WA PHL participation in GenomeTrakr Network for foodborne disease investigations using whole genome sequencing

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1 Introduction to Application 2 The Washington State Public Health Laboratories (WA PHL) were among of the first four laboratories 3 that formed the GenomeTrakr network by entering into a Research Cooperative Agreement (RCA) with FDA- 4 CFSAN in late 2012. In 2013, the WA PHL received a MiSeq instrument, obtained the support of Dr. Zhen Li 5 through the ORISE Fellowship and started receiving reagent support for the sequencing of food/environmental 6 bacterial isolates. 7 The whole genome sequencing (WGS) work performed at WA PHL for GenomeTrakr has the overall 8 objective of building a stronger international rapid surveillance system for pathogen trace back sample 9 collection and sequence cataloging through a publicly available database of food and environmental pathogen 10 isolates. Through this work, WA PHL will continue to expand and improve the outcome of disease cluster trace 11 back to specific sources and will contribute towards the effort of monitoring compliance with FDA’s rules on 12 safe food-handling practices to enhance preventive controls for food safety. The specific aims of this project 13 are 1. To sequence up to four hundred (400) foodborne related bacterial, viral and/or parasite pathogen 14 isolates, 2. To increase collaboration and share live isolate cultures upon request and 3. To actively participate 15 in GenomeTrakr network activities. The overall objective of this work will be possible only if the entire 16 GenomeTrakr network continues to contribute to this goal (through the participation of WA PHL as well as 17 other laboratories). In addition, the successful linkage of current foodborne disease clusters and/or outbreaks 18 to a food or an environmental source hinges upon obtaining WGS data from both food/environmental sources 19 and clinical isolates. As a PulseNet Western Region Area Laboratory; WA PHL also perform WGS on clinical 20 isolates obtained from patients with foodborne disease, therefore; serving as a conduit for the linking of clinical 21 clusters with a source. WA PHL actively shares cluster information with appropriate collaborators locally and 22 nationally to speed foodborne illness outbreak investigations and prevent additional foodborne illnesses and 23 deaths. 24 The GenomeTrakr work is revolutionizing the way in which microbiology is performed at WA PHL and 25 other public health laboratories by providing higher resolution and certainty in molecular epidemiology 26 investigations of disease clusters; by furthering the database of genomic antibiotic resistant markers; and by 27 providing alternative methodologies for the way in which pathogens have traditionally been characterized 28 (serotyping, virulence markers, resistance typing, etc) in the laboratory. Participants of this project have 29 collectively generated massive amounts of data that is publicly available for other researchers to harness for 30 additional applications.