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 = 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.

Keywords: antimicrobial resistance; antimicrobial stewardship; cattle; diarrhea; fecal resistome; metagenomics.