Nanopore sequencing to investigate zoonosis and antibiotic resistance at the wildlife - livestock interface

纳米孔测序研究野生动物-牲畜界面的人畜共患病和抗生素耐药性

• 批准号: 2608383
• 金额: --
• 依托单位: University of Aberdeen
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2021
• 资助国家: 英国
• 起止时间: 2021 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2608383
• 关键词: Nanopore; sequencing; investigate; zoonosis; antibiotic

Project summaryWe are becoming increasingly aware that human, veterinary and environmental health are intrinsically linked. Both farming and food production systems must not only be resilient to environmental changes and threats but the systems themselves must also perform with minimal environmental impact. Climate change events such as flooding and increased temperatures are predicted to bring additional unknown challenges and therefore methods to rapidly and comprehensively characterise microbial risks are vital. Furthermore, farmers are striving to develop sustainable practices that reduce GHS emissions and it is important that these new approaches also limit microbial transmission.This project takes a "One Health" approach by focussing on the interface between wildlife and livestock with a major emphasis on the transmission of zoonotic disease and antimicrobial resistance (AMR) genes. Foodborne pathogens do not often cause overt disease in animals but can be transmitted through the food supply chain and cause human disease. In the same way, AMR genes can potentially be transmitted between wildlife and livestock species and spread to humans. Additionally, some wildlife species act as indicators of environmental health and resilience. By understanding and monitoring contamination of these sentinel species we can more fully understand the impact of pressures such as microbial contaminants arising from farming.Previously, conventional, targeted methods such as laboratory culture and PCR have been used to monitor carriage of bacteria and viruses by animal species. In recent years, development of 3rd generation sequencing technologies has enabled enhanced microbe detection due to the ability to sequence long reads. The key aim of this project is to apply and assess this novel technology to investigate the presence of microbial species and AMR genes within two wildlife populations which represent different dynamics between wildlife and livestock. Firstly, wild bird populations in close proximity to farms1 will be investigated to assess transmission of zoonotic pathogens and AMR genes to livestock. Secondly, grey seals, which are an important sentinel species for coastal marine health, will be investigated to assess environmental microbial contamination. We have previously detected microbial pathogens within grey seal populations as a result of anthropogenic activity2,3, as well as AMR genes in seals and bird populations. The student will optimise and develop laboratory and bioinformatics methods in Nanopore sequencing and evaluate the presence of zoonotic pathogens and AMR genes within wildlife populations. Results will be compared with data from livestock and relevant environmental samples to identify potential transmission routes. Nanopore sequencing outputs will also be compared with gold-standard laboratory methods for pathogen and AMR detection to assess application of Nanopore technology as a surveillance tool. The student will be based at Moredun Research Institute, which is situated just outside Edinburgh. The supervisory team will provide training and expertise in zoonotic pathogens, AMR and Oxford Nanopore Technologies, (Moredun and University of Aberdeen), sequence analysis and bioinformatic pipelines (Biomathematics and Statistics Scotland (BioSS)).

项目摘要我们越来越意识到人类、兽医和环境健康之间有着内在的联系。农业和粮食生产系统不仅必须能够适应环境变化和威胁，而且系统本身也必须对环境影响最小。洪水和气温升高等气候变化事件预计将带来额外的未知挑战，因此快速、全面地表征微生物风险的方法至关重要。此外，农民正在努力开发减少 GHS 排放的可持续做法，重要的是这些新方法也能限制微生物传播。该项目采用“同一个健康”方法，重点关注野生动物和牲畜之间的相互作用，重点关注人畜共患疾病和抗菌素耐药性 (AMR) 基因的传播。食源性病原体通常不会在动物中引起明显的疾病，但可以通过食品供应链传播并导致人类疾病。同样，AMR 基因也有可能在野生动物和牲畜物种之间传播，并传播给人类。此外，一些野生动物物种可以作为环境健康和恢复力的指标。通过了解和监测这些哨兵物种的污染，我们可以更全面地了解农业产生的微生物污染物等压力的影响。以前，实验室培养和 PCR 等传统的、有针对性的方法已被用来监测动物物种携带的细菌和病毒。近年来，第三代测序技术的发展由于能够对长读长进行测序，从而增强了微生物检测能力。该项目的主要目的是应用和评估这项新技术，以调查代表野生动物和牲畜之间不同动态的两个野生动物种群中微生物物种和 AMR 基因的存在。首先，将对农场附近的野生鸟类种群进行调查，以评估人畜共患病原体和 AMR 基因向牲畜的传播情况。其次，将对灰海豹进行调查，以评估环境微生物污染情况，灰海豹是沿海海洋健康的重要哨兵物种。我们之前曾在灰海豹种群中检测到由于人为活动2,3而产生的微生物病原体，以及海豹和鸟类种群中的 AMR 基因。学生将优化和开发纳米孔测序中的实验室和生物信息学方法，并评估野生动物种群中人畜共患病原体和 AMR 基因的存在。结果将与牲畜和相关环境样本的数据进行比较，以确定潜在的传播途径。纳米孔测序输出还将与病原体和 AMR 检测的金标准实验室方法进行比较，以评估纳米孔技术作为监测工具的应用。该学生将在位于爱丁堡郊外的莫尔顿研究所工作。监督团队将提供人畜共患病原体、AMR 和牛津纳米孔技术（莫雷登和阿伯丁大学）、序列分析和生物信息学管道（苏格兰生物数学和统计（BioSS））方面的培训和专业知识。