The goal of this proposal is to obtain funding for the purchase and installation of the Illumina iSeq 100 sequencing platform. This would include training on the iSeq workflow was well as Nextera DNA library preparation. Post installation and training, this proposal includes sequencing 10 E. coli isolates provided by a collaborating Vet-LIRN laboratory. In addition, this laboratory will be providing guidance and training on the Nextera Flex library kit and the workflow, which includes de novo assembly, read and assembly quality statistics, serotype prediction, AMR gene detection, and sequence type determination. The ultimate goal is to produce acceptable E. coli whole genome sequences to be analyzed using a user- friendly tool. This data will be used for both human and animal surveillance as well as on-farm herd management decisions.
As technology has advanced in the veterinary field to include whole genome sequencing (WGS), it is imperative that this technology be deployed in the veterinary field in a collaborative and economical way. The benchtop Illumina iSeq sequencing platform provides an economical way to deliver real-time antimicrobial resistance surveillance. We would like to join the 8 Vet-LIRN laboratories by purchasing, installing and training on the Illumina iSeq sequencing platform. In addition, we will collaborate with other Vet-LIRN laboratories by providing WGS data for validation of the platform and for antimicrobial resistance gene and virulence factor detection. In particular, we will participate with the collaborating Vet-LIRN laboratory in compiling an Escherichia coli virulence factor sequence database to be used with existing tools available in GalaxyTrakr and an integrated E. coli genomic typing pipeline. Alternatively, we will support the Vet-LIRN network to deploy technology and assist in pathogen WGS of most importance to the Vet-LIRN initiative such as Salmonella.