Metagenomic characterization of antimicrobial resistance and bacterial community interactions in Canadian dairy herds

这一研究计划将有助于了解奶牛养殖场抗菌素耐药性(AMR)的流行病学和传播途径。这项NSERC发现赠款(NSERC-DG)计划将建立在AMR监测计划的基础上，并将基于使用新的分子流行病学工具来评估与抗菌素耐药基因(AMRgs)相关的微生物组的多样性和丰度。NSERC-DG计划的结果将促进流行病学建模与基因组信息的整合，以评估动物和动物产品中AMR的风险因素及其传播途径。本研究计划的主要目的是阐明不同来源和传播途径的AMR细菌和基因在不同动物群体、动物产品和奶牛养殖场环境中的贡献。该计划的这一长期愿景将通过一套四个短期目标来实现：1)确定奶牛粪便、奶牛场环境和散装罐装奶(BTM)样本中微生物群落(例如共生微生物和病原体)的多样性(丰富度)和丰度；2)确定从奶牛及其农场环境和散装罐装奶(BTM)样本中AMRgs的频率和分布，并将这些抗性基因与世界其他地区分离的AMRgs进行比较；3)探索牛奶质量参数、微生物多样性和奶牛场AMRgs丰度之间的关系；以及4)利用水平基因转移(HGT)事件确定不同隔间(如动物、环境和BTM)之间的细菌群落之间的相互作用。使用DNA下一代测序(例如，鸟枪式元基因组学)，我努力确定收集的样本中微生物组的多样性和丰度以及AMR基因的丰度，并使用生物信息学和流行病学分析工具确定与抗菌素暴露相关的HGT事件。此外，我还将探索农场微生物群落的HGT网络，以确定不同农场隔间AMR基因转移的热点。使用鸟枪式元基因组学，我将能够表征微生物群落中存在的主要微生物的图谱，以及与奶牛及其牛奶中不同水平的抗生素暴露相关的AMRgs。该计划的结果将有助于理解AMR基因在奶牛场样本微生物群落中的传播途径，也将有助于使用新的分子技术来解决种群水平的问题。NSERC DG的这一发现将对制定在食品、动物农业和风险传播模型中使用抗菌剂的谨慎使用指南非常有用。

This research program will contribute to the understanding of the epidemiology and transmission pathways of antimicrobial resistance (AMR) in dairy farms. This NSERC Discovery Grant (NSERC-DG) program will be built on a surveillance program for AMR and will be based on the use of novel molecular epidemiological tools to assess the diversity and abundance of the microbiome in association with antimicrobial resistance genes (AMRgs). Results from this NSERC-DG program will facilitate the integration of epidemiological modelling with genomic information to assess risk factors for AMR in animals and animal products and its transmission pathways. The main goal of this research program is to elucidate the contribution of different sources and transmission pathways of AMR bacteria and genes in different animal groups, animal products, and the environment in dairy farms. This long-term vision of the program will be achieved through a set of four short-term objectives: 1) to determine the diversity (richness) and abundance of a community of microbes (e.g. commensal and pathogenic microorganisms) present in feces from dairy cattle, the dairy farm environment, and bulk tank milk (BTM) samples; 2) to determine the frequency and distribution of AMRgs from samples obtained from dairy cattle, their farm environments and BTM, and to compare these resistance genes to those isolated in other parts of world; 3) to explore the relationship between milk quality parameters, microbial diversity, and AMRgs abundance on dairy farms; and 4) to determine interactions among bacterial communities using horizontal gene transfer (HGT) events among different compartments (eg, animals, environment and BTM). Using DNA next generation sequencing (e.g. shotgun metagenomics), I endeavor to determine the diversity and abundance of the microbiome and the abundance of AMR genes among the samples collected, and to identify HGT events in association with antimicrobial exposure, using both bioinformatics and epidemiological analytical tools. Moreover, I will explore the HGT network of the microbial communities present in the farm to determine the hot-spots of AMR gene transfer in different farms compartments. Using shotgun metagenomics, I will be able to characterize the profiles of the main microorganisms present in the microbial community, as well as the AMRgs associated with different levels of antibiotic exposure in dairy cattle and their milk. The results from this program will contribute to the understanding of the transmission pathways of AMR genes in the microbial community of samples from dairy farms, and will also help the use of novel molecular techniques to address population-level questions. Findings from this NSERC DG will be very useful for the development of prudent use guidelines for antimicrobial use in food animal agriculture and risk transmission models.