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，抗菌素耐药性导致127万人死亡，如果不进行有效干预，预计到2050年这一数字将上升至1000万人。抗生素通常用于兽医治疗和预防目的，并在许多国家的常规畜牧业中使用。抗生素及其代谢物在动物胃肠道中持续存在，它们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，从而促进抗生素耐药菌（ARB）的维持和抗生素耐药基因（ARGs）的富集。生产粮食的农场动物容易受到病原体感染和抗生素治疗，并可能将抗菌素耐药性病原体相互传播、传播给相关环境和人类，从而增加了对公共卫生的风险。因此，相当一部分抗生素残留物（高达90%）及其相关的ARGs随粪便排出。动物粪便往往未经适当处理就作为肥料撒在土地上，造成通过水平基因转移（HGT）在本地土壤种群之间传播arb和ARGs的风险。在英国，每年用于农业的粪便量超过7000万吨。许多研究表明，粪肥施肥导致土壤微生物组ARB和ARG增加，这成为HGT研究的热点。从环境来看，ARGs可能通过饲料摄入、直接接触、空气传播颗粒和径流到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。需要采取有效的缓解战略，以降低“同一个健康”周期内抗菌素耐药性的水平。该项目将结合英国和加拿大的专业知识，调查奶牛和相关环境中复杂的微生物组，微生物生态相互作用如何影响/控制抗菌素耐药性。将对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的分析和比较。使用霰弹枪宏基因组学工具和高通量多路扩增子测序和ddPCR方法的集体结果将产生关于奶牛场抗菌素耐药性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（提高可重复性和重复性），为生态相互作用和抗菌素耐药性的机制研究创建模型微生物组。该项目将有助于实现减缓抗菌素耐药性传播的长期目标。

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.