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Whole Genome Sequencing Pinpoints Single Case and Potential New Listeria Source

The AMD program, which began in 2014, represents a significant leap forward for CDC’s advanced sequencing and bioinformatics capabilities. Prior to receiving AMD funding, CDC incorporated genetic sequencing methods in some infectious disease outbreak responses. This “AMD in Action” story about CDC’s pre-AMD funded work foreshadows the more robust and far-reaching effort launched in 2014—an escalated attack on infectious disease outbreaks that is proving to be better, quicker, and cheaper.


During routine food testing, the Canadian Food Inspection Agency found Listeria in bagged lettuce that had been grown in the United States. The Canadian scientists had not anticipated finding contamination, but when they did, they worked with the U.S. Food and Drug Administration to conduct a recall.

Still, an important question remained: had anyone gotten sick as a result of eating that lettuce?

Lettuce recalls happen frequently. But health officials had never before seen Listeria cases associated with lettuce. When investigators at the Ohio Department of Health examined data from pulsed-field gel electrophoresis (PFGE) DNA testing, they found a strain of Listeria that had recently infected an Ohio resident had a matching PFGE pattern. The patient had eaten bagged lettuce but could not recall the precise brand. The lettuce had already been recalled; so no one else was at risk.

Because this PFGE pattern is relatively common, Canadian and CDC investigators conducted whole genome sequencing to see if they could strengthen the connection. Scientists found one of closest matches they had ever seen.

Although investigators cannot say with certainty that the patient acquired the illness by eating contaminated lettuce, this event demonstrated that whole genome sequencing can identify single cases at a level of confidence that is not possible with the longstanding PFGE method.

The investigation also identified a likely new vehicle for Listeria infection, prompting CDC officials to add lettuce to questionnaires used to assess sources of Listeria infection.

  • Page last reviewed: August 25, 2014
  • Page last updated: August 25, 2014
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