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2 million base pairs later: CDC stands by DNA evidence

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Last month, when health officials reported they discovered a pathogenic connection between raw milk from a Pennsylvania dairy and two illnesses in 2014 — one in California and the other in Florida — a wave of disbelief and condemnation began rippling out from the raw milk community.

News stories about the announcement from the Centers for Disease Control and Prevention sparked a flurry of online comments from raw milk drinkers and producers who disparaged the government’s science and scientists.

A common thread through many of the posts was disbelief that laboratory analysis could actually prove the pathogen samples from the two patients and the dairy were the same strain of Listeria monocytogenes.

Raw milk advocates questioned why the CDC said only that the samples were “closely related genetically” and that Miller’s Organic Farm in Pennsylvania was the “likely source.” Conspiracy theories about a big government agenda to destroy the raw milk industry emerged as fans of unpasteurized raw dairy products questioned why a specific dairy was being targeted when the CDC would not definitively state their lab analysis was 100 percent correct.

Two million base pairs can’t be wrong
The CDC used whole genome sequencing (WGS) to analyze the DNA of the Listeria from a sample of Miller’s Organic Farm raw milk. That DNA fingerprint of “about 2 million base pairs” was then fed into the PulseNet database, said Matthew Wise, the Outbreak Response Team Lead in CDC’s Division of Foodborne, Waterborne, and Environmental Diseases.

The database already included the DNA fingerprints from the Listeria monocytogenes that sickened the California and Florida patients. When the CDC scientists added the database and ran a search for matches, the connection was discovered.

Matthew Wise

Matthew Wise

“As scientists, we couch it with a little uncertainty, though,” Wise said. “Because we are scientists we know new information can be discovered on Wednesday that we didn’t have on Tuesday.”

Wise said when CDC scientists say something is the “likely source” of an outbreak it has much stronger meaning than the general public probably realizes.

“When we say  ‘a likely source’ it means we have two different lines of evidence showing the same result. It means we are very, very confident we know the source,” Wise said.

Similarly, when the CDC reports a pathogen isolate from sick people is “closely related genetically” to a pathogen isolate from a specific food source, the agency isn’t talking about a shirt-tail relative situation.

“Closely related genetically for us means in the realm of identical twins,” Wise said.

Identical twins are genetically identical because they come from the same egg. They have the same DNA fingerprint, according to the National Institutes of Health, even though their actual fingerprints don’t match.

Raw milk advocates speak out
In addition to doubting the science behind the CDC’s report of the connection between the Pennsylvania raw milk and the Listeria patients in California and Florida, raw milk advocates say the government lied about the Florida patient’s cause of death.

The patient in California reported drinking raw milk before becoming ill, according to the CDC’s report. Family members of the Florida patient, who “died as a result of listeriosis,” told outbreak investigators that the patient drank raw milk before becoming ill. The family “reported purchasing raw milk from Miller’s Organic Farm,” the CDC reported

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Storage area for raw dairy products at Miller’s Organic Farm.

The Weston A. Price Foundation of Washington D.C., which is a non-profit group that annually produces an international raw milk trade show and conference, claims a family member of the Florida patient says the woman died as a result of cancer and chemotherapy treatment.

A woman identified by the Price Foundation as Peggy Stevenson, who purports to be the sister-in-law of the son of the Florida patient, said through the foundation that she was a caregiver for the patient.

“My family member was diagnosed with and died of cancer after a week of chemo,” Stevenson said in the Price Foundation news release. “I am outraged that the CDC is using our tragic situation to damage and try to destroy a farm we love and support.”

Attempts to reach Stevenson were unsuccessful. The Price Foundation did not respond to a request for assistance in reaching Stevenson for comment. The foundation’s president Sally Fallon Morell said in the release that the CDC report is just plain wrong.

“This recent release from the CDC is a deliberate attempt to tarnish raw milk and present false and defamatory information,” Morell said in the release. “This is a witch-hunt against raw milk. This is clearly not a case of illness associated with raw milk, but rather an agency with an agenda.”

