Wastewater surveillance (WWS) has received significant attention as a rapid, sensitive, and cost-effective tool for monitoring various pathogens in a community. WWS is employed to assess the spatial and temporal trends of diseases and identify their early appearances and reappearances, as well as to detect novel and mutated variants. However, the shedding rates of pathogens vary significantly depending on factors such as disease severity, the physiology of affected individuals, and the characteristics of pathogen. Furthermore, pathogens may exhibit differential fate and decay kinetics in the sewerage system. Variable shedding rates and decay kinetics may affect the detection of pathogens in wastewater. This may influence the interpretation of results and the conclusions of WWS studies. When selecting a pathogen for WWS, it is essential to consider it's specific characteristics. If data are not readily available, factors such as fate, decay, and shedding rates should be assessed before conducting surveillance. Alternatively, these factors can be compared to those of similar pathogens for which such data are available.

Antimicrobial resistance (AR) represents a global threat in human and veterinary medicine. In that regard, AR proliferation and dissemination in agricultural soils after manure application raises concerns on the enrichment of endogenous soil bacterial population with allochthonous antibiotic resistance genes (ARGs). Natural resilience of agricultural soils and background concentrations of ARGs play key roles in the mitigation of AR propagation in natural environments. In the present study, we carried out a longitudinal sampling campaign for two crop vegetation periods to monitor spatial and temporal changes in the abundance of seven clinically relevant ARGs (sul1, ermB, vanA, aph(3')-IIa, aph(3')-IIIa, blaTEM-1 and tet(W)) and ribosomal 16S RNA. The absolute and relative abundances of the selected ARGs were quantified in total community DNA extracted from agricultural (manured and non-manured) and forest soils, fresh pig faeces and manure slurry. We observed that ARG concentrations return to background levels after manure-induced exposure within a crop growing season, highlighting the resilience capacity of soil. Naturally occurring high background concentrations of ARGs can be found in forest soil in due distance under low anthropogenic influences. It was observed that pesticide application increases the concentrations of three out of seven ARGs tested (ermB, aph(3')-IIIa and tet(W)). Moreover, we noticed that the absolute abundances of sul1, vanA, ermB and blaTEM-1 resistance genes show an increase by 100- to 10,000- fold, from maturation of fresh pig faeces to manure. Outcomes of our study suggest that agricultural soil environments show a strong capacity to alleviate externally induced disturbances in endogenous ARG concentrations. Naturally occurring high concentrations of ARGs are present also in low human impacted environments represented by the indigenous resistome.