Tetracycline and Sulfonamide Antibiotic Resistance Genes in Soils From Nebraska Organic Farming Operations

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.

Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources

“…The WGS revealed a number of tetracycline and sulfisoxazole resistance genes such as tetA , tetB , tetC , tetR , sul1 , and sul2 (Additional file 2 : Table S2). Of interest, gene mechanisms of tetracycline resistance including the efflux genes, the ribosomal protection and enzymatic genes were suggesting a possible ecological role for specific wide spread of tetracycline resistance [ 47 ]. However, AMR genes especially tetracycline and sulfonamide were also detected in livestock production surrounding even when antimicrobial drugs were not administered to animals [ 47 , 48 ].…”

Resistome in Lake Bolonha, Brazilian Amazon: Identification of Genes Related to Resistance to Broad-Spectrum Antibiotics

“…Antibiotic-resistant bacteria and ARGs have been reported in the environment, such as in soil (Cadena et al, 2018;Djenadi et al, 2018) and aquatic systems (Tacão et al, 2012;Li et al, 2018;Obayiuwana et al, 2018). Antibiotics and resistant bacteria are released into the environment through wastewater effluents and agricultural and livestock flows, altering natural ecosystems and microbial population dynamics, as well as introducing selective pressure that contributes to the diversity of the ARG pool.…”

Research and Technological Advances Regarding the Study of the Spread of Antimicrobial Resistance Genes and Antimicrobial-Resistant Bacteria Related to Animal Husbandry

“…Different ARGs may also possess different ecologies. Tetracycline resistance genes, ribosomal protection, and enzyme inactivation mechanisms are generally more frequently detected in manure and manure-applied soil, while the efflux pump genes are more frequently detected in prairie soil [34]. Perhaps one of the reasons is that efflux pumps are mainly chromosomally-encoded and present a conserved organization, while only a few are in MGEs [35].…”

“…For example, tetM, tetO, tetQ, and tetW are frequently encountered tetracycline resistance genes in pig manure. The tetM gene can be potentially used as an indicator to monitor manure-borne resistance when the manure is land-applied [4,14,34,90,91]. For erythromycin resistance genes, ermB, ermF, and ermG primers could detect 29%, 14%, and 12% of erm sequences, respectively, in swine manure metagenomes [92].…”