Co-sponsored by APHL and the US Centers for Disease Control and Prevention (CDC).
DESCRIPTION
This workshop for PulseNet participants will focus on the laboratory procedure for next generation sequencing (NGS) using Illumina sequencing instruments. NGS technology unlocks the full content of the target genome and can be used to characterize bacterial isolates during foodborne outbreak investigations. The wet laboratory portion of the workshop provides hands-on experience in library preparation using Illumina DNA Prep, DNA library Quality Control (QC), loading an Illumina sequencer and evaluating the quality metrics from the run. The data analysis sessions will cover basic QC of sequence data, analysis of data using PulseNet 2.0 submission of data the PulseNet national databases and National Center for Biotechnology Information (NCBI) and cluster detection and reporting.
AUDIENCE
This workshop is designed for state, local and federal public health laboratory technologists with responsibilities for bench testing of enteric bacterial pathogens who are not yet (but intending to) become PulseNet wet laboratory and analysis certified.
OBJECTIVES
At the conclusion of the program, the participant will be able to:
- Describe the PulseNet laboratory procedures associated with whole genome sequencing (WGS) on multiple Illumina sequencing platforms including library preparation (using the PulseNet Illumina DNA Prep protocol), run setup and run data evaluation
- Develop skills to troubleshoot sequencing errors and suboptimal runs
- Demonstrate data transfer to appropriate workstation or streaming to BaseSpace or the PulseNet FTP sites
- Demonstrate how to maintain and care for Illumina sequencing equipment
- Generate high quality sequence data to be used in foodborne surveillance and outbreak detection
- Perform WGS on the MiSeq and MiSeq i100 Plus in the laboratory
- Identify differences between PulseNet-validated Illumina sequencing instruments’ chemistry, capability and maintenance
- State the requirements and process for WGS Certification (Lab and Analysis) and Proficiency Testing
- Discuss Illumina sequencing technology
- Analyze QC of raw sequence data using FastQC and Fragment Analysis to ensure sequencing runs generate high quality data
- Demonstrate appropriate interpretation of QC results
- Explain how to submit pipelines in PulseNet 2.0
- Describe QC analysis of assembled sequences
- Describe the genotyping tools used to characterize serotype, virulence, resistance determinants and plasmids
- Explain how to publish data to the PulseNet national databases and NCBI
- Demonstrate an ability to navigate and query data using the PulseNet 2.0 platform
- Describe cluster detection in PulseNet 2.0 using cg/wgMLST
- Describe the use of the PulseNet SharePoint use and laboratory-epidemiology communications
FACULTY
Jennifer Adams, BS, manager, PulseNet, APHL
Marcus Collins, MS, biologist/laboratory training facility manager, CDC
Amanda Conrad, MPH, Epidemiologist, CDC
Lori Gladney, MS, data analyst, CDC
Taylor Griswold, MS, bioinformatician, CDC
Jasmine Hensley, BS, microbiologist, CDC
Kelley Hise, MPH, PulseNet database team lead, CDC
Lavin Joseph, DrPH, database coordinator, CDC
Patti Lafon, MS, microbiologist, CDC
Charlotte Lane, MS, microbiologist, CDC
Molly Leeper, MPH, data analyst, CDC
Jo Newkirk-Williams, PhD, bioinformatician, CDC
Jordan Putney, BS, data analyst, CDC
Morgan Schroeder, MPH, database coordinator, CDC
Peyton Smith, MS, microbiologist, CDC
Steven Stroika, BS, pulseNet WGS technical lead, CDC
Courtney Wheeler, MPH, microbiologist, CDC
ACCESSIBILITY
In compliance with the Americans with Disabilities Act, individuals seeking special accommodations must email a request to Amy Bryant (Amy.Bryant@aphl.org) at least three weeks prior to the workshop’s start
CREATE AN ACCOUNT WITH APHL!
If you do not have an account with us, you will need to create an account before attempting to register. Through your account portal you will be able to track your events, invoices, transactions and much more!
If you already have an account, make sure you login before registering!
Contact admin.sp@aphl.org with any login or account questions. Review this guide for help with the registration process.
REGISTRATION CONSENT
By registering for this event, you are consenting to have your information shared with APHL event stakeholders, such as the Centers for Disease Control and Prevention and Public Health Labs. We will not, in any circumstances, share your information with other individuals or organizations without your permission, including corporations or individuals, except when applicable by law. We do not sell, communicate or divulge your information to any mailing lists.