A metagenomic approach for determining prevalence of tetracycline resistance genes in the fecal flora of conventionally raised feedlot steers and feedlot steers raised without antimicrobials

Abstract

To compare prevalence of tetracycline resistance genes in the fecal flora of conventionally raised feedlot steers and feedlot steers raised without antimicrobials. 61 fecal samples from conventionally raised steers and 61 fecal samples from steers raised without antimicrobials at a single feedlot. Total DNA was extracted from each fecal sample and analyzed by means of 4 multiplex PCR assays for 14 tetracycline resistance genes. At least 3 tetracycline resistance genes were identified in all 122 fecal samples. For 5 of the 14 tetracycline resistance genes, the percentage of samples in which the gene was detected was significantly higher for fecal samples from conventionally raised cattle than for fecal samples from antimicrobial-free cattle, and for 1 gene, the percent-age of samples in which the gene was detected was significantly higher for fecal samples from antimicrobial-free cattle than for fecal samples from conventionally raised cattle. The percentage of samples with > or = 11 tetracycline resistance genes was significantly higher for fecal samples from conventionally raised cattle (35/61 [57%]) than for fecal samples from antimicrobial-free cattle (16/61 [26%]). Results suggested that the prevalence of tetracycline resistance genes was significantly higher in the fecal flora of conventionally raised feedlot steers than in the fecal flora of feedlot steers raised without antimicrobials and that a metagenomic approach may be useful in understanding the epidemiology of antimicrobial resistance in food animals.