2019 GenomeTrakr Meeting

​September 17-18, 2019 | College Park, MD

The 2019 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 the transition to whole genome sequencing (WGS) from federal and state partners, the collaboration between partners to solve outbreaks using WGS data, and new technologies that the network may implement, including metagenomics.

Tuesday, September 17, 2019

Independent Submission Strategy from GenomeTrakr
Ruth Timme, FDA CFSAN

PulseNet's Transition to WGS
Kelley Hise, CDC

FSIS Transition Experience and Workflow
Mary Katherine Crews, USDA FSIS

Pilot Laboratory Presentations on Transition Experiences (Panel)

• Samantha Wirth, NYS Dept. of Health, Wadsworth Center

• The WA-PHL Transition: WGS and BN for Everything
  Roxanne Meek, WA Dept. of Health

• Lauren Turner, VA Division of Consolidated Laboratory Services

Adding IFSAC + FoodOn Categories to GenomeTrakr BioSamples
Maria Balkey, FDA CFSAN

Standardizing Metadata: Resistome Trakr
Heather Tate, FDA CVM

So Many Clusters, So Little Time: How to Communicate WGS Data to Your Epidemiologists (Panel) 

• Dave Boxrud and Sean Buuck, MN Dept. of Health

• How VA Communicates WGS Data
  Lauren Turner, VA Division of Consolidated Laboratory Services; Katherine McCombs, VA Dept. of Health

• Hugh Rand, FDA CFSAN; Tyann Blessington, FDA CORE

• Kelley Hise, CDC

WGS Influence on Outbreaks

• Listeria monocytogenes / Avocado Retrospective Outbreak Investigation

  Brooke Whitney, FDA CORE

• E.coli O157:H7/Romaine from Yuma Growing Regions
  Mark Otto, FDA CORE

Wednesday, September 18, 2019

Laboratory Flexible Funding Model Funding Mechanism
Don Burr, FDA ORA/ORS

Updates on Comparisons and Performance of Reagents

• Comparison of Nextera XT and Nextera DNA Flex

  Matt Plumb, MN Dept. of Health

• Illumina Updates
  Dan Schoeffner, Illumina

Current Network-Wide QA/QC Metrics
Ruth Timme, FDA CFSAN

QA/QC Through GalaxyTrakr
Errol Strain, FDA CVM

GalaxyTrakr QA/QC: State User Perspective
Melanie Prarat, OH Dept. of Agriculture

BioNumerics and Quality Control: Overview and Perspective
Rebecca Lindsay, CDC

Proficiency Testing for Foodborne Pathogen Surveillance: An Analysis of the 2019 GenomeTrakr PT Exercise
Joe Baugher, FDA CFSAN

Adaptation of the CFSAN GenomeTrakr PT Pipeline for Internal Assessment of WGS Technical Proficiency
Kevin Libuit, VA Division of Consolidated Laboratory Services

Resequencing Due to Quality Issues—Top Reasons and Impact on Routine Workflow (Panel)

• Sean Wang, MN Dept. of Health

• Mary Katherine Crews, USDA FSIS

NCBI Pathogen Detection Updates: Neighbors, Notifications, Custom Labels and AMR
Arjun Prasad, NCBI

WGS and Non-PulseNet Pathogens

• Cyclospora cayetanensis
  Hediye Cinar, FDA CFSAN

• Clostridium botulinum
  Narjol Gonzalez-Escalona, FDA CFSAN

• Cronobacter sakazakii
  Hyein Jang, FDA CFSAN

• Clostridium difficile
  Nicole Pecora, University of Rochester

Metagenomics

• MetagenomeTrakr: A Pilot Study for the Rapid Detection of Foodborne Pathogens

  Laura Howard, FDA ORA

• Use of Metagenomics in a Veterinary Diagnostic Lab
  Patrick Mitchell, Cornell Vet-LIRN