Canada IPAP: Evolutionary dynamics of antimicrobial resistance in human impacted soils: does the genie go back into the bottle?

抗菌素耐药性（AMR）在环境细菌中已经进化了数十亿年，产生了大量的AMR基因库，这些基因可能被转移到临床病原体中。通过使用粪肥或污水污泥作为肥料，或用再生水灌溉，农业土壤暴露于抗生素。人们担心，这种暴露可能会促进食品生产环境中的AMR，增加AMR通过受污染的作物或环境基质传播到人类微生物组的可能性。越来越多的研究使用体外模型来建立环境中抗生素的最小选择性浓度（MSC），但是很少有证据与土壤中抗生素残留物的原位选择有关。过去10-20年在加拿大农业和农业食品部（AAFC）进行的田间规模试验提供了一个独特的机会来研究抗生素应用对土壤群落和AMR的影响，以及土壤如何从长期应用抗生素中恢复。在这个项目中，最先进的宏基因组学和生物信息学方法将被应用于确定抗生素残留对土壤抗性组的进化影响。这将在三个时间点进行研究：短期暴露（应用后7和30天）;长期暴露（每年暴露10年后）;停止抗生素应用后（暴露后1，2和3年）。将研究大环内酯和氟喹诺酮类抗生素，它们具有非常不同的环境命运，并且都被欧盟水框架指令的危险化合物观察清单标记为优先关注物质。此外，我们将评估是否在体外实验是预测选择在土壤中原位。这项工作将提供最全面的评估抗生素修正土壤中AMR的演变。

Antimicrobial resistance (AMR) has evolved in environmental bacteria over billions of years, producing a vast reservoir of AMR genes that can potentially be transferred to clinical pathogens. Agricultural soils are exposed to antibiotics through the use of manures or sewage sludge as fertiliser, or irrigation with reclaimed water. There is a concern that such exposure may promote AMR in food producing environments, increasing the likelihood of AMR transmission to the human microbiome via contaminated crops or environmental matrices. There is a growing body of research using in vitro models to establish the minimal selective concentrations (MSCs) of antibiotics in the environment, but there is very little evidence relating to selection by antibiotic residues jn situ in soils. The field scale trials undertaken at Agriculture and Agri-Food Canada (AAFC) over the last 10-20 years offers a unique opportunity to investigate the effects of antibiotic application on soil communities and AMR, and how soils recover from long-term application of antibiotics. In this project, state of the art metagenomic and bioinformatic approaches will be applied to determine the evolutionary effects of antibiotic residues on the soil resistome. This will be investigated at three timepoints: short-term exposure (7 & 30 days after application); long-term exposure (after 10 years of annual exposure); and after cessation of antibiotic application (1, 2, and 3 years post-exposure). Macrolide and fluoroquinolone antibiotics will be studied, which have very different environmental fates and which have both been flagged as priority substances of concern by the EU Water Framework Directive's Hazardous Compound Watch List. Furthermore, we will assess whether or not in vitro experiments are predictive of selection in soils in situ. This work will provide the most comprehensive assessment of AMR evolution in antibiotic amended soils to date.