Implementation of affordable whole genome sequencing for front-line genomic analysis of Escherchia coli of veterinary and human importance

University Of Wisconsin-Madison, Madison WI

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Abstract

Project Abstract 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.