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

项目概述我们越来越意识到，人类、兽医和环境健康是内在联系的。农业和粮食生产系统不仅必须对环境变化和威胁具有韧性，而且系统本身也必须在对环境影响最小的情况下运行。洪水和气温升高等气候变化事件预计将带来更多未知挑战，因此，快速和全面地描述微生物风险的方法至关重要。此外，农民正在努力开发可持续的做法，以减少GHS的排放，重要的是，这些新方法也限制微生物的传播。该项目采取“同一健康”方法，重点关注野生动物和牲畜之间的界面，主要强调人畜共患病和抗菌素耐药性(AMR)基因的传播。食源性病原体通常不会在动物身上引起明显的疾病，但可以通过食物链传播并导致人类疾病。同样，AMR基因可能会在野生动物和家畜物种之间传播，并传播到人类。此外，一些野生动物物种是环境健康和恢复能力的指标。通过了解和监测这些哨兵物种的污染，我们可以更充分地了解压力的影响，如养殖产生的微生物污染物。以前，传统的、有针对性的方法，如实验室培养和聚合酶链式反应，被用来监测动物物种的细菌和病毒携带情况。近年来，第三代测序技术的发展由于能够对长片段进行测序，使得能够增强微生物检测。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家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，将对农场附近的野鸟种群进行调查，以评估人畜共患病病原体和AMR基因向牲畜的传播。其次，将对灰海豹进行调查，以评估环境微生物污染，灰海豹是沿海海洋健康的重要哨兵物种。我们之前在灰海豹种群中检测到了微生物病原体，这是人为活动的结果2，3，以及在海豹和鸟类种群中检测到AMR基因。学生将优化和发展纳米孔测序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。纳米孔测序结果还将与病原体和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情况。这名学生将在爱丁堡郊外的莫尔登研究所工作。监督小组将在人畜共患病病原体、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管道(生物数学和苏格兰统计局(BIOSS))方面提供培训和专业知识。

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)).