Effects of chlortetracycline and copper supplementation on the prevalence, distribution, and quantity of antimicrobial resistance genes in the fecal metagenome of weaned pigs

•We used culture independent total community approach to evaluate the impact of chlortetracycline and copper supplementation on the presence of 14 tet genes and quantity of 4 antimicrobial resistance elements (tetA, tetB, blaCMY-2 and pcoD) in the fecal metagenome of weaned pigs.•Diverse number of tet genes with a median of 8 genes were detected per fecal sample and this diversity decreased during treatment and post treatment periods.•Chlortetracycline supplementation, either alone or when combined with copper, differentially impacted the prevalence and quantities of tetA and tetB.•Mean log10 copies of tetA, tetB, blaCMY-2 and pcoD decreased over time.•tetA and blaCMY-2 genes were strongly correlated. Use of in-feed antibiotics such as chlortetracycline (CTC) in food animals is fiercely debated as a cause of antimicrobial resistance in human pathogens; as a result, alternatives to antibiotics such as heavy metals have been proposed. We used a total community DNA approach to experimentally investigate the effects of CTC and copper supplementation on the presence and quantity of antimicrobial resistance elements in the gut microbial ecology of pigs. Total community DNA was extracted from 569 fecal samples collected weekly over a 6-week period from groups of 5 pigs housed in 32 pens that were randomized to receive either control, CTC, copper, or copper plus CTC regimens. Qualitative and quantitative PCR were used to detect the presence of 14 tetracycline resistance (tet) genes and to quantify gene copies of tetA, tetB, blaCMY-2 (a 3rd generation cephalosporin resistance gene), and pcoD (a copper resistance gene), respectively. The detection of tetA and tetB decreased over the subsequent sampling periods, whereas the prevalence of tetC and tetP increased. CTC and copper plus CTC supplementation increased both the prevalence and gene copy numbers of tetA, while decreasing both the prevalence and gene copies of tetB. In summary, tet gene presence was initially very diverse in the gut bacterial community of weaned pigs; thereafter, copper and CTC supplementation differentially impacted the prevalence and quantity of the various tetracycline, ceftiofur and copper resistance genes resulting in a less diverse gene population.