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Short history of PulseNet USA

By the beginning of the 1990’s, Pulsed-Field gel electrophoresis (PFGE) had become the gold standard for subtyping of bacterial pathogens and was increasingly used by the Central Reference Laboratory at the Foodborne and Diarrheal Diseases Branch, the Centers for Disease Control and Prevention (CDC), for investigations of outbreaks of bacterial foodborne disease. An increasing number of outbreaks, especially of Shiga toxin-producing E. coli O157, were being investigated and it became impossible for the CDC laboratory to subtype all strains received in real-time,.which slowed down the investigations. It was therefore decided.to decentralize subtyping activities for foodborne pathogens to where the outbreaks were occurring: the states. This decentralization signaled the birth of PulseNet USA in 1996.

Established in 1996, PulseNet USA, is the national molecular subtyping network for foodborne disease surveillance. It is coordinated by CDC and the Association of Public Health Laboratories (APHL). It now has more than 70 participants including state and local public health departments, federal food regulatory agency laboratories, as well as agricultural and veterinary laboratories. Since its inception, PulseNet USA has become an indispensible part of the surveillance of foodborne infections in the United States by facilitating the detection and investigation of outbreaks, as well as the confirmation of their source,

How does PulseNet USA work?
  1. PulseNet participants perform DNA "fingerprinting" by pulsed-field gel electrophoresis (PFGE) on disease-causing bacteria isolated from humans and from suspected food using highly standardized methodology and equipment.
  2. Once the PFGE patterns are generated, they are entered into an electronic database of DNA fingerprints at the local PulseNet laboratory.
  3. The patterns are then uploaded to a national database located at CDC.
  4. Laboratorians in the states perform regular searches on their local databases, looking for clusters of patterns that are indistinguishable. If an outbreak is suspected, the results are reported to the state epidemiologists, CDC, and the whole PulseNet community on the PulseNet listserv. An outbreak investigation is initiated.
  5. Database managers at CDC also perform cluster searches at least once every week. This allows the detection of geographically dispersed clusters that are not apparent locally, as well as the linking of seemingly local clusters occurring in different states but originating from the same source to each other. If an outbreak is suspected, the results are reported back to the laboratories, the epidemiologists at CDC and to the PulseNet listserv triggering an outbreak investigation..


Before a participant is allowed to submit data to PulseNet, he/she must be trained and certified. Since 1996, more than 400 participants have been trained in the PulseNet subtyping protocols, and the use of the PulseNet customized software, BioNumerics (Applied Maths, Sint-Martens-Latem,,Belgium) for data analysis

As of January 2008, the national database contained approximately 500,000 entries. The Salmonella database has reached over 180,000 entries; E. coli and Shigella each have over 30,000 entries. Databases also exist for Listeria monocytogenes,Campylobacter, Vibrio cholerae, Vibrio parahaemolyticus and Yersinia pestis.

PulseNet USA facilitates the maintainance and expansion of PulseNet International by:
  • Supporting and participating in strategic planning meetings of the regional PulseNet networks
  • Training international participants at CDC
  • Supporting and participating as trainers in workshops held throughout the regional PulseNet networks
  • Sharing protocols and BioNumerics customizations
  • Hosting the QA/QC program for coordinating laboratories of the regional networks
  • Chairing the PulseNet International Steering Committee
  • Assisting in international outbreak investigations


For further information please contact:

Peter Gerner-Smidt, PulseNet USA.


Links to Associated USA Organisations

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Visit APHL website(external link)Visit FDA website(external link)Visit USDA website(external link)


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