Research project Antibiotic residues, antibiotic resistant bacteria and antibiotic resistance genes in manure, soil and plants and the potential exposure of humans

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Main research question

When livestock manure is used on agricultural land, in addition to the known attention to environmental problems, concern is increasing about antibiotic residues and antibiotic resistance genes that may end up in the environment with the manure. In this project we investigated the impact of manure with antibiotic residues and resistance genes. What do we observe in the agricultural soil on which this manure is spread, and what are the effects on the crops that are then grown on it?

Research approach

We analyzed samples of manure of different animal origin as well as from the agricultural soil before and after fertilization. We also grew leek under experimental controlled conditions on fertilized soil inoculated with relevant antibiotic concentrations. We analyzed the samples to quantify the antibiotic residues, to investigate the (antibiotic-resistant) bacterial shifts and to quantify antibiotic resistance genes. In addition, commercially available leek was also investigated for the presence of antibiotic residues.


In conclusion, we observed that manure used for fertilization, especially from pigs and veal calves, often contains several antibiotic residues and multidrug resistant (possibly pathogenic) bacteria, such as E. coli resistant to antibiotics which are critically important in human medicine. Further, we noticed that agricultural fields may contain antibiotic residues even before fertilization, probably due to previous fertilization events. Two to three weeks after fertilization, we noticed that some antibiotic residues brought into the soil by fertilization were still present in the soil. This is strongly dependent on the properties of the soil as well as the physicochemical properties of the residue itself. We also observed an increase in resistance genes in the soil which was more likely due to the simultaneous introduction of antibiotic residues and resistance genes by fertilization than by the subsequent selection of antibiotic resistance in the soil. However, tetracyclines, fluoroquinolones and lincomycin were detected in concentrations in soil that might provoke a selection pressure contributing to antibiotic resistance selection, although this should be further studied. In addition, the effect of repetitive fertilization on the presence and gene copy number of resistance genes should be studied over a longer period. When cultivating leek in a controlled greenhouse experiment in soil fertilized with manure spiked with antibiotic residues, the crop did not contain antibiotic residues at harvest, nor the studied resistance genes. Also, antibiotic residues in leek for consumption were only sporadically detected in small amounts. Further research should also be conducted with other vegetables for example those with a shorter growing season.