Introducing Whole Genome Sequencing

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

Note that Table 1. referenced in the text, is published in the full article in Food New Zealand, Oct/Nov 21 issue

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.

Lucy spends a lot of her time explaining WGS technology and the results of sequencing to commercial food clients. While it’s a nobrainer for big industries and companies, it can be a hard sell to small companies where every dollar counts. Although the cost of sequencing has come down, it’s not cheap either. WGS is expensive compared to other microbiological tests, but then it is very different to most standard tests.

Cost–benefits

The Centre has commissioned an independent expert to evaluate the technology’s cost-benefits, with a view to giving members hard data from which to build a business case for their executive and board. The costs of foodborne disease to victims and taxpayers are well known. It is harder to generalise the costs for producers related to outbreaks and recalls, and each scenario varies. Early findings from the Centre’s evaluation demonstrate that there have been situations in which a pathogen has been detected and led to the removal and destruction of product, at a cost to the companies interviewed of between NZ$0.5M - $2.37M. The companies involved in these incidents noted that with WGS findings in hand, they have now implemented a range of strategies to combat these pathogens and minimise further lost batches and costly recalls. These strategies include changing sanitation regimes to help eradicate the pathogen from the processing environment, replacing problematic infrastructure, and the identification of ‘hot spots’ to target for regular testing. The Centre’s report will soon be available to members.

Lucy says, “The cost-benefit ratio is particularly worthwhile if a company is facing chronic contamination issues in its processes. The accuracy and confidence of elucidating the source of contamination in a system is greater if a broad range of isolates from different locations are sequenced. This can drive up initial costs for isolation and sequencing but consequently offers a powerful dataset with which to compare new isolates prospectively. Not only can WGS implicate a source of contamination, it can also exonerate a potential source, which can be equally valuable, especially as it can narrow down further sampling.”

Debunking the push–back

There are reasons other than cost why many companies have not lined up yet to use WGS – most of them understandable. They worry about confidentiality, and being implicated in and held to account by media and regulators for current and historical outbreaks. The time it takes to get results is another block. The Centre has found through its work with individual companies that most concerns, such as confidentiality, are able to be addressed and mitigated.

The rapid sequencing of COVID-19 positive samples has raised expectations about the time it should take. “Why can’t I get results overnight?” clients ask Lucy. But sequencing bacteria requires a different approach which is more labour intensive than sequencing a COVID-19 sample. Between 90 and 100 bacterial isolates are run once a week in a single batch. Like a dishwasher, it’s uneconomic to run the machine unless it’s fully loaded. The standard ESR processing time of about two weeks includes expert analysis and reporting, without which the raw data would mean very little to clients. Lucy explains, “Sequencing of COVID-19 samples does not need any prior isolation of the virus, as required for bacteria, which can add days to weeks of waiting time for food companies. This timeline means that WGS is predominantly used by companies for retrospective investigations and not for product release decisions.” She says they are looking at ways to speed up the process.

What are the future developments for WGS?

Sequencing technology will undoubtedly continue to improve and so will the turnaround time as it becomes faster, potentially decreasing the overall cost of sample analysis. Beyond this, the field of metagenomics, where the sequencing is performed on an entire sample to provide a snapshot of a bacterial community, will allow the detection and sequencing typing of many different pathogens in a single assay. Eventually these developments will make the need for isolating pathogens and the use of WGS for individual pathogens obsolete.

As food is a global commodity, there are many consortia working towards establishing common technology and standards with respect to WGS. A shared online global repository or database has been proposed1 and may make in-depth bioinformatic training unnecessary, as well as providing an inexpensive way to store sequencing data. But this also highlights the need for well-controlled, secure and standardised database management, and clear and easy processes to

Whole genome sequencing can help with identifying a source of infection. Bacteria of interest can be isolated from various sources throughout the food chain and their whole genome sequences can be compared to establish whether they are genetically related

upload data to platforms, without advanced technical infrastructure and programming requirements2. Broader acceptance of shared or ‘open data’ would facilitate collaboration across multiple sectors and countries and thus improve the entire process for all users, including industry, the regulators and research organisations. However, there are many complex issues to resolve with respect to data sharing and ownership. The Centre’s Listeria database which enables industry to compare their genomes on a confidential basis, is a good start on this journey.

Director of the NZ Food Safety Science & Research Centre, Dr Catherine McLeod, says, “Despite the daunting list of challenges, genomics and bioinformatics technologies have unstoppable momentum, and will continue to transform our capacity to track and respond to foodborne disease threats worldwide. The Centre will do all it can to help members embrace this future.”

1. Black, A., MacCannell, D.R., Sibley, T.R., Bedford, T. 2020. Ten recommendations for supporting open pathogen genomic analysis in public health. Nature Medicine. 26: 832-841. 2. Food and Agriculture Organization of the United Nations, Applications of Whole Genome Sequencing (WGS) in food safety management 2016: Italy. 1688.