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

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