John Besser, CDC, 2018 Food Safety Consortium

CDC: Quite a Year for Outbreaks, Exciting Time in Food Safety

By Maria Fontanazza
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John Besser, CDC, 2018 Food Safety Consortium

2018 was a busy year for multistate foodborne illness outbreaks, and the CDC has been leveraging whole genome sequencing in its traceback investigations.

This year Salmonella outbreaks hit chicken, shell eggs, ground beef, pre-cut melon, dried and frozen coconut, pasta salad, chicken salad, turkey, ground beef, raw sprouts and breakfast cereal. There were also significant Cyclospora infections linked to salads sold at McDonalds as well as vegetable trays. For the first time in 10 years, a Listeria outbreak was linked to an FSIS regulated product (deli ham); ground beef was affected by E. coli O26. And perhaps the most notable outbreak of the year was the E.coli O157:H7 outbreak linked to romaine lettuce from the Yuma growing region.

“It’s been quite a year for outbreaks,” said John Besser, Ph.D., deputy chief, enteric diseases laboratory branch, at CDC, referring to the pathogens that have plagued a variety of consumer products in 2018. “Out of this group, there are a lot of the things you’d expect, but also some brand new unexpected [products affected] like shredded coconut and Honey Smacks cereal.”

Despite the number of outbreaks that have hit the food industry in 2018, “this is a really exciting time to be in public health and food safety, because there are a lot of tools we can use to help make food safer,” said Besser. Most of the diseases that impact the food industry are preventable if their source can be identified, and using big data can have a tremendous impact on improving food safety.

Yesterday John Besser informed attendees at the 2018 Food Safety Consortium about CDC’s latest efforts in foodborne disease surveillance, which he defines as the
systematic collection, analysis and interpretation of health data. The agency is actively working to identify unrecognized gaps in the food supply chain and provide the industry with information it can use to make products safer. “The most important reason for detecting outbreaks is so we can identify the problem and fix it,” said Besser.

There are two ways that CDC detects outbreaks. The first is via the “citizen reporters” who are observant and alert the agency. (This is actually how E.coli O157 was discovered). The second is through pathogen-specific surveillance where CDC takes lab information and links cases that are geographically diverse. These cases are often widely dispersed and are the most effective way to find food production and distribution problems, and are often easier to address than local issues, according to Besser.

He went on to review the successes of PulseNet and the promise of whole genome sequencing (WGS) and metagenomics. The CDC’s PulseNet nationwide WGS implementation project is underway and will result in a “tsunami of data”, with the timeline as follows:

  • January 15, 2018: Listeria monocytogenes
  • October 15, 2018: Campylobacter jejuni/coli
  • January 15, 2019: Diarrheagenic E.coli (including STEC)
  • March 15, 2019: Salmonella enterica

Metagenomics will continue to play a large role in enabling unbiased sequencing of all nucleic acids in an environment. It will help to directly characterize sequences from samples, food and people (i.e., the gut), and could aid in pathogen discovery.

“I think within just a few years, it’s going to be the standard for tests,” said Besser. “My prediction is that you’ll be able to do this test in the production environment.”

Deadly Outbreaks and the Role of Metagenomics

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Maria Fontanazza, Food Safety Tech

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