Canada_IPAP Constructing model microbiomes to study microbial interactions and AMR in dairy production systems

世界卫生组织认为，抗菌素耐药性（AMR）是对健康、生计、经济和环境的紧迫全球威胁，也是对可持续发展目标进展的威胁。2019年，有127万人死于AMR，如果不采取有效干预措施，预计到2050年这一数字将上升至1000万。在许多国家，抗生素通常用于兽医学中的治疗和预防目的，并用于常规畜牧业。抗生素及其代谢产物在动物胃肠道中持续存在，其在肠道中以亚致死浓度积累会对微生物群产生选择性压力，促进抗生素耐药菌（ARB）的维持和抗生素耐药基因（ARG）的富集。食用家畜易受病原体感染和抗生素治疗，并可能将AMR病原体相互传播、传播给相关环境和人类，从而增加公共卫生风险。因此，相当一部分抗生素残留（高达90%）及其相关的ARG会在粪便中脱落。动物粪便通常作为肥料撒在土地上，未经适当处理，造成ARB和ARG传播的风险-通过水平基因转移（HGT）与土著土壤种群/在土著土壤种群之间传播。在英国，每年用于农业的粪肥量超过7000万吨。大量研究表明，有机肥施用会引起土壤微生物数量的增加，这也成为HGT研究的热点。从环境来看，ARG可能会通过饲料摄入、直接接触、空气中的颗粒物和径流进入水中等途径循环回到动物体内，除了食物链传播外，后三种途径也对人类构成威胁。本项目将结合英国和加拿大的联合收割机的专业知识，研究在奶牛和相关环境中复杂的微生物组中，微生物生态相互作用如何影响/控制AMR。将对来自英国和加拿大有机和传统奶牛场的现场样本进行微生物组和抗菌素耐药性分析和比较。使用鸟枪宏基因组学工具和高通量多重扩增子测序和ddPCR方法的集体结果将产生奶牛场AMR负担的概述和详细信息。该项目旨在构建分离文库和合成微生物群落（提高再现性和复制性），以创建用于生态相互作用和AMR机制研究的模型微生物组。该项目将有助于实现减缓AMR传播的长期目标。

The World Health Organization considers antimicrobial resistance (AMR) as an urgent global threat to health, livelihood, economies, and environment and a threat to the progress of Sustainable Development Goals. In 2019, 1.27 million deaths were attributed to AMR and this number is predicted to rise to 10 million by 2050 without effective intervention. Antibiotics are routinely used in veterinary medicine for therapeutic and prophylactic purposes, and during routine animal husbandry in many countries. Antibiotics and their metabolites persist in the gastrointestinal tract of animals, and their accumulation at sub-lethal concentrations in the gut induces a selective pressure on the microbiota that facilitates the maintenance of antibiotic-resistant bacteria (ARB) and enrichment of antibiotic resistance genes (ARGs). Food-producing farm animals are prone to pathogen infections and antibiotic treatment, and potentially transmit AMR pathogens to each other, the associated environment, and humans, raising risks to public health.Consequently, a substantial fraction of antibiotic residues (up to 90%) and their associated ARGs are shed in manure. Animal manure is often spread on land as fertiliser without proper treatment, posing risks of disseminating ARBs and ARGs - with/between indigenous soil populations through horizontal gene transfer (HGT). In the UK, the annual amount of manure used in agriculture is pegged at over 70 million tonnes. Many studies have demonstrated ARB and ARG increases in soil microbiome induced by manure fertilising, which becomes a hotspot for HGT. From the environment, ARGs may be cycled back to animals through fodder ingestion, direct contact, airborne particles, and runoff to water, the latter three routes also become threats to humans, in addition to the food chain transmission. Effective mitigation strategies are required to reduce AMR levels in the One Health cycle.This project will combine the expertise from UK and Canada to investigate, in complex microbiomes in dairy cattle and associated environments, how AMR can be affected/controlled by microbial ecological interactions. Field samples from organic and conventional dairy farms in UK and Canada will be analysed and compared on microbiome and AMR. Collective results using shotgun metagenomics tools and high-throughput multiplexed amplicon sequencing and ddPCR methods will generate an overview and detailed information on AMR burden in dairy farms. The project aims to construct isolation libraries and synthetic microbial communities (which improves reproducibility and replications) to create model microbiomes for mechanistic investigations of ecological interactions and AMR. This project will contribute to the long-term goal of AMR transmission mitigation.