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Workpackage 4 Overview: PulseNet Europe

Development of a linked molecular surveillance database system for food-borne infections

In Med-Vet-Net News December 2004 we gave a first overview of Workpackage 4: now at the project completion we outline the achievements and benefits to stakeholders.

Multinational outbreaks of food-borne infections have become frequent events with the increasing trade of raw, semi-processed and ready-to-eat foods between countries. Early detection and response to food-borne infections are therefore important both for public health and for trade of food products.

Workpackage 4 achievements

Participants at the curators training course at SSI in April 2006.

In Europe, for many years the problem has been that molecular typing results from different countries have not been comparable, even when the same method was used. Further, it is impractical to exchange bacterial strains over long distances to perform the real-time typing necessary for outbreak detection and control. However, it is possible to do molecular typing according to defined and standardized protocols in many places at one time and to send DNA fingerprints electronically to a central database enabling a comparison of profiles of strains isolated in different countries in real-time.

PulseNet Europe is a network of food, public health, and veterinary laboratories dedicated to molecular surveillance of food-borne infections. It is a unique multi-disciplinary network in the EU and which combines high discriminatory molecular typing with a truly ‘farm-to-fork’ approach to the existing surveillance at an international level. Strains isolated from patients and food are locally typed by pulsed field gel electrophoresis (PFGE) using a standardized protocol and images of the PFGE-profiles are electronically submitted via the web to the PulseNet Europe central database to be compared with profiles submitted by other laboratories. Comparison is made in real-time using sophisticated image analysis software.

The data are also comparable internationally through PulseNet International (PulseNet Asia–Pacific region, PulseNet Canada, PulseNet Latin America and PulseNet USA).
Partners have direct access to the PulseNet Europe central database containing specific databases for Salmonella, verocytoxin-producing Escherichia coli and Listeria monocytogenes. This direct access ensures a uniform nomenclature for PFGE-subtypes in all participating countries, provides portable data and allows partners to check and compare their own data to the data that are stored in the database when alerts of infection clusters are posted on the communication forum. This direct access to comparable typing data for isolates from human infections as well as food and animals will significantly improve the surveillance and trace-back of food-borne infections at the national, European and international level. Further, international clusters of food-borne infections that have too few cases in each country to be recognized by the national surveillance systems will be detected through the central PulseNet Europe surveillance system.

PulseNet Europe partners are laboratories submitting typing data for one or more of the pathogens under surveillance in the network. The partnership represents public health, food, and veterinary laboratories across Europe. Partners expressing interest represent 60 institutes from 30 countries. This includes 12 institutes participating in Med-Vet-Net.

The quality of the PFGE gel images and correct band assignments are critical when data is uploaded to the central database for comparison. The six database curators from AFSSA, DFVF, HPA, IP, SSI and VLA, who were chosen to take care of the quality of the central databases, perform the uniform naming and confirm the PFGE profiles submitted by partners, and perform central cluster detection of all pathogens at regular intervals. In addition, the curators organize training courses and are involved in troubleshooting for participant laboratories whenever requested.

Website

The PulseNet Europe homepage (http://www.pulsenet-europe.org/) has been established. It contains general information of PulseNet Europe, participants, organization structure, the PNE forum, links to other networks and documents such as protocols, a gel analysis manual (BioNumerics PNE manual) and a troubleshooting help function.

Communication

The PulseNet Europe communication system, PNE forum, http://www.pulsenet-europe.org/pneforum, has also been set up. Through the PNE forum, partners will be alerted by email when an international cluster is detected, and the images from clusters of PFGE profiles can be attached to the alert email. It is also a forum where discussions and questions can be asked concerning the PulseNet protocols and the database. The forum contains a public site and a confidential site, the latter is only accessible to PulseNet Europe partners. Curators and administration also have their own confidential discussion forums.

Curator Group

A curator group of six curators from different institutes was trained in 2006 and additional funding from Med-Vet-Net also enabled a training course for 15 PulseNet Europe participants.

A European Quality Assurance System

A European Quality Assurance System (EQAS) has been created and certification started in order to insure the comparability of the data that are uploaded from different laboratories.

Central database

A trial run of the PulseNet Europe central database has been performed and the system is fully functional. Customized BioNumerics software has been developed with full compatibility with other PulseNet networks and a manual of the customized PulseNet BioNumerics software has been written for partners. The certified partners, who have signed the memorandum of understanding have been given passwords to access the central database

Memorandum of Understanding

A memorandum of understanding (MoU) which defines the rules for collaboration allowing exchange of information and molecular typing data between PulseNet Europe partners is ready for signatures and an MoU with PulseNet USA has been drafted.

Integraton of PulseNet Europe database and activities with ECDC

The European Centre for Disease Prevention and Control (ECDC) has the mandate to detect, assess and respond to health threats including multi-national food-borne outbreaks. The operation of PulseNet Europe supports rapid detection of outbreaks associated with food and animal sources, therefore, close links to ECDC were built up and the integration of PulseNet Europe with ECDC was carefully explored. In November 2006, the PulseNet steering committee was informed that ECDC had included PulseNet Europe in their 2007 action plan. The plan will be made public in December and it includes one co-ordinator and three curators (full time).

Stakeholder benefits from Workpackage 4

The knowledge that has been gained on how to build customized BioNumerics databases with server access via the internet could be valuable for other groups (collaborators from different institutes and countries) aiming to create a place for sharing information on species, strains and different molecular and typing techniques. The structure exemplified by PulseNet Europe databases is easily modified for other pathogens including non-food-borne pathogens and the spectrum of typing methods can be easily expanded.

It is anticipated that the direct access to comparable typing data for isolates from human infections as well as food and animals generated by PulseNet Europe, will significantly improve the surveillance and trace-back of food-borne infections at national, European and international level.

Susanna Lukinmaa

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Page Contact: Jennie Drew - Last modified: 2007-06-04