Innovations in the lab and digital technologies such as artificial intelligence are transforming the detection, tracking, and response to food safety threats, according to scientists.
Experts from Canada, the United Kingdom, and Oman shared their thoughts during the World Health Organization’s (WHO) Alliance for Food Safety webinar on foodborne disease surveillance and contamination monitoring.
The webinar was held as part of the alliance’s annual general meeting this past week, hosted by the Food Safety and Quality Centre of Oman. The event brought together representatives from 40 countries and 90 participants from regional and international organizations.
Celine Nadon, director, enteric diseases, national microbiology laboratory at the Public Health Agency of Canada (PHAC), said taking innovations from the lab to operations is often a critical piece of the lifecycle that gets overlooked.
“All scientists who develop novel approaches are met with a similar frustration, when advancements they know will make a difference are not instantly implemented,” she said.
Navigating change
About eight years ago, PHAC moved from molecular subtyping to genomics.
“Introducing new science into this well-oiled machine was disruptive and created a lot of confusion. Activity can’t stop until we wait for everyone to become experts in genomics. There was a large period where it was very busy with lots of training, knowledge translation and feeling like we were sailing a ship as we were still building it,” said Nadon.
However, Nadon said the outcome was worth it.
“That switch to genomics changed our understanding of strain relatedness and our ability to take public health and food safety action. The change was obvious within weeks. We were able to detect dozens of outbreaks and hundreds of cases and link them to one category of poultry products,” she said.
“This new information led to a collective effort across government that resulted in a change to national food safety policy. After that change, contaminated products and the illnesses associated with them plummeted. This gives concrete evidence to our decision-makers, instead of discussing the potential.”
Nadon said epidemiologists measured the impact of the move one year later. Disease incidence fell by 20 percent and 26,000 illnesses were prevented, corresponding to a saving of CAD $20 million (U.S. $14 million) because of avoided medical costs and lost productivity.
CIDT challenge
Nadon also revealed ongoing work on innovations in the lab.
“The first has to do with genomics and augmented microbiology, this overlays digital information on the microorganisms. We still do microbiology with petri dishes at the lab bench but we now have in-silico. That means doing the work digitally. In the past if you had a foodborne pathogen, you are doing at least five experiments at the bench, determining the species, serotype, molecular subtype, virulence and antimicrobial resistance profile. Now we are doing one test at the bench, extracting the sequence, and the other experiments are done by bioinformatics techniques in-silico.”
The second paradigm shift stems from the split between patient care and public health with culture-independent diagnostic tests (CIDTs).
“In previous decades, the same test used to diagnose the patient with a foodborne disease was also used to inform the public health response and the associated food safety actions. You get a culture from the patient and then it is identified and characterized. Innovations in diagnostic technology now enable you to get that result, bypassing the need for culture. The benefits to healthcare are immense but it leaves nothing for public health,” said Nadon.
“This has put some urgency on the development of new science that would enable public health labs to also bypass the need for culture, using metagenomics and then use bioinformatics to separate the pathogen of interest from everything else.”
Earlier outbreak detection
Amy Douglas, lead epidemiologist, gastrointestinal infections, Food Safety and One Health Division at the UK Health Security Agency (UKHSA), spoke about the use of artificial intelligence.
A 2022 E. coli O157 outbreak with 259 cases linked to UK grown lettuce sold through national fast-food chains prompted scientists to wonder if online reviews could be used for earlier outbreak identification. They used data from Yelp and, after filtering, the team found one million reviews related to eating out or restaurants and 10,000 with foodborne illness related keywords.
“We would identify the relevant premises, sample reviews from those premises, the tool would work through and classify them into those likely reporting gastrointestinal illness and then annotate them with the symptoms and food items mentioned. Outputs would be shared with gastrointestinal scientists or epidemiologists for review, that would be taken forward for risk assessment and it may trigger public health action,” said Douglas.
“We could see how the use of AI alongside traditional epidemiological investigations could facilitate earlier detection of outbreaks and expedite implementation of control measures. However, due to issues with data access the tool is available but not deployed.
“The biggest gains for surveillance and outbreak management will be making better use of the WGS data we hold on gastrointestinal pathogens. That will be through the development of new tools to analyze genomic data. There are a number of considerations when thinking about how to develop and implement AI for public health, such as being aware of its limitations, the outputs still need validation and approval by humans.”
Oman and Qatar
Adel Ben Saed Al Wahibi, director, Epidemiological Surveillance Directorate, at the Ministry of Health in Oman, told attendees about Tarassud, a system used to provide information on infectious diseases.
Oman imports more than 60 percent of its food and must also contend with tourism, mass gatherings, high temperatures and long supply chains. Surveillance challenges include underreporting and weak community reporting, fragmented data flow and deficiencies in lab and analytical capacity.
During the annual meeting, Qatar’s Ministry of Public Health officially joined the alliance for 2025 to 2027. The agency joins network members from countries such as Australia, Denmark, France, Germany, Mexico, Singapore, and Saudi Arabia.
Wasan Abdulla Al Baker, director of the Food Safety Department at the Ministry of Public Health, said: “Our participation in the alliance’s annual meeting represents an opportunity to strengthen international cooperation and exchange expertise and best practices in the field of food safety. It also enables us to contribute effectively to accelerating the implementation of the Global Strategy for Food Safety 2022–2030, enhance Qatar’s global role in the field of food safety, broaden its vision within the international community and increase its impact in promoting global food safety standards.”
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