Antibiotic Resistance in Agricultural and Non-Agricultural Settings.

The use of antibiotics in animal agriculture is an issue that has captured national attention, with the primary concern being the transfer of antibiotic resistance from animals to humans via food or water.  It has also been proposed that antibiotic resistance genes themselves be considered an environmental contaminant.  While there is a general mechanistic understanding about how the use of veterinary antibiotics can impact human health, the specific details of how antibiotic resistant bacteria and antibiotic resistance genes are transported through agroecosystems and the food chain remains unclear.  Characterizing antibiotic resistance phenotypes or genotypes is one method that has been used to help determine if fecal contamination is derived from agricultural, human, or environmental sources, but many questions remain to be answered before these methods can be routinely applied to understand the epidemiology of antibiotic resistance in animal agriculture.  Here we report on which bacteria are carrying specific antibiotic resistance genes, and begin to characterize how antibiotic resistance in agricultural settings compares to antibiotic resistance in natural settings.  Using publicly available metagenomic data sets and analysis tools we quantified antibiotic resistance genes from agricultural, environmental, human, and food-associated samples and determined the phylum and class-level taxonomic assignments for each gene fragment.  We also report on culture-based studies that quantify and characterize antibiotic resistant bacteria from beef cattle feedlots and ungrazed prairie soils.  Results indicate that some types of antibiotic resistance are broadly distributed across many taxa, while other types are limited to only a few taxa. Antibiotic resistant bacteria and antibiotic resistance genes are found across all samples and habitats studied, and there is variation in the temporal distribution of antibiotic resistance in soils.