Wednesday, December 6, 2023

Whole genome sequencing and food safety

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ATLANTA — “We are transitioning from pulse field gel electrophoresis to whole genome sequencing, which is faster and has a reduced cost and increased discriminatory power,” said Dr. Haley Oliver, associate professor of food science, Purdue University, during her presentation at the “Whole Genome Sequencing-Food Safety Implications” education program held during the 2017 International Production & Processing Expo. The event was sponsored by U.S. Poultry & Egg Association and the North American Meat Institute.

Oliver discussed the human health burden of known foodborne diseases in the U.S. and the progress achieved to identify them, particularly through whole genome sequencing (WGS). She observed that all states will soon have this technology available to them through Genome Trackr.

The data housed in public databases can be accessed by researchers and public health officials for real-time comparison and analysis that promises to speed foodborne illness outbreaks investigations and reduce foodborne illnesses and deaths.

Oliver remarked that WGS will become less expensive and databases will grow rapidly with the inclusion of environmental isolates. Thus, more outbreaks will be linked from environmental samples.

In his presentation on “Whole Genome Sequencing Use in Outbreak Investigations,” Dr. Matthew Wise, outbreak response team lead, Centers for Disease Control & Prevention, discussed the changing landscape around foodborne diseases in the U.S. He remarked that food production and distribution has changed substantially during the last several decades. There are fewer producers, but they have wider distribution. There is also more “ready-to-eat” food and industrially-produced food. These changes have influenced the types of outbreaks that occur.

Wise stated that WGS has helped increase the confidence that bacteria from people and foods are connected in some way. “Sequence-based surveillance is going to result in detecting more outbreaks, which will be smaller and more ‘solvable.’ Illnesses, too, that are far apart in both time and geography will be linked together to investigate a potential common source,” commented Wise.

From an industry perspective, both USPOULTRY and NAMI expressed concern that WGS will alter the way investigations are conducted, specifically the role it may have in epidemiological investigations as the technology advances. The industry will need to learn the technology, its uses and impacts and how best to interpret the results. Among other concerns are questions such as: How balanced is the data? How secure is Genome Trakr? Are there any legal ramifications of test results?

“We need industry concerns addressed before we can proceed with any activity related to WGS. Most importantly, we need the time and space to learn how to use WGS to improve public health and protect our industries,” remarked Rafael Rivera, manager of food safety and production programs, USPOULTRY.

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