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

Abstract

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&#x2009;=&#x2009;7-8 per sampling point) were used. Samples were obtained before AMU reductions and 12&#x2009;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&#x2009;=&#x2009;0.02) and fluoroquinolones (0%-0.1%, q&#x2009;<&#x2009;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&#x2009;=&#x2009;0.006) and fluoroquinolones (0.77%-0.12%, q&#x2009;=&#x2009;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.