Molecular typing techniques are essential support for foodborne outbreak investigations both at the national and international level. New technologies develop fast, particularly next generation sequencing techniques (NGS), which allow more accurate delineation of outbreaks and provide sustainable source of data for further studies on pathogen characteristics and molecular epidemiology. To support the integration of NGS into food- and waterborne diseases and zoonoses surveillance, ECDC has established an expert group, the FWD NEXT, which provides guidance on practical implementation of NGS and analytical steps.
Well standardised and agreed procedures/analytical pipelines for public health purposes are not yet available for these new techniques, therefore ECDC continues to support the existing molecular typing methods over the transition period.
Expert Opinion on the introduction of next-generation typing methods for food- and waterborne diseases in the EU and EEA
This report describes many of the aspects that should be taken into account. It systematically covers the entire process from sample provision and sequencing to data analysis and collaboration with other organisations.
ECDC has endorsed the use of the following standard molecular typing protocol, which has been technically and epidemiologically validated:
EU protocol for harmonised monitoring of antimicrobial resistance in human Salmonella and Campylobacter isolates – June 2016
Laboratory standard operating procedure for multiple-locus variable-number tandem repeat analysis of Salmonella enterica serotype Enteritidis