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.Historically, public health laboratories look for matching genetic fingerprints usingPulsed Field Gel Electrophoresis (PFGE). However, by the time this grant starts, PFGEwill have been largely abandoned and replaced by surveillance based on WholeGenome Sequencing (WGS).WGS is being adopted by state and federal public health laboratories because of itsgreater genetic resolution when compared to PFGE, as well as its demonstrated abilityto improve source attribution. WGS is described as offering the ultimate resolution sinceeach nucleotide in the genome can be queried and phylogenetic relationships can beinferred using well-established computational models. However, to achieve the fullpromise of this technology, large well-curated databases are required that harborsequence and associated metadata from isolates collected at diverse locations andtimes. Such databases aid in source attribution, understanding the natural history of theorganisms, 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 four 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) in real-time.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 reduce pathogen-borne illness.