiotics in antimicrobial resistance (AMR), empirical evidence is lacking. This study examined microbiome and resistome dynamics in fecal samples of gilts from an organic farming operation, where AI is the primary source of antimicrobial exposure. Metagenomics was used to analyze microbial communities and antibiotic resistance genes (ARGs) across quarantine, breeding pen introduction, and post-AI production phases. The fecal microbiome was dominated by Bacillota and Bacteroidota. Microbial shifts were likely due to environmental and dietary adaptation, with no major changes observed post-AI. Among 168 identified ARGs, 89% were linked to drug resistance, primarily targeting tetracyclines, aminoglycosides, and macrolides, lincosamides and streptogramins (MLS). The abundance of most ARGs decreased between arrival at the operation and 10 days after introduction into the breeding pen, with no major resistome changes post-AI. Neither exposure to previously inseminated females nor antibiotics in semen extenders increased fecal ARGs. This study found no evidence that rational antibiotic use in swine semen extender contributes to increased antimicrobial resistance in the swine fecal microbiome.