PulseNet Surveillance for Listeria: Introduction to Interpretation - - PowerPoint PPT Presentation

National Center for Emerging and Zoonotic Infectious Diseases

PulseNet Surveillance for Listeria: Introduction to Interpretation and Reporting of Whole Genome Sequencing (WGS) Data Preconference Workshop

June 2, 2018 • 8:00–11:30 am PT Pasadena Convention Center

Find Related Cases by Pulsed-Field Gel Electrophoresis (PFGE)

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Limitation of PFGE: Genetically Unrelated Isolate Might Appear Same by PFGE

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Limitation of PFGE: Genetically Related Isolate Might Appear Different By PFGE

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What Subtype Data Can I Get From My Sequence?

 Genus and Species  Serotype  Virulence  AMR  MLST

 Started September 2013  Goal: Sequence all Listeria monocytogenes isolates  Near real-time (<1 week for patient isolates)

National Center for Biotechnology Information

Listeria WGS Pilot Project

Public Health Agency of Canada

 >4,300 Listeria patient isolates sequenced to

date

 >9,500 Listeria food and environmental

isolates

 Nearly all available on NCBI website  Main CDC analysis methods

• High-quality single nucleotide polymorphism

(hqSNP) – Salmonella, Escherichia, Vibrio spp.

• Whole-genome multilocus sequence typing

(wgMLST) – Campylobacter, Listeria

Listeria Sequencing

WA OR MT WY CO UT AZ ID CA NV ND SD KS NE TX NM OK MN MO IA LA AR WI IN KY MI OH IL TN GA AL MS SC FL PA NC WV VA DE

MD

NJ ME VT NY NH MA CT AK HI RI Modified: May 23, 2018

WGS certified, BioNumerics 7.6 pilot site WGS certified

PR

Tally of certified labs: 46 states 52 labs

PulseNet, WGS and Enhanced Epidemiological Capacity

OutbreakNet Enhanced or FoodCORE

DC

Area Laboratories PulseNet Central

NYC CA2 CAOC CASC LAC HU

Where Are We With Implementing Real-Time WGS Surveillance Nationwide?

 Transition to use of wgMLST by the end of calendar year 2018

• Testing combined (PFGE and WGS) national databases
• Validating allele databases
• Validating Reference ID database
• Testing and validating WGS nomenclature (Allele Codes)

 Once above has occurred, PHLs can create combined databases in BioNumerics v7.6

• Get analysis certified for WGS
• Sequence all PulseNet organisms in as real-time as possible and upload to the

combined national databases (goal 7 working days from DNA extraction)

 PFGE will continue to be the gold standard for surveillance until enough testing has been done to fully transition to wgMLST

Presentation Outline

 Basics of wgMLST  WGS Workflow at CDC: What happens to your sequence data  Basic Tree Interpretation  Exercise 1: Tree Interpretation  NCBI Pathogen Detection Pipeline  Exercise 2/Demo: NCBI Pathogen Detection Pipeline  Reporting  Q & A

Speakers for the Session

Kelley Hise, MPH PulseNet Database Unit Chief Steven Stroika, BS WGS Technical Lead Jasmine Huffman, BS Listeria Database Manager

Heather Carleton, MPH, PhD Bioinformatics and Metagenomics Team Lead

For more information, contact CDC 1-800-CDC-INFO (232-4636) TTY: 1-888-232-6348 www.cdc.gov The findings and conclusions in this report are those of the authors and do not necessarily represent the

• fficial position of the Centers for Disease Control and Prevention.

Thank You

#PulseNet Telephone: 404-639-4558 E-mail: PulseNet@cdc.gov Web: www.cdc.gov/pulsenet

#PulseNet