Enriched Shotgun Sequencing to Assess the Effects of Interventions to Reduce Antimicrobial Use in Neonatal Dairy Calves

Background Neonatal diarrhea accounts for 20%–25% of morbidity among calves, and antimicrobial drugs (AMDs) are often administered for treatment. Systematic approaches that mitigate antimicrobial use (AMU) can be effective in decreasing antimicrobial resistance (AMR). Hypothesis/Objectives To determine the effects of an algorithmic farm‐based intervention that reduced AMU for diarrhea on the community structure of antimicrobial resistance genes (ARGs) identified in the feces of healthy dairy calves. Animals Thirty‐one fecal dairy calf samples collected at two timepoints and farms ( N = 7–8 per sampling point) were used. Samples were obtained before AMU reductions and 12 months afterward. Methods Target‐enriched shotgun sequencing was performed to characterize all ARGs in samples. Bioinformatics processing and statistical analysis were performed using the AMR++ pipeline, MEGARes AMR database, and R. Results Pre‐intervention comparisons showed increased relative abundances (RA) consistent with the AMU on each farm. Intra‐farm results showed that on Farm 1, there were significant increases in the RA of ARGs for tetracyclines (22.1%–27.4%, q = 0.02) and fluoroquinolones (0%–0.1%, q < 0.0001) in the Post period. On Farm 2, significant decreases were seen over time in the RA of ARGs for sulfonamides (9.6%–5.1%, q = 0.006) and fluoroquinolones (0.77%–0.12%, q = 0.004). Conclusions and Clinical Importance Despite similar reductions in AMU on both farms, implementing an antimicrobial stewardship algorithm was associated with differing effects on and changes to the fecal resistome.