Effects of Ceftiofur and Chlortetracycline on the Resistome of Feedlot Cattle

Treatment of food producing animals with antimicrobial drugs (AMD) is controversial because of concerns regarding promotion of antimicrobial resistance (AMR). To investigate this concern, resistance genes in metagenomic fecal samples during a clinical trial were analyzed to assess the impacts of treatment on beef feedlot cattle resistomes. Four groups of cattle were exposed, using a 2x2 factorial design, to different regimens of antimicrobial treatment. Injections of ceftiofur crystalline free acid (a third generation cephalosporin) were used to treat all cattle in treated pens vs. only a single animal, and chlortetracycline was included in the feed of all cattle in a pen vs. no treatment. On days 0 and 26, respectively, pre- and post-trial fecal samples were collected and resistance genes were characterized using shotgun metagenomic sequencing.