Molecular Surveillance of Foodborne Infections Peter Gerner-Smidt, MD, PhD Chief of PulseNet USA CDC...
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Transcript of Molecular Surveillance of Foodborne Infections Peter Gerner-Smidt, MD, PhD Chief of PulseNet USA CDC...
Molecular Surveillance of Foodborne Infections
Peter Gerner-Smidt, MD, PhDChief of PulseNet USA
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:EpidemiologyLaboratory
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” electronicallyDynamic database of DNA “fingerprints” at CDCDatabase available on-demand to participants
Role of PulseNet USA
Detect foodborne disease case clusters by PFGE– Facilitate early identification of common source
outbreaksAssist 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
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Day of Outbreak
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ases
outbreak detected 1993 726 ill, 4 deaths
1993 Western States E. coli O157 Outbreak
39 d
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Day of Outbreak
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ases
outbreak detected 2002 44 ill, no deaths
18 d
2002 Colorado E. coli O157 Outbreak
Philadelphia
West Mountain South Central North Central Midwest Mid-Atlantic Southeast Northeast
The National Molecular Subtyping Network forFoodborne Disease Surveillance
COLORADO
OREGON
CALIFORNIA
NEVADA
IDAHO
UTAH
ARIZONA
MONTANA
WYOMING
WASHINGTON
NEW MEXICO
NORTH DAKOTA
SOUTH DAKOTA
NEBRASKA
KANSAS
OKLAHOMA
MINNESOTA
IOWA
MISSOURI
ARKANSAS
ILLINOIS
WISCONSIN
MICHIGAN
IND
IAN
A
ALASKA
TEXAS
HAWAII
LOUISIANA
KENTUCKY
OHIO
WEST
VIRG
INIA
VIRGINIA
TENNESSEE
NORTH CAROLINA
PENNSYLVANIA
NEW YORK
MAINENEW HAMPSHIRE
MIS
SIS
SIP
PI
ALABAMA
MASSACHUSETTS
RHODE ISLANDCONNECTICUT
NEW JERSEY
DELAWARE
MARYLAND
GEORGIA
SOUTH CAROLINA
FLORIDA
Los Angeles County
San Diego County
Santa Clara County
Houston
New York City
Tarrant County
Tampa
USDA-AMS
USDA-ARS/FSIS
Orange County
Washington D.C.
FDA-CFSAN
FDA-ORA
FDA-ORA
FDA-ORA
FDA-ORA
FDA-ORA
FDA-CVM
FDA-ORA
Milwaukee
Florida Ag Lab
Area Laboratories
PulseNet Central
County/City Laboratories
USDA Laboratories
FDA Laboratories
FDA-ORALas Vegas
PUERTO RICO
VERMONT
Culture growth
+
Cell Suspension AgaroseCells Trapped in Plug-Lyse cells
Restriction
SpecimenPatient Specimen Collection
=
Finished
Product! ….TCTAGA….….AGATCT….
(XbaI)
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
PulseNet Laboratory Network
Local Databases
PulseNet National
Databases (CDC)
PulseNet National
Databases (CDC)
Participating LabsParticipating Labs PFGE PatternsPFGE Patterns
PulseNet Activity 1996-2010
'96 '97 '98 '99 '00 '01* '02 '03 '04 '05 '06 '07 '08 '09 '100
10000
20000
30000
40000
50000
60000
70000
80000
PFGE patterns submitted to PulseNet Databases
PulseNet is a cluster detection tool, not an
outbreak detection system
A PulseNet CLUSTER is a group of patterns that are found indistinguishable by PFGECLUSTERS of cases identified by PulseNet are investigated by epidemiologists If epidemiologic links are found between cases, the cluster is classified as an OUTBREAK
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
PulseNet: Communication
On-line databasesPulseNet 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
PulseNet Metadata
No PI’s1. Specimen ID2. Organism3. Serotype4. Toxin profile5. Gender of patient6. Age of patient7. City/County/State8. Type of specimen9. Date (collection/received/upload)10. Cluster code11. Pattern names12. Free text comments
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
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 5th XbaI pattern of STEC
O157 ever named• EXHX01.0006 is the 6th XbaI pattern of STEC O157
ever named
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
Weekly cluster report
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.”