Risks of antibiotic residues, antibiotic resistance genes and pathogens when using pig manure as fertilizer on crop fields

    Project Details


    Main research question/goal
    Every year, fertilisation with pig manure is responsible for depositing about 60 kilotons of nitrogen on arable lands in Flanders, including vegetable fields. In pig production, antibiotics are very often used to prevent or treat diseases and a significant amount of these antibiotics are excreted as active metabolites. Does this use of pig manure as a fertilizer have an effect on the spread of antibiotic residues and antibiotic resistance genes in the environment? A related issue is the survival of zoonotic pathogens like Salmonella in pig manure and after spread on the fields. The purpose of this study called VARMEST was to elucidate if and how pig manure can be used safely in agriculture.

    Research approach
    This project has now ended. We developed and validated a liquid chromatography tandem mass spectrometry method for the detection of multiple antibiotic residues in manure and soil samples. Next, pig manure was screened for antibiotic residues, antibiotic resistance genes and zoonotic pathogens before spreading it on the field. This happened several times: the soil was sampled immediately before and after fertilization, and one, two and four months after fertilization (at harvest). Last, we assessed the effect of manure processing on antibiotic residues, antibiotic resistance genes and pathogens by analyzing the manure before and after processing.


    The results showed that high concentrations of antibiotic residues could be present in pig manure which are further diluted in the soils after fertilization. These can be detectable in the soils up until harvest. However, this is dependent of the antibiotic and soil type. The presence of antibiotic resistance genes in manure were similar for the pigs which were administered antibiotics and the ones which were not. Although the antibiotic resistance genes studied were already present in the soil environment prior to fertilization, an increase in the relative abundances of most of the antibiotic resistance genes studied was observed immediately after fertilization. This increase was followed by a gradual decline to initial levels over time. These results may indicate that the input of resistance genes through fertilization with manure is more important with regard to dissemination of resistance than the selection pressure exerted through the antibiotic residues present in the manure. Pathogens present in the manure could be detected in the soil environment directly after fertilization but not after one month. 

    Finally, it was demonstrated that biological nitrogen removal from pig manure as a manure treatment process is able to slightly reduce the concentration of certain antibiotic residues and several antibiotic resistance genes and to largely reduce the amount of zoonotic bacteria in the effluent.

    Effective start/end date1/09/1331/12/18