Scientists have given a preview of a forthcoming publication on the use of Whole Genome Sequencing (WGS) in food safety.
The World Health Organization (WHO) will launch a guide in July that outlines the capacities that need to be in place before WGS can be useful for foodborne disease surveillance and outbreak response; options for implementing it; and how to integrate WGS within existing systems.
Dr. Eric Brown, from the Center for Food Safety and Applied Nutrition (CFSAN) at the U.S. Food and Drug Administration, said WGS has been one of the greatest recent impacts in science.
“For us, WGS has been tantamount, to an advancement in food safety, as the Hubble telescope has been for astronomy, to put it in perspective and that is not an understatement. There is no question that WGS has revolutionized the way we can monitor and survey for contamination in the food supply,” he told attendees of a WHO Health Talks webinar.
Development of WGS use
Two incidents highlighting the power of WGS in the early days of its use were shared by Brown.
“One involved nut butter, because we saw illnesses across multiple parts of the country, just 2 or 3 illnesses, we were able to put those together with high-resolution WGS, figure out a nut butter contamination event was beginning to emerge, and stop it before it became an outbreak. The second was a Latin-style cheese event where we were able to link multiple states on the East Coast back to a common cheese provider. It meant we could now sort through a large area of geography quickly and link related illnesses and contaminated products as quickly as possible.”
Brown said the paradigm shift was using WGS for traceability with data openly available in real-time.
“This gave rise to the field of genomic epidemiology, where instead of epidemiology always leading the way, sometimes a genomics signal could be produced early that might show a linkage, and then epidemiology can trace that back and forward,” he said.
“A few characteristics of WGS that make it so powerful are fewer clinical cases are needed, much higher unambiguous scope and definition of an outbreak, we can determine what is related or not more quickly, we can also do source tracking now. Raw ingredients can be traced and this gives rise to enhanced root cause analysis because it can tell you what raw ingredient from what part of the world contamination might be coming from. Complex food vehicles like a salad can have ingredients that start anywhere around the world.”
Brown cited two recent examples of data sharing in the GenomeTrackr database.
“In a series of events related to tahini that was exported internationally, multiple countries were able to identify a common source of tahini contamination. Another example is the Listeria outbreaks associated with enoki mushrooms. This involved four countries in particular: Australia, South Korea, Canada, and the U.S. who shared their data and you could see a linkage from a root cause that came out across multiple countries,” he said.
“Right now we continue to improve the process and the database with greater data integrity, capacity building to get the technology in more people’s hands around the world and make sure we can share as much as we can in real-time. As my FDA colleague Marc Allard likes to say, for every thousand genomes we can get into the database, we can prevent six more illnesses each year. We now know increased use of WGS leads to more outbreaks and contamination events that we can identify and that equates to fewer sick people.”
Key components of the WHO guide
Dr. Kirsty Hope, manager of the Foodborne and Waterborne Diseases and One Health Branch in New South Wales, Australia, said early detection helps to reduce the burden of disease in the community.
“WGS has greater sensitivity and specificity in foodborne pathogen sub-typing. It gives a lot of information on virulence factors and antimicrobial resistance. It allows us to compare strains nationally or internationally. The module enhances our routine surveillance in place already for foodborne pathogens, allows for outbreak detection, helps in outbreak response, and incorporates the One Health response, with animal health and food safety people, laboratories, and databases of sequences and isolates that allow early detection,” she said.
The WHO guidance document covers principles to consider when deciding if it is appropriate to use WGS. Countries need an established surveillance and response system that can be built on. There is a need for political and financial buy-in and a resource burden when using WGS. Three modules include the introduction, surveillance and outbreak investigations.
“We tried to recognize that countries are all at different places in their development and use of WGS, the modules are set up so you can pull out a component and use it solely or you can use the whole document. The first module defines the minimum capabilities that are needed before a country can embark on this journey of WGS to enhance outbreak investigations and routine surveillance. It also gives them options of different ways to implement WGS,” said Hope.
“The second module is about outbreak investigations and how to use WGS. It is meant for countries at the initial stages of lab-based surveillance for food pathogens so you can start building on that. It talks about how you can use it to detect outbreaks and the response process. The third module is around surveillance. It is for countries that have a lab-based surveillance system and it has been in use for quite some time. There is some overlap between the outbreak and surveillance modules. The modules are used as a process to help you step through, think about, and plan within your countries and different agencies on how to move forward with WGS.”
Case studies by the CDC, UKHSA, and PHAC and mock outbreaks are included in the guidance.
“For surveillance and response, we are trying to stop illnesses from occurring and taking public health action. To do that we use information from epidemiologists and our food safety and animal health colleagues. WGS is one part and is helping to do our work with more precision but traditional epidemiology and collaboration is still required. It’s also important to be clear on the questions you are asking to get the answers you want or you may get more questions,” said Hope.
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