• Open Access

Scientific Opinion on the evaluation of molecular typing methods for major food-borne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance: Part 1 (evaluation of methods and applications)


  • EFSA Panel on EFSA Biological Hazards (BIOHAZ)

  • Panel members: Olivier Andreoletti, Dorte Lau Baggesen, Declan Bolton, Patrick Butaye, Paul Cook, Robert Davies, Pablo S. Fernandez Escamez, John Griffin, Tine Hald, Arie Havelaar, Kostas Koutsoumanis, Roland Lindqvist, James McLauchlin, Truls Nesbakken, Miguel Prieto Maradona, Antonia Ricci, Giuseppe Ru, Moez Sanaa, Marion Simmons, John Sofos and John Threlfall
  • Correspondence: biohaz@efsa.europa.eu
  • Acknowledgement: The Panel wishes to thank the members of the Working Group on the evaluation of molecular typing methods for major food-borne pathogens: Dorte Lau Baggesen, Patrick Butaye, Robert Davies, Tine Hald, Arie Havelaar, Bjørn-Arne Lindstedt, Martin Maiden, Eva Møller Nielsen, Gaia Scavia and John Threlfall for the preparatory work on this scientific opinion and European Centre for Disease Prevention and Control (ECDC) staff: Marc Struelens, and EFSA staff: Luis Vivas-Alegre, Ernesto Liebana Criado and Maria Teresa da Silva Felicio for the support provided to this scientific opinion.
  • Adoption date: 5 December 2013
  • Published date: 18 December 2013
  • Question number: EFSA-Q-2013-00032
  • On request from: EFSA


An evaluation of molecular typing methods that can be applied to the food-borne pathogens Salmonella, Campylobacter, Shiga toxin-producing Escherichia coli and Listeria monocytogenes is presented. This evaluation is divided in two parts. Firstly, commonly used molecular typing methods are assessed against a set of predefined criteria relating to discriminatory capacity, reproducibility, repeatability and current or potential suitability for international harmonisation. Secondly, the methods are evaluated for their appropriateness for use in different public health-related applications. These applications include outbreak detection and investigation, attribution modelling, the potential for early identification of food-borne strains with epidemic potential and the integration of the resulting data in risk assessment. The results of these evaluations provide updated insights into the use and potential for use of molecular characterisation methods, including whole genome sequencing technologies, in microbial food safety. Recommendations are also made in order to encourage a holistic and structured approach to the use of molecular characterisation methods for food-borne pathogens; in particular, on the importance of structured co-ordination at international level to help overcome current limitations in harmonisation of data analysis and interpretation.