Structure of manure resistome and associated mobilome in the context of the risk assessment of drug resistance transmission to crops. The raw metagenomic data of manure resistome and associated mobilome.

Due to the unmonitored use of antibiotics and the release of residuals into the environment,widespread antibiotic resistance genes (ARGs) and emerging antibiotic-resistant bacteria (ARB) havebecome a great public concern. Globally, action is being taken by international and regional agencies,such as the World Organization for Animal Health and the World Health Organization, to improve theregulation of antibiotics and to preserve the efficacy of antibiotics. Now, ARB and ARGs arerecognized as emerging environmental pollutants. This study determined the impact of bovine andpoultry manure fertilization on the quantitative and qualitative composition of ARGs andenvironmental mobilome associated with antimicrobial resistance in the soil and crops. The aim of thestudy was the metagenomic characterization of poultry and bovine manure in the context of estimatingthe risk of transmission of ARGs and bacterial drug resistance carriers to the fertilized soil and thecultivated plants. This study was conducted as a field experiment to reflect the actual environmentalconditions that influence changes in the composition of pollutants. Soil supplementation with manure,both without and with the addition of antibiotics, had a direct impact on the level of MRGs and thediversity of ARG types appearing in the soil. Fertilization only with manure resulted in the appearanceof ARGs and integrase genes in the soil in greater proportions than in the case of supplementation withmanure enriched with antibiotics. Endomicrobials of underground parts of crops constituted a richerreservoir of ARGs than endomicrobes of above-ground parts, which may pose a risk related to theconsumption of unprocessed root crops. As a result of fertilization with manure, large amounts ofinsertion sequences introduced into the soil, including those related to the mobility of ARGs in theESKAPEE group of pathogens, show stability in the soil environment for up to several months, whichindicates that supplemented manure, especially of poultry origin, may pose a huge risk of rapidmobility ARGs in the environment generating a serious health risk.