Friday, May 13, 2016

Listeria Tracking and Whole Genome Sequencing - How Close is Close

As the CRF frozen produce recall has resulted in a cascade of recalls and millions of pounds of produce being pulled from shelves across the country, one can look at what triggered this - an Ohio Lab finding Listeria in frozen foods and an investigation of a frozen food plant that led to finding the organism in the plant.
According to CDC: Epidemiological and laboratory evidence available at this time indicates that frozen vegetables produced by CRF Frozen Foods of Pasco, Washington and sold under various brand names are one likely source of illnesses in this outbreak. This is a complex, ongoing investigation, and updates will be provided when more information is available.
Further in that report
Whole genome sequencing showed that the Listeria isolate from the frozen corn was closely related genetically to seven bacterial isolates from ill people, and the Listeria isolate from the frozen peas was closely related genetically to one isolate from an ill person. This close genetic relationship provides additional evidence that some people in this outbreak became ill from eating frozen vegetables produced by CRF Frozen Foods.
Whole genome sequencing has had a huge impact on outbreak investigations.  It allows investigators to match the organism involved in an outbreak back to the organisms found in the plant.  Using this output, one can look in time to past illness and do the same matching, what is termed retrospective analysis. But just because that organism is found in food or in the food plant, does that implicate that food? And how close is close when CDC says there is a close genetic relationship? We asked Dr. Edward Dudley of Penn State to provide some insight.
"A 5 base pair difference (or 5 SNPs) is strong evidence that the two are related. [Listeria has 3 million base pairs]  Even within an outbreak, it isn’t unusual for clones to vary by a few SNPs. This is one of the reasons the FDA is sequencing large collections of food borne pathogens including Listeria, in order to get a handle on how much genetic variation exists in natural populations. As we collect more of this data, it will tell us how quickly the DNA of these pathogens change in foods, food processing environments or during an outbreak, informing us how many SNPs should be allowed for us to still make strong case that two isolates are related."
"Keep in mind though, that genome sequencing should not be used by itself to make any conclusions. We still need the epidemiological (epi) data that provides a statistical link between the patient and an event, for example "did patients with Listeria eat frozen vegetables more commonly than healthy individuals during the time frame of the outbreak?”. The genome sequencing of isolates obtained from patient and foods is used to support the conclusions of the epi investigation when isolates from linked sources are found to be highly related on the DNA level."
So in the end, old fashion epidemiological evidence is still needed.   And there is still understanding is needed.  As for produce, many of the companies forced into a recall are doing so without knowing if there is actually Listeria in their product and in the absence of illnesses associated with their product.

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