Chemical residues in agricultural land in Germany between 2022 and 2024 – prevalence of selected antibiotic resistance genes in soil

Growing concern about antibiotic resistance genes (ARGs) in agricultural soils, particularly due to application of organic fertilizers-has increased the need to better understand environmental reservoirs and mechanisms of antimicrobial resistance and their potential risks to human and animal health. In this study, soils from 51 agricultural sites across Germany were sampled between 2022 and 2024 aiming to determine the antibiotic resistance occurrence and pharmaceutical product contamination in the soils, and to evaluate the influence of different fertilization practices (mineral, organic, or combined). In addition, three reference soils from the German Environmental Specimen Bank (ESB) were investigated to provide background levels with minimal anthropogenic influence. The relative abundance of targeted ARGs was quantified using quantitative PCR (qPCR). Resistance genes associated with macrolides (ermB) and tetracyclines (tetA) were most frequently detected, whereas aminoglycoside (aacC4, aadA1) and trimethoprim (dfrA1) resistance genes occurred only sporadically. Other ARGs, including those conferring resistance to β-lactams (blaCTX-M1), quinolones/fluoroquinolones (qnrS), and colistin (mcr-3), were not detected, indicating low abundance or absence in the evaluated sites. The class 1 integrase gene (intI1), indicative of mobile genetic elements (MGE), was detected at nearly all sites. ARG abundances varied among sites and were generally higher in soils receiving slurry/manure, while reference soils showed consistently lower ARG prevalence. Although direct causal links between antibiotic residues and ARG occurrence could not be established due to generally rare detections of antibiotics, the observed spatial co-occurrence of high ARG findings and high sales of veterinary antibiotics underscores the importance of jointly evaluating chemical exposure, agricultural management and resistance determinants in risk assessments of soils.