Characterization of the resistome and of antibiotic-resistant bacteria in top soil improvers and irrigation waters devoted to food production: a case-study from Italy

Biosolids and reclaimed waters are seen as precious resources to reintroduce organic matter into soils used for agriculture and to reduce the water footprint of intensive agricultural food system. While the circular economy is a virtuous exercise, it cannot be excluded that the adoption of such a practice can introduce vulnerabilities in the food chain, by exposing crops to zoonotic agents and antimicrobial resistance determinants. This option is far from being a speculation and evidence start to accumulate indicating that the risk is tangible. In this work we add further evidence that the circular economy practices of reusing biomass and reclaimed waters in agricultural setting may be vectors for the spreading of antimicrobial resistance genes targeting molecules used to treat human bacterial infections and demonstrate that such genes, identified through metagenomics screening of these samples, are present into live bacterial organisms, harbouring multi drug resistance genes clusters. Moreover, we observed that most of the antibiotic-resistant bacteria identified belonged to species with an environmental diffusion, which were not supposed to be exposed to the antimicrobials, suggesting that inter-specie transfer occurred.