Antibiotic Resistance Genes and Associated Phenotypes in and from Cattle at Different Production Stages on a Dairy Farm in Central California.

The objectives of this study were to characterize overall genomic antibiotic resistance profiles of fecal and spp. from dairy cattle at different production stages using whole-genome sequencing and to determine the association between antimicrobial resistance (AMR) phenotypes and their corresponding genotypes. The Comprehensive Antibiotic Resistance Database (CARD) and ResFinder, two publicly available databases of antimicrobial resistance genes, were used to annotate isolates. Based on the ResFinder database, 27.5% and 20.0% of tested isolates ( = 40) harbored single and ≥3 antimicrobial resistance genes, respectively; for spp., we observed 87.8% and 8.2%, respectively. The highest prevalence of AMR genes in was for resistance to tetracycline (27.5%), followed by sulphonamide (22.5%) and aminoglycoside (20.0%); the predominant antimicrobial resistance genes in spp. targeted macrolide drugs (77.6%). Based on the CARD database, resistance to ≥3 antimicrobial classes was observed in all and 77.6% in spp. isolates. A high degree of agreement existed between the resistance phenotype and the presence of resistance genes for various antimicrobial classes for but much less so for isolates of . Consistent with prior work, fecal and spp. isolates from calves harbored a wide spectrum of resistance genes, compared to those from cattle at other production stages, based on the cross-sectional samples from the studied farm.