Influence of Whole Genome Sequencing growing beyond listeria – The Packer

CHICAGO The rise of whole genome sequencing is changing the way state and federal health officials are responding to foodborne illness outbreaks.

Speaking at the May 8-11 Food Safety Summit in Chicago, Matthew Wise, lead for outbreak response team at the Centers for Disease Control and Prevention, said the use of whole genome sequencing is an improvement over DNA sequencing techniques in trying to connect potentially related illnesses.

That DNA fingerprinting system has been very very successful but there are times that it doesnt work very well, Wise said. The whole genome sequencing really has the opportunity to address some of the gap.

Calling whole genome sequencing a much higher resolution picture of the bacteria making people sick, Wise said the CDC can compare the bacteria found in victims with bacteria found in food production environments. It gives us more confidence to be able to (know) that those in fact are connected in some way or another, he said.

For testing of listeria, whole genome sequencing started in 2013 with a pilot project between the Food and Drug Administration, the CDC, the U.S. Department of Agriculture and the National Institutes of Health.

Essentially all the agencies agreed to sequence all the listeria starting in 2013 and now it is a routine part of public health surveillance.

In coming years, Wise said there will be more and more investment by state and local health departments to have sequencing capacity.

We are getting to a point where salmonella and all Shiga toxin-producing E. coli will be sequenced, just as is being done for listeria, he said.

I think potentially this will mean (the ability) to identify a lot more outbreaks, and give us more confidence when starting (outbreak) investigations.Whole genome sequencing is having an impact on the decisions that the CDC makes every day concerning outbreak investigations, he said.

The technology has helped the CDC exclude people that are not a part of an outbreak, and also has demonstrated that some (events) that look like an outbreak actually were not.

The other thing it has showed us is that there are people that might appear unrelated to one another that we wouldnt have thought were connected in the past when we get that high-resolution genomic data we see that they are connected and we should investigate them together.

The technology also has helped the CDC understand the pathology of pathogen reservoirs in the environment of food protection, and whether those trouble spots have been around a long time.

Outbreak response capacity is increasing, with 28 states or jurisdictions getting extra money from the federal government to have more boots on the ground to interview people when they get sick.

The FDA also is giving money to the states to increase the capacity of rapid response teams that give additional resources for state level outbreak investigations, Wise said.

Wise said the growing role of food and environmental isolates in outbreak investigations is largely a function of whole genome sequencing.

Now we have so much more confidence that a food or environmental isolate is linked to cases with that same bacteria. It gives us more of a toehold to ask the right questions about what might be causing the outbreak, he said. In the past, health officials looked for an outbreak by seeing a lot of people get sick at once and interviewing them to try to figure out what happened.

Now we are having more outbreaks where we might find a bacteria in a food or environment and then look backward to see if they are linked to those (illnesses), almost reverse investigations conducted sometimes, he said. Wise said the CDC is really trying to move toward methods of outbreak response that are targeted at getting actionable information quickly.

When we find there is actionable advice that consumers can take to protect themselves, thats the point where we think about pulling the trigger and communicating, he said. We have made a lot of efforts to make that process more systematic and have more identifiable triggers to decide to take that action, he said.

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Influence of Whole Genome Sequencing growing beyond listeria - The Packer