Molecular Surveillance of Foodborne Infections

Peter Gerner-Smidt, MD, PhDChief of PulseNet USA

CDCplg5@cdc.gov

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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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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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.”