Metagenomics and Other Methods for Measuring Antibitoic Resistance in Agroecosystems.

Background: There is broad concern regarding antibiotic resistance on farms and in fields, however there is no standard method for defining or measuring antibiotic resistance in environmental samples.   

Methods: We used metagenomic, culture-based, and molecular methods to characterize the amount, types and taxonomic distribution of antibiotic resistant bacteria and antibiotic resistance genes in cattle feces, water, and soil

Results:  Assessment of whether one site has more resistance than another depends heavily on the specific parameter chosen to assess resistance. Metagenomic studies reveal that antibiotic resistance genes are common in agricultural, human, and coastal-marine metagenomes, but although the types of resistance are fairly consistent across habitats, there are differences in the kinds of bacteria that likely carry the resistance genes.  Culture-based studies in native Nebraska prairies support the idea that antibiotic resistance is ubiquitous in soil, even in non-agricultural sites.  Phenotypic and genotypic characterization of prairie soils highlight that resistance can vary even in samples collected from the same prairie, and provide specific examples of how resistance changes depending on what gene or bacteria is measured.

Conclusions:  By more precisely defining how antibiotic resistance is measured we can better assess the impacts that agricultural best management practices have on the specific types of antibiotic resistant bacteria and antibiotic resistance genes that are most important for animal and human health.