Antimicrobial (AM) agents (e.g. antibiotics) are used to treat bacterial infections in both humans and animals which has led to their widespread use and misuse. Drugs not completely absorbed by the animal are excreted in urine and feaces that may be used in manure, which is then applied as fertilizer to agricultural land, releasing the bacterial to the soil. Antimicrobial resistance (AMR) is the ability of microorganisms such as bacteria, viruses and some parasites to stop an antibiotic, from working against them and can trigger the development of AMR. Globally, about 70 000 deaths per year from resistant infections and unless action is taken, the estimated annual deaths attributable to AMR will be 10 million by 2050.
Soil is the most important vector when antibiotics are used, or when manure and slurry used as fertilizers contain antibiotics from veterinary medicine and agricultural use.  While AMR has been widely studied from the angles of human and animal health, little is known about the impacts it has on the soil, the environment and on health. Current conventional chemical methods to analyse antibiotics and study ARB can analyze a broad range of target compounds, are very sensitive and allow precise quantification over a large linear range of concentrations, it cannot elucidate the fate, dynamics and persistence of antimicrobials and AMR in agricultural systems. The compound specific stable isotope analysis (CSIA) technology is a powerful tool that can provide answers, through stable isotope fingerprint, to the fate and dynamics of AM when existing molecular biological methods for monitoring methods fall short. The new proposed CRP “Isotopic Techniques to Assess the Fate of Antimicrobials and Implications for Antimicrobial Resistance in Agricultural Systems” be overall objective is to use CSIA and related techniques to trace and understand the fate, dynamics and persistence of antimicrobials and AMR in agricultural systems, and develop strategies to mitigate the spread of AM in the environment. The specific objectives are (1) to develop, evaluate and standardize integrative isotopic and conventional approaches for tracing the sources  and persistence of antimicrobials and AMR in agricultural systems, (2) to apply a combination of approaches of isotopic and bioanalytical/molecular  biological methods (gene detection) to different agricultural systems for assessing the dynamics of AM and implications for AMR and (3) to  provide knowledge and guidance and for informed decisions that help mitigate the spread of AM and AMR in agricultural systems. The main nuclear techniques to be use is the CSIA with complementary molecular biology methods.