Tetracycline and sulfonamide antibiotic resistance genes in soils from Nebraska organic farming operations

Authors: CADENAS, MARLYNN - University Of Texas - El Paso; Durso, Lisa; Miller, Daniel; Waldrip, Heidi; Castleberry, Bobbie - Lana; DRIJBER, RHAE - University Of Nebraska; WORTMAN, CHARLES - University Of Nebraska

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/25/2018
Publication Date: 6/27/2018
Citation: Cadenas, M., Durso, L.M., Miller, D.N., Waldrip, H., Castleberry, B., Drijber, R.A., Wortman, C. 2018. Tetracycline and sulfonamide antibiotic resistance genes in soils from Nebraska organic farming operations. Frontiers in Microbiology. 9:1283.
DOI: https://doi.org/10.3389/fmicb.2018.01283

Interpretive Summary: The ability to use antibiotics to control microbial infections has led to longer lifespans and better overall health in both humans and animals. However, the continued use of antibiotics provides a selective pressure for the development of antibiotic resistance. Increased resistance is associated with potential risks in both the clinical aspect and the environmental aspect. As the focus of this study, the environmental aspect can be explored through the process of identifying the presence of antibiotic resistant genes in organic farm soil to create a baseline of information regarding the amount of antibiotic resistance that occurs naturally in the environment. Soil samples from 13 different organic farms in Nebraska were collected for DNA detection of antibiotic resistance genes. The microbiological analysis revealed that antibiotic resistance genes were detected in all 13 Nebraskan organic farms that were part of this study. Of the 198 samples tested, 93% were positive for at least one antibiotic resistance gene and 81% of the samples had 2 or more antibiotic resistance genes present. These results characterize baseline of antibiotic resistance in farming systems that do not routinely use antibiotic drugs.

Technical Abstract: There is widespread agreement that agricultural antibiotic resistance should be reduced, however it is unclear from the available literature what an appropriate target for reduction would be. Organic farms provide a unique opportunity to disentangle questions of agricultural antibiotic drug use from questions of antibiotic resistance. In this study, soil was collected from 12 certified organic farms in Nebraska, evaluated for the presence of tetracycline and sulfonamide resistance genes (n=15 targets), and correlated to soil physical, chemical, and biological parameters. Tetracycline and sulfonamide antibiotic resistance genes (ARGs) were found in soils from all 12 farms, and 182 of the 196 soil samples (93%). The most frequently detected gene was tet(Q) (49% of samples), followed by tet(S) (46%), tet(X) (30%), and tetA(P) (29%). Soil was collected from two depths. No differences in ARGs were observed based on soil depth. Positive correlations were noted between ARG presence and soil electrical conductivity, and concentrations of calcium, sodium and Mehlich-3 phosphorus. Data from this study point to possible relationships between selected soil properties and individual tetracycline resistance genes, including tet(B), and tet (O). We compared organic farm results to previously published data from prairie soils and found significant differences in detection frequency for 12 genes, eight of which were more commonly detected in prairie soils. Of interest, when tetracycline ARG results were sorted by gene mechanism, the efflux genes were generally present in higher frequency in the prairie soils, while the ribosomal protection and enzymatic genes were more frequently detected in organic farm soils, suggesting a possible ecological role for specific tetracycline resistance mechanisms. By comparing soil from organic farms with prairie soils, we can start to determine baseline effects of low-chemical input agricultural production practices on multiple measures of resistance.