Molecular typing


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

Typing food-borne 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 specific strains and specific food types, it is possible to estimate the role of different foods in human infections. This is known as “source attribution”.

This has been illustrated 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.

 molecular typing
Interactive infographic: molecular typing


EFSA has been piloting the collection of molecular typing data from food and animals together with European Union reference laboratories since the end of 2014. In the long run, EFSA will manage the database containing data submitted by national reference laboratories.

The European Commission requested EFSA to provide technical support for the collection of molecular typing results of food and animal isolates of Salmonella, Listeria monocytogenes, and Shiga-toxin producing E. coli. EFSA worked closely with the EU reference laboratories to develop harmonised procedures that allow the interpretation and analysis of data obtained with different typing methods.

The European Centre for Disease Prevention and Control (ECDC) is carrying out similar work for human isolates.

The systems in place for typing data from food, animals and humans are compatible and complementary. This allows joint analysis using both databases.


In December 2013, EFSA’s Panel on Biological Hazards reviewed molecular typing methods applied to Salmonella, Campylobacter, Shiga-toxin producing E.coli and Listeria monocytogenes.

Experts assessed the methods based on specific criteria: their discriminatory capacity (ability to distinguish between pathogens), reproducibility and suitability for international harmonisation. They also evaluated 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. 

The Panel concluded that there are no current typing methods for foodborne pathogens that meet all the criteria. Several methods are often used in combination to obtain the result needed and they depend on the pathogen and the application sought.

In August 2014, EFSA evaluated the requirements for the design of surveillance activities for food-borne pathogens when molecular typing methods are applied. Experts also reviewed the requirements for harmonised data collection and analysis, which are needed to compare trends over time and geographical areas. 

Whole genome sequencing (WGS)

June 2014 – about 90 leading scientists, risk assessors, policy makers and risk managers working in the field of foodborne zoonoses attended a Scientific Colloquium at EFSA to discuss the use of the whole genome sequencing of food-borne pathogens for the protection of public health. Participants discussed benefits and challenges related to the use of WGS for public health, the analysis and interpretation of WGS data and the integrated use of these techniques in the food, veterinary and human health sectors.


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.

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.