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

加拿大 IPAP：受人类影响的土壤中抗菌素耐药性的进化动态：精灵会回到瓶子里吗？

• 批准号: BB/X012719/1
• 负责人: Alison Mather
• 金额: $ 19.08万
• 依托单位: Quadram Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2023
• 资助国家: 英国
• 起止时间: 2023 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FX012719%2F1
• 关键词: Canada; IPAP; Evolutionary; dynamics; antimicrobial

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.

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，这些基因可能会转移到临床病原体。通过使用粪便或污水污泥作为肥料，或用再生水灌溉，农业土壤暴露在抗生素下。有人担心，这种暴露可能会在食品生产环境中促进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群的可能性。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浓度(MSCs)，但很少有证据与土壤中抗生素残留的选择有关。过去10-20年在加拿大农业和农业食品公司(AAFC)进行的田间规模试验提供了一个独特的机会，可以调查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，将应用最新的元基因组学和生物信息学方法来确定抗生素残留对土壤抗药性的进化影响。这将在三个时间点进行调查：短期暴露(使用后7-30天)；长期暴露(每年暴露10年后)；以及停止使用抗生素后(暴露后1、2和3年)。将研究大环内酯类和氟喹诺酮类抗生素，这两种抗生素的环境命运截然不同，都已被欧盟水框架指令的危险化合物观察名单标记为优先关注的物质。此外，我们将评估体外实验是否可以预测在土壤中的选择。这项工作将提供迄今为止对抗生素改良土壤中AMR进化的最全面的评估。