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 pangenomic 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