Assessment of Zoonotic Risk of Emerging Infections in Companion Animals

项目概要/摘要 该项目评估了两种重要的可能的伴侣病原体的人畜共患病的影响 动物：E.大肠杆菌和冠状病毒。E.大肠杆菌是最常见的病原体测试的抗生素敏感性， 兽医诊断实验室它也是最令人关注的多药耐药性之一;几个分离株 迄今为止，在Vet-LIRN主动监测中捕获的病毒预计对人类使用的所有药物都具有泛耐药性。 或动物医学。本课题组发表了第一个动物宿主特异性E.大肠杆菌毒力数据库 与可以挖掘全基因组测序数据的工具兼容。我们现在提出一个比较 进化基因组研究，以评估E.编码新的耐药机制 并导致人类疾病。这些数据将采用细菌泛- 基因组分析，以及细菌GWAS。分析结果将揭示是否存在E.适应狗的大肠杆菌基因座， 这些基因座是否具有提示致病潜力的功能特征，以及犬是否可能 潜在致病机制或抗生素耐药性的储存库。 目前由SARS-CoV-2（COVID-19）引起的冠状病毒病爆发是第三次 在过去，有记录的动物冠状病毒对人类的溢出导致了重大流行病， 二十年描述伴侣动物冠状病毒的物种多样性， 这是提高我们对病毒-宿主相互作用的认识和加强我们 为未来疫情做好准备。我们将在三种不同的宿主物种中进行这种表征- 马、猫和狗-利用一组广泛的时间序列样本（呼吸和粪便）， 包括AHDC的收藏。冠状病毒基因组序列将通过两种方法获得： 呼吸道病毒组的RNAseq和呼吸道和粪便样本的多重扩增子方法; 前者可让我们识别每种宿主的冠状病毒种类，包括识别 任何新的冠状病毒物种，后者将提供详细探索多样性方面的能力， 和主机之间。数据的比较进化基因组分析将为各种各样的生物学提供信息。 与其人畜共患病潜力相关的问题，包括例如：（1）哪些冠状病毒物种更容易 宿主间的传播以及这种传播是否有方向性(2)它们的宿主是 病毒种类？(3)有重组的历史吗？(4)有着分子进化史 以及病毒的蛋白质是什么 我们的最终目标是为其他八个Vet-LIRN测序实验室提供试剂和培训 能够独立测序和分析细菌和病毒基因组，包括SARS-CoV-2。所有 该项目的三个目标直接支持FDA确保我国食品安全的使命 供应和保护公共卫生。

Project Summary/Abstract This project evaluates the zoonotic implications of two important possible pathogens of companion animals: E. coli and coronaviruses. E. coli is the most common pathogen tested for antibiotic susceptibility in veterinary diagnostic labs. It is also one of the most concerning for multi-drug resistance; several isolates captured thus far in Vet-LIRN active surveillance are predicted to be pan-resistant to all drugs used in human or animal medicine. Our group has published the first animal host specific E. coli virulence database compatible with tools that can mine whole genome sequencing data. We now propose a comparative evolutionary genomic study to assess the potential of E. coli in dogs to encode novel resistance mechanisms and cause disease in humans. The data will be explored employing the latest developments in bacterial pan- genomic analysis, as well as bacterial GWAS. Such analysis will reveal if there are E. coli loci adapted to dogs, whether such loci have the functional character suggestive of pathogenic potential, and whether dogs may be a reservoir of potential pathogenesis or antibiotic resistance. The present outbreak of coronavirus disease caused by SARS-CoV-2 (COVID-19) is the third documented spillover of an animal coronavirus to humans to have resulted in a major epidemic, within the past two decades. Characterizing the species diversity of coronaviruses from companion animals, represents an important necessary step towards improving our understanding of virus–host interactions and to enhance our preparedness for future outbreaks. We will undertake this characterization in three different host species – horses, cats, and dogs – making use of an extensive set of time series samples (respiratory and feces) that comprise the AHDC’s collection. Sequences of coronavirus genomes will be acquired using two approaches: RNAseq of the respiratory virome and multiplexed amplicon approaches of both respiratory and feces samples; the former will allow us to identify the coronavirus species repertoire of each host, including the identification of any new coronavirus species, the latter will provide the ability to explore aspects of diversity in detail, within and between hosts. Comparative evolutionary genomic analyses of the data will inform on a wide variety of issues related to their zoonotic potential, including for example: (1) Which coronavirus species are more prone to inter-host transmission and is there a directionality to that transmission? (2) Are their host reservoirs for any of the virus species? (3) Which have a history of recombination? (4) Which have a history of molecular adaptation and what viral proteins does that involve? Our final aim is to provide eight other Vet-LIRN sequencing laboratories with the reagents and training to be able to independently sequence and analyze bacterial and viral genomes, including SARS-CoV-2. All three Aims of this project directly support the mission of the FDA to ensure the safety of our nation's food supply and protect public health.