Practical Experience with Whole Genome Sequencing in the Food Industry

There has been an increased interest in the use of Whole-genome Sequencing (WGS) in public health and food safety applications in recent years. This has been driven by advances in the technology, its reducing costs and the increase in discriminatory power. Obtaining genomes from pure cultures of prokaryotes does not present technological barriers anymore. WGS has been demonstrated as a useful tool for microbial source tracking in foodborne outbreaks, enabling a more targeted investigation. Conventional microbial typing tools are also regularly used in the food industry for investigative purposes (source attribution), factory ecology and trend analysis.  For the food industry, WGS can, through its increased discriminatory power, its potential analytical economies of scale and speed, offer advantages for the industry. Furthermore on a global scale such a technology, when harmonized, will offer considerable benefits for food safety and public health. The WGS application for foodborne source tracking is relatively new and is an especially complex analysis compared to the conventional typing technologies. The bioinformatics and IT infrastructure involved in the WGS analysis forms a ‘black box’ for many food microbiologists. The goal is to open this ‘black box’ of the so called “WGS analysis pipelines” to understand the parameters utilized for foodborne pathogens source tracking such as Salmonella and Listeria. Subsequently, there is a need to establish guidelines to align on each of the parameters within the WGS analysis pipeline (such as the minimal coverage, reference selection, cluster analysis and etc.). Scientific data regarding pathogenic mutation rate and background population diversity would help to define parameters and criteria. Validation by means of case studies would be needed to enable internationally accepted WGS analysis for routine applications and finally to obtain standardization ensuring consistent clustering of isolates. Investigation carried out by Nestle with regards to the different parameters of the WGS analysis pipeline will be elaborated. Industrial case studies will be illustrated to show the value of the WGS technology for source tracking and food safety purposes.