Presence and abundance of antibiotic resistance genes at an organic goat dairy farm

Abstract

How does the use of antibiotics in animal husbandry impact antibiotic resistance genes (ARGs) and integron prevalence? This article examines the prevalence of nine ARGs (OXA-2, tetB, tetG, blaCMY-2, ereB, NDM, ermB, sul1, and sul2) and two class one integron sequences (intI1 and CS) at an organic goat dairy farm. To provide insight on how antibiotic use is contributing to the abundance of ARGs and integrons outside of where they are used, we made a comparison between our findings and the prevalence of ARGs and integrons at conventional farms from previously published studies. Samples were collected from an organic goat dairy farm in the Willamette Valley from the goat bedding and goat pellets, as well as non-agriculture soil from the Pacific University campus. DNA extraction, followed by PCR and agarose gel electrophoresis, was used to determine the ARG and integron presence in samples. Quantitative PCR was used to determine the ARG and integron abundance in the samples. Out of nine ARGs and two class 1 integron sequences, we found that four ARGs (tetG, ermB, sul1, and sul2) and both class 1 integron sequences (intI1 and CS) were present in the bacterial populations in our samples. tetG, intI1, and sul1 were chosen for qPCR analysis, and revealed equal or higher concentrations when compared to conventional farms. This study highlights the need to compare various practices to determine their impact on ARG prevalence.