Molecular Surveillance of Foodborne Infections

1. Molecular Surveillance of Foodborne Infections Peter Gerner-Smidt, MD, PhD Chief of PulseNet USA CDC plg5@cdc.gov

2. Surveillance of foodborne infections • The ongoing systematic collection and analysis of data leading to action being taken to prevent and control foodborne infections  Two components working together: • Epidemiology • Laboratory

3. What is PulseNet USA? • A national laboratory network coordinated by CDC • State health departments, Local health departments, Federal agencies (CDC, USDA, FDA) • Perform standardized molecular typing of foodborne disease-causing bacteria by Pulsed-field gel electrophoresis (PFGE) [and other methods] • Share DNA “fingerprints” electronically • Dynamic database of DNA “fingerprints” at CDC • Database available on-demand to participants

4. Role of PulseNet USA • Detect foodborne disease case clusters by PFGE • Facilitate early identification of common source outbreaks • Assist epidemiologists in investigating outbreaks • Separate outbreak-associated cases from other sporadic cases • Assist in rapidly identifying the source of outbreaks • Act as a rapid and effective means of communication between public health laboratories

5. 1993 Western States E. coli O157 Outbreak outbreak detected 1993 726 ill, 4 deaths 39 d 2002 Colorado E. coli O157 Outbreak outbreak detected 2002 44 ill, no deaths 18 d

6. The National Molecular Subtyping Network for Foodborne Disease Surveillance NEW HAMPSHIRE Milwaukee MAINE FDA-ORA WASHINGTON MINNESOTA MONTANA NORTH DAKOTA MASSACHUSETTS Philadelphia OREGON WISCONSIN NEW YORK RHODE ISLAND MICHIGAN IDAHO SOUTH DAKOTA CONNECTICUT FDA-ORA WYOMING New York City IOWA NEW JERSEY PENNSYLVANIA FDA-CVM NEBRASKA OHIO NEVADA DELAWARE ILLINOIS INDIANA FDA-CFSAN WEST VIRGINIA UTAH FDA-ORA MARYLAND Washington D.C. FDA-ORA COLORADO VIRGINIA Las Vegas KANSAS KENTUCKY Santa Clara County CALIFORNIA MISSOURI NORTH CAROLINA USDA-AMS TENNESSEE SOUTH CAROLINA ARKANSAS OKLAHOMA FDA-ORA ARIZONA NEW MEXICO Los Angeles County USDA-ARS/FSIS FDA-ORA MISSISSIPPI ALABAMA Area Laboratories Orange County GEORGIA FDA-ORA San Diego County TEXAS PulseNet Central LOUISIANA FLORIDA Florida Ag Lab County/City Laboratories Tarrant County ALASKA USDA Laboratories Houston Tampa FDA Laboratories HAWAII PUERTO RICO West Mountain South Central North Central Midwest Mid-Atlantic Southeast Northeast VERMONT

7. Culture growth Patient Specimen Collection Specimen + = Cells Trapped in Plug -Lyse cells Cell Suspension Agarose Restriction Finished Product! ….TCTAGA…. ….AGATCT…. (XbaI)

8. PFGE Patterns of E. coli O157:H7 * * * Fragment Sizes (in kilobases) 1135 Kb 452.7 Kb 216.9 Kb 76.8 Kb 33.3 Kb *Global Reference Standard DNA “fingerprints”

9. PulseNet Laboratory Network PulseNet National Databases (CDC) Participating Labs PFGE Patterns Local Databases

10. PulseNet Activity 1996-2010

11. PulseNet is a cluster detection tool, not an outbreak detection system • A PulseNet CLUSTER is a group of patterns that are found indistinguishable by PFGE • CLUSTERS of cases identified by PulseNet are investigated by epidemiologists • If epidemiologic links are found between cases, the cluster is classified as an OUTBREAK

12. What is a Cluster Search? • Patterns submitted electronically • 60- or 120-day cluster search performed • Visually compare indistinguishable patterns • Patterns and clusters are named by CDC Cluster of indistinguishable patterns

13. PulseNet: Communication • On-line databases • PulseNet Web-Portal (database without images) • WebBoard postings • Cluster detection • Outbreak investigations • Technical support • Quarterly/Annual Reports from CDC • “PulseNet News” Newsletter • Tri-annual publication • PulseNet Websites • www.cdc.gov/pulsenet or www.pulsenetinternational.org • Annual meetings

14. PulseNet Metadata • No PI’s • Specimen ID • Organism • Serotype • Toxin profile • Gender of patient • Age of patient • City/County/State • Type of specimen • Date (collection/received/upload) • Cluster code • Pattern names • Free text comments

15. PulseNet Syntax • A way to provide unique identifiers to • PFGE patterns without images • PFGE patterns are now and then renamed since PFGE analysis is partly subjective • Outbreaks/clusters

16. PulseNet Syntax • Pattern name: XXXYYY.#### • XXX ~ organism, e.g., EXH = STEC O157 • YYY ~ restriction enzyme, e.g., X01 = XbaI • .#### ~ consecutive number • i.e., patterns with like names are usually not related • EXHX01.0005 is the 5thXbaI pattern of STEC O157 ever named • EXHX01.0006 is the 6thXbaI pattern of STEC O157 ever named

17. PulseNet Syntax • Cluster Code: <YY><MM><LabID><organism code>-<number of cluster in month> • YY = year • MM = month • LabID = laboratory/state where the cluster was identified (ML if multi state) • organism code is the same as used in pattern name • 0909MAJPX-1 = the first Salmonella Typhimurium cluster identified in Massachussetts in September 2009

18. Weekly cluster report

19. Acknowledgements • All PulseNet & OutbreakNet participants at CDC, FDA, USDA, and in the State Public Health Laboratories Disclaimer: “The findings and conclusions in this presentation have not been formally disseminated by the Centers for Disease Control and Prevention and should not be construed to represent any agency determination or policy.”