Food Safety
The power and potential of whole genome sequencing This article was written exclusively for Food New Zealand by Dr Lucia Rivas, ESR, Dr Catherine McLeod, Director of the NZ Food Safety Science & Research Centre, and science writer, Glenda Lewis Dr Lucia (Lucy) Rivas, ESR, leads the team that is building the Listeria database
Dr Catherine McLeod, Director of the NZ Food Safety Science & Research Centre
Introducing Whole Genome Sequencing COVID-19 has been a phenomenal spur for the introduction of whole genome sequencing (WGS). In the early stages of the pandemic, The Institute of Environmental Science and Research (ESR) prompted the government to invest in WGS, and quickly outfitted and upskilled three centres to provide a 24-hour turn-around service for urgent testing of COVID samples. WGS is the brains behind our track and trace system and has given confidence to agonising lockdown decisions. The power and potential of WGS is not as well understood in the food industry. New Zealand food-producing companies are at quite different stages in applying WGS, or even thinking about applying it. There are individual champions, like Denver McGregor of NZ King Salmon, who actively sought it out and sold the benefits to his boss. Fonterra has established a completely independent and integrated sequencing and bioinformatics facility. For many other companies, there are still a lot of barriers, perceived or real. Chief among them are lack of understanding of the technology, and cost-benefit information to justify the extra expense.
What's in it for me? Companies who have experienced a disease outbreak or product recall are quick to appreciate the virtues of WGS. In a survey commissioned by the NZ Food Safety Science & Research Centre (the Centre), companies who have adopted WGS generally report that the benefits have met or exceeded expectations. It may well be that late adopters will soon be obliged to come on board by increasingly risk-averse food importers and insurers. Meanwhile, the technology is just getting better and faster all the time – undercutting even Moore’s Law. There is a foreseeable future in which food producers will have cheap handheld devices that give immediate readings of samples in processing facilities. But that is still tech talk, not 2021 reality. The Centre is helping New Zealand companies get to grips with WGS technology in the here and now, and how to apply it in their unique production context. In 2020-2021, WGS was used in eight collaborative research projects within industry settings. Distinguished Professor Nigel French, the Centre’s chief scientist, is a world expert in the application of WGS for
food safety. He says it is a no-brainer when it comes to understanding and reducing the risk of pathogen transmission in a long and complex food chain, such as poultry, dairy or meat. The main benefit of WGS is that it provides an unprecedented level of resolution – right down to one DNA or RNA ‘letter’ (nucleotide) difference between isolates. As an example, a company can analyse pathogens collected from different areas of a processing chain and determine whether a particular source, like a piece of equipment or an ingredient, is responsible for contaminating a food product and whether it is a persistent resident strain. Companies can then focus cleaning efforts in these specific areas. The Centre is soon to launch a WGS database resource for members to help manage one of our main food safety risks – Listeria monocytogenes. The isolates are from historical clinical cases and anonymous company environmental and food samples. This is designed to be a confidential reference repository for Centre members. The database is not a public health surveillance tool and in order to protect contributing members’ data no sensitive or identifiable information, such as company names or locations, food products or sectors, are included, and authorised access to the database is required.
The Listeria project ESR is the science partner in much of the Centre’s research, and is one of the principle providers of sequencing services – clinical, forensic and commercial. Dr Lucia (Lucy) Rivas at ESR leads the team that is building the Listeria database, which now has over 1000 isolate sequences uploaded. There is some work still to do before it is available for authorised Centre members to use. A lot of the software up till now has been developed by, and for, academic research so the aim is to make the site as user-friendly as possible, so that companies can view their own data easily, without needing too much bioinformatic training. Centre members will be able to compare and visualise WGS data from their isolates, independently, or with other isolates of interest, to obtain a ‘bigger picture’ as to how common a particular type or strain is in NZ. User feedback will continue to improve the resource, which may eventually include international, publicly available data. The platform could also serve as a start-point for an in-house analysis tool that displays the data onto maps of food production and processing facilities to help clearly identify sources and trends of contamination. The Centre itself wants oversight into how this troublesome bacterium is moving and evolving in New Zealand. There is a lot of potential to analyse the genomic data further to find out what drives Listeria to stubbornly persist in a factory, in some instances, and work out better ways to control or eliminate it. Funds forthcoming, the Centre’s aim is to expand this database to other pathogens of concern for the food industry, such as Cronobacter and Salmonella. October/November 2021
23
