The 2018 GenomeTrakr Meeting featured presentations from federal, state and academic partners who participate in FDA’s GenomeTrakr Network, the first distributed network of laboratories utilizing whole genome sequencing for pathogen characterization. Meeting participants heard about new data generation and analysis tools, networked with peers, discussed best practices and common challenges, and learned how their data is utilized to detect and speed up response in various foodborne outbreak investigations.
Wednesday, September 26
Federal Updates
Welcome and Cooperative Agreement Updates
Don Burr and Christina Megalis, FDA
Gen-FS Overview
Eric Brown, FDA
Update on GenomeTrakr Submissions and Bioinformatics Tools
Errol Strain, FDA
USDA FSIS Updates
Glenn Tillman, USDA FSIS
CDC PulseNet Updates
Steven Stroika, CDC
Updates on the NCBI Pathogen Detection Pipeline
Bill Klimke, NCBI
Ask Me Anything for Federal Agencies
Panel: Don Burr(FDA), Christina Megalis (FDA), Eric Brown (FDA), Errol Strain (FDA), Glenn Tillman (USDA FSIS), Steven Stroika (CDC), Bill Klimke (NCBI), Ruth Timme (FDA)
Thursday, September 27
Outbreak investigations and WGS
Adiam Tesfai, FDA
WGS and Federal Regulatory Activities
Asha Dwarka, FDA
Impact of WGS in New York
Maria Ishida, New York Department of Agriculture and Markets
Impact of WGS in Florida
Brian Caudle, Florida Department of Agriculture and Consumer Services
GenomeTrakr Workflows
Bringing Whole Genome Sequencing on Board in a State Regulatory Laboratory
Brian Sauders, New York Department of Agriculture and Markets
Managing the Transition to WGS & Maintaining Multiple Workflows in USDA FSIS
Glenn Tillman, USDA FSIS
Implementation of WGS for Foodborne and Environmental Isolates in FDA ORA ORS Laboratories
Karen Jinneman, FDA
Integration of WGS into an Establish Public Health Laboratory Testing Process – Virginia's Perspective
Leigh-Emma Lion, Virginia Division of Consolidated Laboratory Services
Academic Applications of GenomeTrakr Data
Scalable Metagenomics of Foodborne Pathogens and Antimicrobial Resistance Using Supercomputing with Bayesian and Error Correction Methods
Zaid Abdo, Colorado State University Veterinary School
GenomeTrakr in PA: Public Health—Academic Collaboration in Integrated Surveillance to Enhance Food Safety
Edward Dudley, Pennsylvania State University
Recent Updates in Bacterial Tolerance to Industrial Cleaners and Other Stressors
Genomic Mapping of Adaptive Changes in Food and Environmental-borne Salmonella for Identification of Preventive Controls
Julie Haendiges, NSF International
High-throughput Assay to Determine Susceptibility of Salmonella and E. coli to Biocides
Jonathan Frye, USDA
Assessing Purity of Isolates from International Sources (Panel Session)
Brian Sauders, New York Department of Agriculture and Markets
Bill Wolfgang, New York Department of Health, Wadsworth Center
Laboratory Experiences with Automation in Sequencing Workflows
Automating FDA Extraction
George Kastanis, FDA
Adjustable Tip Spacing Pipettes, an Alternative to Automated Library Prep
Valerie Reed, State Hygienic Laboratory at the University of Iowa
WGS and ISO – Putting WGS Methods on Scope
Putting WGS Methods on Scope – Where to Start?
Maria Ishida, New York Department of Agriculture and Markets
ISO 17025 Bacterial WGS Accreditation Experience in Veterinary Diagnostics
Derek Rothenheber, Cornell University
Metagenomics Applications
Application of Metagenomic Sequencing to an Outbreak of E. coli O157:H7
Kelly Oakeson, Utah Public Health Laboratory
Pipelines: Understanding Which to Use and How They Differ
Bioinformatics Approaches to Support Outbreak Investigations: CFSAN-SNP and the Lyve-Set Pipeline
Kevin Libuit, Virginia Division of Consolidated Laboratory Services
Benchmark Datasets for Phylogenomic Pipeline Validation
Ruth Timme, FDA
Friday, September 28
Utilizing NCBI Pathogen Detection Browser
Updates to the NCBI Pathogen Detection System
Arjun Prasad, NCBI
Utilization of NCBI Pathogen Detection Tool in USDA FSIS
Glenn Tillman, USDA FSIS
Utilizing GalaxyTrakr
GalaxyTrakr: Scalable Public Health Bioinformatics in the Cloud
Justin Payne and Jimmy Sanders, FDA
GalaxyTrakr for State Public Health Bioinformatics: Data Analytics, Introductory Trainings, and University Collaborations
Kevin Libuit, Virginia Division of Consolidated Laboratory Services
New and Unusual Organisms
Vibrio Outbreak and Surveillance: Maryland's Collaborative Approach
Catherine Dominguez, Maryland Department of Health and Mental Hygiene
James Pettengill, FDA
Cyclospora cayetanensis and Cyclosporiasis Outbreaks: Why Do We Need Genomics?
Alex da Silva, FDA
Clostridium perfringens Whole Genome Sequencing Improves Outbreak Source Attribution: A Case for Including C. perfringens in the GenomeTrakr Database
Bill Wolfgang, New York Department of Health, Wadsworth Center
Adoption of WGS Tools for Toxin Profiling in Food Products
Sandra Tallent, FDA
Development of a GenomeTrakr Pipeline for Foodborne Viruses
Mark Mammel and Zhihui Yang, FDA
Looking to the Future
Moez Sanaa, FDA