Structure of manure resistome and associated mobilome in the context of the risk assessment of drug resistance transmission to crops

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.

由于抗生素使用缺乏监管且其残留物被排放至环境中，广泛分布的抗生素抗性基因（antibiotic resistance genes, ARGs）与新型耐药菌（antibiotic-resistant bacteria, ARB）已引发公众的广泛担忧。全球范围内，国际与区域机构（如世界动物卫生组织、世界卫生组织）已采取行动，以加强抗生素监管并维持其临床疗效。目前，ARB与ARGs已被认定为新型环境污染物。

本研究探究了牛、家禽粪便施肥对土壤与作物中与抗菌耐药性相关的ARGs及环境迁移组（environmental mobilome）的定量与定性组成的影响。本研究的研究目的为：在评估ARGs与细菌耐药载体向施肥土壤及栽培作物传播风险的背景下，对家禽与牛粪便开展宏基因组学表征。本研究采用田间试验设计，以真实反映影响污染物组成变化的实际环境条件。

向土壤施加未添加与添加抗生素的粪便，均会直接影响土壤中多重耐药基因（multidrug resistance genes, MRGs）的丰度与ARG类型的多样性。仅施用粪便的施肥方式，相较于添加了抗生素的粪便施肥，会使土壤中ARGs与整合酶基因的占比更高。作物地下部分的内生微生物相较于地上部分的内生微生物，拥有更为丰富的ARGs储存库，这可能对未加工块根类作物的食用安全构成风险。

施用粪便施肥会将大量插入序列引入土壤，其中包括与ARGs在ESKAPEE病原体群中迁移相关的序列；这些插入序列可在土壤环境中稳定存在长达数月之久。这表明，施加的粪便（尤其是家禽粪便）可能会快速推动ARGs在环境中的迁移，进而引发严重的健康风险。