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

Biosolids and reclaimed waters are valuable resources for reintroducing organic matter into agricultural soils and reducing the water footprint of intensive agricultural food system. While the circular economy is a sustainable practice, it may 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. This study provides further evidence that the circular economy practices of reusing biomass and reclaimed waters in agricultural setting may be vectors for the spreading of antibiotic resistance genes (ARGs) targeting molecules used to treat human bacterial infections. We screened biosolid and water samples for ARGs presence using shotgun metagenomic sequencing. We demonstrated that the identified ARGs are present in live bacterial organisms, harbouring multidrug-resistant gene clusters, confirmed through phenotypic testing and whole-genome sequencing of isolated bacteria. Additionally, we observed that most of the antibiotic-resistant bacteria identified belonged to environmentally widespread species, which were not expected to be exposed to the antimicrobials, suggesting that inter-species transfer of resistance genes.