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) =

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

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

What Subtype Data Can I Get From My Sequence?  Genus and Species  Serotype  Virulence  AMR  MLST

Listeria WGS Pilot Project  Started September 2013  Goal: Sequence all Listeria monocytogenes isolates  Near real-time (<1 week for patient isolates) National Center for Biotechnology Information Public Health Agency of Canada

Listeria Sequencing  >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

PulseNet, WGS and Enhanced Epidemiological Capacity WGS certified, BioNumerics 7.6 pilot site WGS certified OutbreakNet Enhanced or FoodCORE AK WA ME ND NH MT VT NY MN OR MA ID WI CT SD RI MI NJ NYC WY PA IA NE MD OH CA NV IN DE IL WV CA2 DC UT VA CO CASC MO KS KY NC TN CAOC OK SC AZ NM AR HI LAC GA MS AL TX LA HU FL Tally of certified labs: Area Laboratories 46 states PulseNet Central PR 52 labs Modified: May 23, 2018

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 Heather Carleton, MPH, PhD Jasmine Huffman, BS Steven Stroika, BS PulseNet Database Bioinformatics and Listeria Database WGS Technical Lead Metagenomics Team Lead Unit Chief Manager

Thank You For more information, contact CDC 1-800-CDC-INFO (232-4636) TTY: 1-888-232-6348 www.cdc.gov #PulseNet The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention. Telephone: 404-639-4558 E-mail: PulseNet@cdc.gov Web: www.cdc.gov/pulsenet #PulseNet