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

抗菌素耐药性（AMR）已被联合国和世界卫生组织确定为最重要的全球威胁之一，需要采取全球应对措施，以遏制其在人群中的传播。这项研究计划将有助于了解抗菌素耐药性在奶牛场的传播途径。这项独特的NSERC计划是基于使用新的分子流行病学工具来评估与抗菌素耐药性基因（AMRgs）相关的微生物组的多样性和丰度。这项NSERC发现基金（NSERC- dg）项目的结果将使我们能够将流行病学建模与基因组信息相结合，以评估动物和动物产品中AMR的风险因素及其传播途径。这项NSERC-DG提议的研究的主要目标是确定AMRgs在动物、动物产品和奶牛群中细菌群落的不同生态位之间的传播途径。短期目标是1)确定奶牛粪便、奶牛场环境和散装罐奶（BTM）样品中存在的微生物群落（如共生微生物和致病微生物）的多样性（丰富度）和丰度；2)确定从奶牛、其农场环境和BTM中获得的样本中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抗性基因进行比较；3)利用基因组序列之间的水平基因转移（HGT）事件确定细菌群落之间的相互作用；4)探讨奶牛场牛奶品质参数、微生物多样性和AMRgs丰度之间的关系。使用DNA下一代测序（例如霰弹枪宏基因组学），我努力确定所收集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药物暴露相关的HGT事件。此外，我将探索农场中存在的微生物群落的HGT网络，以确定不同农场隔间中AMR基因转移的热点。使用散弹枪宏基因组学，我将能够描述微生物群落中存在的主要微生物的概况，以及与奶牛及其牛奶中不同程度的抗生素暴露相关的AMRgs。该项目的结果将有助于了解AMR基因在奶牛场样品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群体水平的问题。NSERC-DG的研究结果将有助于制定食品动物农业中抗菌药物使用的谨慎使用指南和政策制定的风险评估模型。

Antimicrobial resistance (AMR) has been identified by the United Nations and World Health Organization as one the most important global threats that require a global response to curb the spread in populations. This research program will contribute to the understanding of the transmission pathways of AMR in dairy farms. This unique NSERC initiative is 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 Discovery Grant (NSERC-DG) program will allow us to integrate epidemiological modeling with genomic information to assess risk factors for AMR in animals and animal products and its transmission pathways. The main goal of this NSERC-DG proposed research is to determine the pathways of transmission of AMRgs between animals, animal products, and different ecological niches of the bacterial communities within the dairy herds. The short-term objectives are 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 determine interactions among bacterial communities using horizontal gene transfer (HGT) events amongst the genomic sequences; and 4) to explore the relationship between milk quality parameters, microbial diversity, and AMRgs abundance on dairy farms. 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 beneficial for the development of prudent use guidelines for antimicrobial use in food animal agriculture and risk assessment models for policy development.