Antibiotic resistance : The role of soil use in antibiotic resistance

Soils have been implicated as a source of antibiotic resistance, particularly when amended with manure or dung. Despite the limitation of prior studies to very few genes and sites, presumed links between soils and public health risks are being drawn. A broader understanding of soil resistomes in their microbial habitat, subject to environmental conditions, is needed to develop sustainable agricultural as well as antibiotics policies.

The aim of the “Antibiotic resistance” project was to describe the diversity of antibiotic resistance genes in representative of Swiss agricultural soils and to evaluate the effects of agricultural practices on resistance gene dynamics.

Total soil DNA sequencing and analysis methods were optimised to obtain metagenomes for cultivated and uncultivated land. A hierarchical assessment of the impact of soil parameters and soil amendments relevant to antibiotic resistance abundance and shifts was made. Swiss soils carry a natural background of diverse antibiotic resistance genes but these are at very low levels and are not clinically relevant genes. Manure application introduces antibiotic resistance genes but this is a transient effect, with these genes being flushed from the system within a few days and soils returning to normal levels. Soil management practices have little impact on antibiotic resistance genes, or on microbial communities that play an important role in key soil functions.

Inadequate information is available on antibiotic resistance in soils for a scientific assessment of links with public health. The project provides data on resistance gene biodiversity and dynamics, as affected by soil management practices. This data can now be used to develop risk mitigation strategies and animal waste application guidelines.

Protecting soil as a safe resource: Antibiotic resistome metagenomics and impact of land use on resistance dynamics