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Molecular typing

Molecular typing of microbes, also known as microbial fingerprinting, has developed rapidly in recent years.

Typing foodborne pathogens (“disease-causing”) such as Salmonella, Listeria, E. coli and Campylobacter helps identify the specific strains that are responsible for foodborne outbreaks and detect emerging health threats. By establishing a link between strains and food types, it is possible to estimate the role of different foods in human infections. This is known as “source attribution”.

This technique has been employed on many occasions. During the 2011 Shiga-toxin producing E. coli outbreak, which resulted in 4,000 cases and over 50 deaths, molecular typing played a central role in the identification of cases, and in demonstrating that the same strain was responsible for the German and French clusters.

Interactive infographic: molecular typing
Interactive infographic: molecular typing


  1. 2022


    EFSA launches a platform for the collection and analysis of Whole Genome Sequencing (WGS) data on Salmonella, Listeria monocytogenes, and Escherichia coli in food and animals, following a request from the European Commission. The platform is accessible to national competent organisations in the field of food safety, which will be uploading data that come from the annual monitoring of foodborne diseases. It will interact with the equivalent ECDC data collection system.

    The platform will support the work of EFSA and ECDC on rapid outbreak assessments, and ultimately help protect European consumers.

  2. 2019


    Experts evaluate the possible use of whole genome sequencing and metagenomics to investigate foodborne outbreaks, in source attribution analysis and microbiological risk assessment. They also analyse the advantages and limitations of next generation sequencing-based methodologies for characterising Salmonella and STEC and detecting antimicrobial resistance genes in bacteria.

  3. May

    Following a request from the Commission, EFSA and the European Centre for Disease Prevention and Control (ECDC) provide technical support for the collection and analysis of whole genome sequencing (WGS) data. Experts assess the state of the art of existing tools and identify needs and requirements for the joint EFSA-ECDC data collection system.

  4. 2018


    The European Commission and EFSA, supported by the European Union Reference laboratories (EURLs), publish a report on a survey among the EU/EFTA laboratory networks for the main foodborne pathogens. The survey is aimed at gathering information on the WGS capacity of food safety/veterinary laboratories in the EU and associated countries (EFTA).

  5. 2014


    EFSA evaluates the requirements for the design of surveillance activities for foodborne pathogens when molecular typing methods are applied. Experts also review the requirements for harmonised data collection and analysis, which are needed to compare trends over time and geographical areas.

  6. June

    About 90 leading scientists, risk assessors, policy makers and risk managers working in the field of foodborne zoonoses attend a scientific colloquium at EFSA to discuss the use of the WGS of food-borne pathogens for the protection of public health.

  7. 2013


    EFSA reviews molecular typing methods applied to SalmonellaCampylobacterShiga-toxin producing E. coli and Listeria monocytogenes.

    Experts assess the methods based on specific criteria: their discriminatory capacity (ability to distinguish between pathogens), reproducibility and suitability for international harmonisation. They also evaluate their appropriateness in different public health applications — such as outbreak detection and investigation, estimating the contribution of various sources to illnesses and predicting which strains may cause epidemics.

EFSA's role

EFSA provides the tools and databases to support the collection of data on molecular typing of foodborne pathogens in food and animals. Ultimately, EFSA’s work in the field of foodborne diseases helps decision-makers in the European Union to set policies and take measures to protect consumers.

EFSA coordinates the collection of traditional molecular typing results (pulsed-field gel electrophoresis, or PFGE) of food and animal isolates of Salmonella, Listeria monocytogenes and Shiga-toxin producing E. coli (STEC) submitted by national reference laboratories and other official laboratories.

ECDC runs the collection of similar data for human isolates. Data are harmonised across sectors (from food, animals and humans).

Upon submission, data are validated and gathered in a joint ECDC-EFSA database, so that joint analysis of human and non-human isolates can be carried out.

EU framework

The European Commission prepared a vision paper on the development of databases for molecular testing of foodborne pathogens in view of outbreak preparedness. EFSA, ECDC and the European Union reference laboratories contributed to the paper, which sets the contexts for the work in this field at EU and national level.

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