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

6. VERMONT

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

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

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

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? Cluster of indistinguishable patterns Patterns submitted electronically 60- or 120-day cluster search performed Visually compare indistinguishable patterns Patterns and clusters are named by CDC

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 1.Specimen ID 2.Organism 3.Serotype 4.Toxin profile 5.Gender of patient 6.Age of patient 7.City/County/State 8.Type of specimen 9.Date (collection/received/upload) 10.Cluster code 11.Pattern names 12.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 5 th XbaI pattern of STEC O157 ever named EXHX01.0006 is the 6 th XbaI pattern of STEC O157 ever named

17. PulseNet Syntax Cluster Code: - –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.”