Molecular-based Surveillance in Food Manufacturing Facilities Using Next Generation Sequencing Techniques and Software

Next generation sequencing (NGS) techniques can provide significant insights for safety and quality programmes in food manufacturing facilities, by characterising specific bacterial isolates using Whole Genome Sequencing (WGS) or by examining the complete microbiome of a facility using metagenomics. The Origin Green Micro Surveillance project, commencing in 2016 for a period of three years, is a multi-disciplinary, multi-partner initiative with the aim of gathering and integrating WGS and metagenomics data from manufacturing environments into a harmonised risk and quality assessment system and software application. Industry partners in the project include a global leader in paediatric nutrition, three international infant formula grade ingredient suppliers, an international cooked and fermented meat supplier and an SME nutritional ingredient supplier. The project will identify a sampling plan that will be used to capture the dynamics of bacterial adaptation and microbial population changes over time and space, using WGS and metagenomic analysis. Specific isolates, identified from monitoring, will be sequenced in parallel with a microbiome characterisation of production environments. The molecular epidemiology will be described and predictive models based on both bacterial isolates and their connection with the microbiome will be developed. All gathered data and models will be housed in a risk and quality assessment software application built on a cloud computing architecture, for use by industry to analyse, monitor and improve food safety and quality in specific manufacturing environments.