MEtaGenome-informed Antimicrobial resistance Surveillance: Harnessing long-read sequencing for an analytical, indicator and risk assessment framework

基于 MEtaGenome 的抗菌药物耐药性监测：利用长读长测序构建分析、指标和风险评估框架

• 批准号: MR/Y034457/1
• 负责人: Alison Mather
• 金额: $ 46.69万
• 依托单位: Quadram Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2024
• 资助国家: 英国
• 起止时间: 2024 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FY034457%2F1
• 关键词: MEtaGenome; informed; Antimicrobial; resistance; Surveillance

Antimicrobial resistance (AMR) is a threat to humans, animals, and crops, and requires a coordinated One Health approach. AMR affects many of the goals of the WHO 2030 Agenda for Sustainable Development. Levels of AMR are generally quantified by culturing indicator organisms like E. coli, and determining its resistance. Looking at only one indicator organism in all human, animal, food and environmental samples is like studying ocean life by looking at a single droplet of seawater with a microscope. Interesting differences can be found between droplets but is it really the entire picture?Metagenomic sequencing is a technique that allows identification and quantification of AMR genes and species in a sample without culturing. Currently the use of short read sequencing is more common but limited when AMR quantification is required. One can only quantify genes, not where they are. On a chromosome? Or in a transmittable plasmid or transposon, which can easily spread to pathogens?We propose to use long-read Nanopore sequencing to develop a 'one stop shop' surveillance method. Long reads contain both resistance genes and flanking sequences, thereby identifying the original organism or mobile genetic element, the location, but also genes associated with high transmission risk. We propose integrating into traditional methods to expand surveillance into non-model-organisms.By working with stakeholders in government, industry and academia, this project will support translation of long-read metagenome data into actionable surveillance information for the reduction of risk to human health.

抗菌素抵抗（AMR）是对人，动物和农作物的威胁，需要一种协调的一种健康方法。 AMR影响了2030年WHO 2030年为可持续发展议程的目标。通常通过培养指标（如大肠杆菌）和确定其耐药性来量化AMR的水平。在所有人类，动物，食物和环境样品中只查看一个指标生物，就像研究海洋生命是通过使用显微镜的一滴海水来研究海洋生命。可以在液滴之间找到有趣的差异，但是它确实是整个图片吗？宏基因组测序是一种允许在不培养的情况下识别和量化样品中AMR基因和物种的技术。当前，短读测序的使用更为常见，但是当需要AMR量化时，使用限制。一个人只能量化基因，而不是它们所在的位置。在染色体上？或在可透射的质粒或转座子中，可以很容易地扩散到病原体上？我们建议使用长阅读的纳米孔测序来开发“一站式商店”监视方法。长读数既包含抗性基因又包含侧翼序列，从而识别原始生物或移动遗传元素，位置，以及与高传输风险相关的基因。我们建议将监视扩展到非模型生物的传统方法中。通过与政府，工业和学术界的利益相关者合作，该项目将支持将长阅读元素数据数据转换为可行的监视信息，以减少人类健康的风险。