Whole genome sequencing as a typing tool for foodborne pathogens like Listeria monocytogenes – The way towards global harmonisation and data exchange

Background: Various molecular typing methods are used for the surveillance of foodborne pathogens and outbreak investigations, differing widely in information content and discriminatory power. Presently, not least because of the rapid technological development, the focus is shifting to whole genome sequencing (WGS) as an analytical tool. As a result of globalisation of food trade, a comprehensive understanding of the association between the occurrence of human infections and causative pathogens has to be established to monitor and to prevent their spread. In this respect, the accuracy of WGS clearly supersedes that of previous tools. Scope and approach: Our review describes the status quo of WGS in surveillance and outbreak investigations of foodborne pathogens through the example of Listeria monocytogenes. It highlights the value of WGS in trace-back of infections to food sources and provides an overview of methods used for data generation (wet lab) and analysis (dry lab). Altogether, progress but also challenges in the worldwide practical application of WGS for bacterial typing are described. Key findings and conclusions: The current status of WGS differs widely between countries and even laboratory sites. A consensus has to be found concerning methods, quality measures, thresholds for data generation and analysis as well as rules for data sharing. International harmonisation is going to be indispensable on the way to data exchangeability which will finally support global control of foodborne pathogens.