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 the soil. 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 tetG (55% of samples), followed by tet(Q) (49%), 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 Ca, Na, and Mehlich-3 phosphorus. Data from this study point to possible relationships between selected soil properties and individual tetracycline resistance genes, including tet(O) which is a common target for environmental samples. 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.
Highlights
The global emergence of antibiotic resistance has led to the immediate need to find ways to mitigate resistance in the environment
The presence of antibiotic residues in manure may lead to selection and proliferation of strains of antibiotic resistant bacteria (ARB); manure from livestock facilities is a source of antibiotic drugs, ARB, and antibiotic resistance genes (ARGs) excreted into the environment (Binh et al, 2008; Heuer et al, 2011)
Organic farms present a unique opportunity to determine impacts of agriculture on antibiotic resistance in soil, without the routine antibiotic drug inputs associated with conventional production practices
Summary
The global emergence of antibiotic resistance has led to the immediate need to find ways to mitigate resistance in the environment. Agricultural antibiotic resistance is an issue that has gained national and international attention (Topp et al, 2017), and there is concern that resistance from cropland and livestock will be transferred through the environment and cause untreatable infectious disease in people and animals (Durso and Cook, 2014). There is widespread agreement and support for the idea that agricultural antibiotic resistance should be reduced, with an emphasis on reducing transfer of resistance from practices such as land application of animal manures (Heuer et al, 2011; Pruden et al, 2013; Marti et al, 2014), and spraying of antibiotics to control bacterial disease in fruit crops (Stockwell and Duffy, 2012). There remain many knowledge gaps surrounding the basic ecology of antibiotic resistance on farms and in fields, such as how variable is any particular measure of resistance within or between farms? And from a human and animal health standpoint, which types of resistance should be measured or tracked?
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