A spokeswoman with the CDC said the agency does not routinely determine the cause of death, which is reported to the federal agency by the state where the death occurred.

“In this outbreak where raw milk was implicated, the Florida Department of Health informed CDC that an ill person in Florida died as a result of listeriosis. This is typically based on information gathered through a review of medical records and the death certificate,” the CDC spokeswoman said.

Florida officials confirmed Monday that they reported to the CDC that there was a Listeria patient in 2014 who died, but the state cannot release extensive details to the public.

“We cannot comment on details relating to a specific individual due to patient confidentiality,” said Mara Gambineri, communications director for the Florida Department of Health. “

“However, I can confirm that we did have a case of listeriosis in Florida related to Miller’s Organic Dairy Farm and that the person did pass away. We cannot comment on cause of death.”

The CDC didn’t find the connections between the 2014 illnesses in Florida and California until early this year because sequencing the listeria DNA in the raw milk from Miller’s Organic Farm didn’t begin until late in 2015. In November, public health officials in California collected samples of the unpasteurized raw milk from Pennsylvania during the Price Foundation’s annual raw milk conference.

DNA sequencing helps detect outbreaks faster
In addition to discovering outbreaks after the fact, officials and scientists from local to federal levels say DNA fingerprinting of pathogens helps identify outbreaks while they are happening, which means fewer people are exposed.

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The Listeria Whole Genome Sequencing Project, launched in September 2013, had cracked the DNA code on about 2,300 isolates by February 2015, according to the CDC’s project website. State laboratories, the CDC, the Food and Drug Administration, the U.S. Department of Agriculture’s Food Safety and Inspection Service, and the National Center for Biotechnology Information are collaborating on the project.

“What we eat and how we eat in the United States has changed. In the early 1900s, most food was consumed close to where it was produced. Food safety gaps were usually discovered only when groups of people in the same location became ill, such as picnics or schools,” according to the CDC’s website.

“In the last half-century, food production has become increasingly centralized, and food products are often transported great distances before arriving at our dinner tables. Illnesses caused by errors in food production can sicken people over a wide area and may not be recognized as a problem in any one community.”

Before technology advances made whole genome sequencing (WGS) fast and affordable, the CDC and FDA mostly relied on pulsed-field gel electrophoresis (PFGE) molecular typing to identify foodborne pathogens.

The CDC’s Wise said PFGE was helpful, but not even in the same ballpark as WGS in terms of detecting or investigating foodborne illness outbreaks. He said some Salmonella, for example, have PFGE results that are very similar when the Salmonella isn’t related and vice versa.

“WGS gives us more certainty that two isolates are the same,” Wise said. “And it shows us more than PFGE, such as antibiotic resistance. WGS is altering the landscape of foodborne outbreak investigation. It’s an incredible toe hold for investigators.”

The value of WGS had already been proven

As more isolates of pathogens such as Listeria monocytogenes, E. coli and Salmonella are decoded by WGS, the more connections between seemingly unrelated illnesses will be discovered, Wise said.

The WGS technique helped detect a Listeria outbreak in 2014 linked to caramel apples. In that outbreak, 35 people in 12 states contracted listeriosis from eating caramel apples. Seven people died.

Ultimately the California apple grower-shipper who supplied the apples recalled its entire crop of galas and granny smiths, which health officials say reduced the number of people who got sick.

In 2015, WGS connected 24 illnesses reaching back to 2010. The source was found to be soft cheeses produced by Karoun Dairies of San Fernando, CA.

“Suddenly, we went from just a few cases … to upwards of 20,” epidemiologist Brenda Jackson told Food Safety News in 2015. “Once we had those numbers, it was fairly easy to see that there was a signal for soft cheese.”

Whole genome sequencing also helped investigators with the 2011 E. coli O104:H4 outbreak in Europe, which prompted a rapid scientific response.

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