Whole Genome Sequencing For State Food Testing Laboratories Competition B

The long-term goal of this project is to reduce the frequency of disease outbreakscaused by food and other environmental sources contaminated with enteric pathogens.Identification and removal of sources of contamination is key to achieving this goal. Tolink sources and patient disease, public health laboratories look for matching geneticfingerprints using pulsed field gel electrophoresis (PFGE). While PFGE basedsurveillance has been successful at reducing the number of outbreaks, its low resolutionis a barrier to further gains. This leads to many sources remaining unidentified.Whole Genome Sequencing (WGS) is being adopted by state and federal public healthlaboratories because of its greater genetic resolution when compared to PFGE anddemonstrated ability to improve source attribution. WGS is described as offering theultimate resolution since each nucleotide in the genome can be queried andphylogenetic relationships can be inferred using well established computational models.However, to achieve the full promise of this technology large well curated databases arerequired that harbor sequence and associated metadata from isolates collected atdiverse locations and times. Such databases aid in source attribution, understanding thenatural history of the organisms, and provide a valuable resource for data mining.One such database is curated by the GenomeTrakr Network. The immediate goal of thisproject is to add eight hundred unique and diverse draft genomes from food andenvironmental bacterial pathogens to this database. This will be accomplished bysequencing well characterized isolates at the Wadsworth Center and sharing thesequence and metadata with the GenomeTrakr network and the National Center forBiotechnology Information (NCBI).The expected outcome of this project will be to expand the GenomeTrakr database ofhigh quality scaffold genomes that are linked to metadata. This will allow more accuratesubtyping to link patient pathogens to specific foods or environmental sources andultimately a reduction pathogen borne illness.!