Pulsenet - Tracking of Foodborne Disease

The US surveillance system for tracking foodborne illnesses, or PulseNet, is 20 years old.  Through time, the technology has improved and its reach is now global. 

In the US, the system is comprised by a network of 83 laboratories linked to the CDC in Atlanta.  Using genetic identification technology, including Whole Genome Sequencing or WGS, it can identify outbreak clusters through matching bacterial isolates involved in cases.  This information is then used to help identify the source of the outbreak.

This article in EMBO is a nice summary of Pulsenet and how it has impacted food safety.

EMBO Reports
http://onlinelibrary.wiley.com/doi/10.15252/embr.201643128/full
Future challenges for tracking foodborne diseases

PulseNet, a 20-year-old US surveillance system for foodborne diseases, is expanding both globally and technologically

Authors - Efrain M Ribot and Kelly B Hise
Centers for Disease Control and Prevention, Atlanta, GA, USA
First published: 19 September 2016Full publication history

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.

Soft Cheese Listeria Outbreak Extends Back 5 Years - The Power of Whole Genome Sequencing

This past week, a California cheese company recalled cheese due to Listeria related illnesses.  CDC released information that there have been 24 cases in 9 different states caused by 5 closely related strains of Listeria.  The cases occurred over a five year period!  

 

The ability to combine this data into one outbreak is incredible!  Whole Genome Sequencing has become a game changer with regard to solving foodborne illness outbreaks.  The entire DNA sequence from pathogens responsible for past foodborne illness cases can be evaluated and matched with those from more recent cases. 

 

This technology also raises the ante for facilities with low level pathogen contamination issues.  Just as was seen with the Blue Bell ice cream facilities, it is more than a matter of checking the environment for Listeria, but enacting a proactive strategy that when contamination is found.  This includes an examination to determine if product has been exposed as well as a carrying out a seek-and-destroy mission to determine all potential sources/ contributing factors within the process environment (recognizing the fact that it is often an on-going battle of control rather than complete elimination).

 

This strategy also includes prevention of contamination - all of those things that come into process environment from outside - whether that is raw materials or even non-food (workers, inspectors, pallets, maintenance tools, carts, forklifts, used equipment, etc).  Who knows, some of this may be coming from a facility fighting its own endemic contamination issue.

 

People infected with the outbreak strains of Listeria monocytogenes, by month of specimen collection*

 

CDC Outbreaks

http://www.cdc.gov/listeria/outbreaks/soft-cheeses-09-15/index.html

Multistate Outbreak of Listeriosis Linked to Soft Cheeses

Posted September 18, 2015 9:00 AM ET

  

Read the Advice to Consumers, Restaurants, and Retailers»(http://www.cdc.gov/listeria/outbreaks/soft-cheeses-09-15/advice-consumers.html)

CDC is collaborating with public health officials in several states and the U.S. Food and Drug Administration (FDA) to investigate a multistate outbreak of Listeria monocytogenes infections (listeriosis). Listeria can cause a serious, life-threatening illness.

• Five rare DNA fingerprints of Listeria are included in this investigation.
• Whole genome sequencing showed that the Listeria strains with the five rare DNA fingerprints are closely related genetically.
• Twenty-four people infected with one of the closely related Listeria strains have been reported from nine states since August 8, 2010.

Blue Bell Ice Cream Recalls All Products, Additional Cases Linked Through Retrospective DNA Matching

The CDC is reporting that 10 Listeria related illnesses dating back to 2010 have been attributed to Blue Bell Ice Cream.  While 8 cases had been reported, the additional 2 cases were identified through a 'retrospective analysis' using DNA data (verified via whole genome sequencing) to match isolates to different illness cases.

Blue Bell had recalled all of its products at all of its facilities.  A very bold move done due of the uncertainty of findings in the facility and inability to find the exact source.

 

 

CDC News Release

http://www.cdc.gov/listeria/outbreaks/ice-cream-03-15/index.html
Multistate Outbreak of Listeriosis Linked to Blue Bell Creameries Products
Posted April 21, 2015 11:45 AM ET
Highlights
Read the Advice to Consumers, Institutions, and Retailers>>(http://www.cdc.gov/listeria/outbreaks/ice-cream-03-15/advice-consumers.html)
Read the Information for Health Professionals>>(http://www.cdc.gov/listeria/outbreaks/ice-cream-03-15/health-professionals.html)
On April 20, 2015, Blue Bell Creameries voluntarily recalled all of its products currently on the market made at all of its facilities, including ice cream, frozen yogurt, sherbet, and frozen snacks, because they have the potential to be contaminated with Listeria monocytogenes. Blue Bell announced this recall after sampling conducted by the company revealed that Chocolate Chip Cookie Dough Ice Cream half gallons produced on March 17, 2015 and March 27, 2015 contained the bacteria.