Technical specifications for the pilot on the collection of data on molecular testing of food-borne pathogens from food, feed and animal samples

Molecular typing or microbial DNA fingerprinting has developed rapidly in recent years. Data on the molecular testing of food-borne pathogens such as Salmonella, Listeria monocytogenes and Shiga toxin-producing Escherichia coli could substantially contribute to the epidemiological investigations of food-borne outbreaks and to the identification of emerging health threats. The molecular testing data could also be very useful for source attribution studies when estimating the contributions of different food categories or animal species as sources of human infections. The European Food Safety Authority received the mandate from the European Commission to provide technical support to the development of a database on molecular typing data on isolates of Salmonella, Listeria monocytogenes and Shiga toxin-producing Escherichia coli from food, feed, animals and the related environment. For the purposes of the data collection and subsequent linkage with correspondent data from human isolates, ensuring comparability of typing data from food-borne pathogens isolated from food, feed, animals and the related environment as well as from human sources is essential. The project on database development comprises two phases: a pilot data collection phase and database set-up, followed by a fully functional data collection and database management. The present report addresses the pilot phase that will cover molecular typing data based on Pulsed Field Gel Electrophoresis for Salmonella, L. monocytogenes and Shiga toxin-producing Escherichia coli, together with Multiple Loci variable-number tandem repeat Analysis for Salmonella Typhimurium. The purpose of the pilot phase is to test the functionality of the database, including its technical components, as well as the operational process underlying the collection, exchange, curation and analysis of the data. This report addresses all technical aspects for the design of the database and its functionalities. In addition, specific information about the procedures for data submission and accessibility are also covered.