Occurrence and horizontal gene transfer of carbapenemase and ESBL genes in soil microbiomes

该项目旨在了解环境水库的潜力以及AMR在原生土壤微生物群成员中的传播，以及进入环境的瞬时异地人和动物病原体之间的传播，例如从农业粪便或家养或野生动物和鸟类的粪便进入。它还试图了解各种土壤微生物群中的潜在病原体与包括粘土、壤土和沙质土壤在内的复杂基质之间的水平基因转移是否成功发生。这项工作将利用现代分子生物学和基因组学来筛选微生物种群，并定义第三代ESBL和第四代碳青霉烯酶大肠杆菌和肺炎克雷伯菌供体菌株，以一株大肠杆菌敏感菌株为接受者。南安普顿大学的团队由一个成熟的科学小组组成，该小组专门研究土壤和水中粪便病原体的生存，以及不同物种之间ESBL和碳青霉烯酶抗性基因的HGT，并与一名在土壤微生物学和过程方面具有专业知识的早期职业研究人员以及稳定同位素探测(SIP)合作，以了解群落的生存能力、代谢周转和基因获取。UKWIR和Defra/FSA之前的工作已经形成了粘土、壤土和沙土的草地土壤微观世界，并证明了人畜共患病病原体在粪便灌溉后在其中存活了几个星期。随后使用一种新颖的、温和的脉动程序将这些病原体从复杂的土壤基质中释放出来，然后在适当的选择性琼脂培养基上进行膜过滤和定量复苏。该提案将有助于确定HGT和β-内酰胺酶选择过程的具体环境驱动因素，包括对人为(畜牧业、人类废水处理)和非人为(野生动物和鸟类粪便进入)驱动因素的影响。这项工作还将包括确定对肺炎克雷伯氏菌和大肠杆菌等具有临床和/或兽医重要性的病原体的影响。这项研究将有助于为AMR政策和管理战略提供信息，并将形成随后的大型研究提案的基础，以更全面地解决这些政策和战略。该提案中开发的途径和方法可以转化为AMR资助机构感兴趣的其他环境、抗菌药或其他细菌群落。

This project aims to understand the potential of environmental reservoirs and transmission of AMR in members of autochthonous soil microbiomes and between transient allochthonous human and animal pathogens entering the environment, for example from faecal agricultural wastes or domesticated or wild animal and bird faecal ingress. It also seeks to understand if horizontal gene transfer occurs successfully between potential pathogens in the various soil microbiomes and complex matrices encompassing clay, loam and sandy soils. The work will utilize modern molecular biology and genomics to screen microbiome populations and defined third generation ESBL and fourth generation carbapenemase E. coli and Klebsiella pneumoniae donor strains, with an E. coli sensitive strain as the recipient.The University of Southampton team comprises an established scientific group with expertise in survival of faecal pathogens in soil and water, and HGT of ESBL and carbapenemase resistance genes between different species, in collaboration with an Early Career Researcher with expertise in soil microbiology and processes, and stable isotope probing (SIP) to understand community viability, metabolic turnover and gene acquisition. Previous work for UKWIR and Defra/FSA has developed grassed soil microcosms of clay, loam and sandy soils and demonstrated survival of zoonotic pathogens therein for several weeks following faecal waste irrigation. These pathogens were subsequently released from the complex soil matrices using a novel, gentle pulsification procedure followed by membrane filtration and quantitative resuscitation on appropriate selective agar media. This proposal will help identify the specific environmental drivers of the HGT and beta lactamase selection processes, including implications for both anthropogenic (animal husbandry, human wastewater disposal) and non-anthropogenic (wild animal and bird faecal ingress) drivers. The work will also include identifying the implications for pathogens of clinical and/or veterinary importance such Klebsiella pneumonia and E. coli. The research will be able to help inform AMR policy and management strategies, and will form the basis of a subsequent large research proposal to address these policies and strategies more fully.The approaches and methodologies to be developed in this proposal could be translated to other environments, antibacterials or other bacterial communities of interest to the AMR funding bodies.