PathoSeq: Food safety with high precision - Pathogenomics for the food industry

Public health and food safety authorities have implemented whole genome sequencing (WGS) of foodborne pathogens for use in source tracking, epidemiological surveillance, and outbreak investigations, due to its superior sensitivity, specificity and accuracy compared with traditional methods. In the food industry sector, the use of WGS for preventative contamination controls could aid identification of contamination sources and routes, potentially stopping foodborne outbreaks before they occur. WGS may also supplement risk analyses by describing relevant properties of problem organisms. However, significant barriers remain before WGS can be implemented on a wide scale in the food industry. The aim of the PathoSeq project is to identify and resolve technical, biological, practical, commercial, legislative, and regulatory barriers to the use and benefit of WGS technology in the food industry, and with that, prepare Norwegian food industry for the challenges and possibilities of using WGS. To achieve this, we have combined biological and technological expertise with social science and legal research perspectives, as well as active engagement of key Norwegian food industry players. Listeria monocytogenes in meat and salmon factories was selected as a case study. A barrier to effective use of WGS in the food industry is the lack of knowledge about the origin, diversity, and distribution of L. monocytogenes in food chains. Also, effective control will require earlier detection of L. monocytogenes and easy access to information about the properties of individual strains, such as resistance, persistence, and virulence. Furthermore, microbial genetic data must ultimately be shared and compared; cross-sectionally, in real-time, and across sectors. This will require sharing of knowledge, building trust, and the development of guidelines for interactions between key stakeholders. PathoSeq has mapped and addressed challenges for legislation and governance policy relevant for implementation of WGS technology for food safety regulation and pointed towards potential paths going forward that strike a balance between different stakeholder interests. The project has generated knowledge that will contribute to unlocking the full potential of WGS for food safety and public health. The project has sequenced nearly 800 environmental isolates of Listeria monocytogenes from 15 different Norwegian food processing plants, collected over a period of 30 years. This has resulted in increased knowledge of the origin, diversity, and distribution of L. monocytogenes in Norwegian food chains (WP1). Mapping of genetic relationships between the individual isolates showed that over half of the isolates were very closely related to bacterial isolates collected from different factories. The genetic similarity between isolates from different factories were at the same level as that often seen among isolates linked to the same listeriosis outbreak, showing that a broad overview over the L. monocytogenes clones circulating in a food chain is important background knowledge needed for interpretation of WGS results. Examination of genetic determinants showed that the dominant L. monocytogenes variants established as persistent house strains in more than one factory were adapted to the production environment. Investigation into the use of WGS data to identify specific genes associated with disease severity was performed to examine the possibility of using this information as part of risk-based food safety management in the industry showed that the virulence gene profiles did not always correlate with experimental data for invasion efficiency (WP3). The potential of metagenomic sequencing based methods for faster and more sensitive analysis results has been examined and showed that it was possible to detect L. monocytogenes after four hours of enrichment using Nanopore sequencing technology (WP2). The project has been involved in development of tools for visualization and handling of WGS results in the food industry and prepared practical guidelines for how food business operators may use and integrate WGS data into their food safety management systems (WP4). As part of the work to facilitate the use of WGS in food industry, mapping of relevant legal questions and Norwegian food safety legislation relevant for the use of WGS in food industry has been performed. Interviews were conducted with all industry partners of the project, as well as other relevant stakeholders, to gather information on practice and perceived challenges linked to the legal framework (WP5).

PathoSeq has provided Norwegian food producers with increased knowledge, competence, and tools needed to effectively cope with upcoming global digital pathogen surveillance systems, and provided first-hand experience in the use of WGS data for food safety management, contributing to Norwegian food businesses currently being at the forefront worldwide in implementation of WGS technology for pathogen control in the food industry. Together with dissemination of the generated scientific knowledge on the genetic diversity of Listeria monocytogenes found within Norwegian food chains to food safety authorities and other actors, this should reduce the risk of Norwegian food producers being wrongly suspected by customers or authorities for being sources of contaminations and outbreaks, and will contribute to prevention of foodborne disease and increased sustainability through reduction in recalls and food waste. Project outcomes include reinforcement of Nofima’s role as a leading actor supporting the food industry on how to manage Listeria monocytogenes, increased interdisciplinary research collaboration (law and microbiology) and international research collaboration (Norway and Austria). Within the field of food microbiology, the project has generated significant contributions to the scientific knowledge and understanding of the diversity, hazard characterization, and spread of Listeria monocytogenes in food chains. Within the field of law, the project constitutes pioneering work on the topic of food safety legislation and constitutes a foundation for further research on the topic.

The long term vision of PathoSeq is that the Norwegian food industry move to the forefront on implementation of modern DNA sequencing technology for pathogen surveillance and source tracking. The project will provide a scientific and legal basis for enabling use of whole genome sequencing (WGS) technology to control foodborne pathogens. PathoSeq will focus on Listeria monocytogenes (Lm), the most important pathogenic challenge for Norwegian industry. We will build a genomic database giving an overview of the origin, diversity and distribution of Lm in the Norwegian food industry, and across different food chains. We will test the potential of metagenomic sequencing based methods for faster and more sensitive detection of Lm, investigate how WGS can give added value through information about virulence and persistence traits and clarify practical and legislative barriers for implementation of WGS in the food industry. A transdisciplinary and multi-actor approach will be used to produce and translate science into practical recommendations for the food industry. This project will, through revealing and removing barriers (biological, technical, legal and other regulatory issues) for implementation of WGS, prepare the Norwegian food industry for the ongoing revolution within sequencing, transparency and global digital surveillance systems. By building competence and resolve conflicts of interest between different stakeholders, it will be easier to prevent foodborne outbreaks, thus decrease health burden and economic losses both for the public health system and food companies. Furthermore, a more sustainable food production will be achieved through reduced food waste due to recalls and consumer mistrust.