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How the CDC Stops Foodborne Illness From Spreading

And why the Trump administration’s budget cuts could put diners at risk

What happens when you get sick after eating out? For many people, the answer is, “I write a poor review on Yelp.” Unfortunately, that is not the best course of action from a public health perspective. A visit to the emergency room for a proper diagnosis is the first step in the process of protecting the public from foodborne illness.

In the United States, diners can be relatively sure that any establishment they visit for a meal undergoes regular health inspections, and that the food supply itself is safe. But people still get ill from eating contaminated food, and most are unaware of the system that engages when something goes awry.

Operated by the Centers for Disease Control (CDC), PulseNet is a network of laboratories and a database that works to protect diners from foodborne illness in the U.S. When a person gets sick and goes to the doctor or emergency room, historically, a stool sample is taken, and a sample is grown in a petri dish. The result is called an isolate, or molecular fingerprint, and it is sent to a public health laboratory where its DNA is tested to figure out if it is the same type of bacteria or subtype of bacteria that is making other people sick. The molecular fingerprint of the bacteria is then sent to the CDC, and added to a database to be stored for future comparisons.

Without PulseNet, outbreaks could occur more frequently, spread more rapidly, and be more costly — in dollars and lives. A report from the CDC describes the investigation that discovered an outbreak of salmonella from contaminated truffle oil. It began in a restaurant in Washington, DC and was eventually linked to other locations of the same restaurant chain, Fig & Olive, across the country. Cooperation between local health departments, emergency departments, and the media, along with the use of PulseNet led to a quick containment of the outbreak.

There are some challenges currently facing the system, though, primarily due to the Trump administration’s ongoing promise to repeal the Affordable Care Act (ACA), which supplies a chunk of PulseNet’s funding. A change in how labs carry out diagnostic tests and a shift to more precise and accurate technology — which requires state approval — are other areas of concern.


“Changing diagnostics are making it difficult to do the [molecular] fingerprinting,” says Shari Shea, director of food safety at the Association of Public Health Laboratories (APHL). There’s an important distinction between PulseNet labs getting an actual specimen from an individual, and getting the isolate from a lab. She says that the industry is “moving away from culturing and getting isolates to doing molecular tests directly on your stool. That’s one of the challenges facing PulseNet right now.”

Since the early 1980s samples have been cultured in labs. This is a tried-and-true method, used all over the world. However, new tests have been developed that allow testing to happen in physician’s offices, or in hospital labs. These direct tests are fast, and from the doctor’s and patient’s perspectives, great news: complete the test, find out what is making the patient sick, move forward with a treatment.

Peter Kyriacopoulos, senior director of public policy at APHL, says these new tests disrupt the flow of information to the public health laboratories. “That means is that, yes, an individual has been successfully treated,” he says, “but we don’t have the right information to stop other people from getting sick.”

An ongoing outbreak of E. coli infections related to I.M. Healthy Brand SoyNut Butter illustrates the importance of information flowing to public health laboratories. In the course of that investigation, two people who had consumed I.M. Healthy Brand SoyNut Butter the week before becoming ill were excluded from the CDC case count because no bacterial isolates were available for DNA fingerprinting.

Kyriacopoulos says that this is especially challenging “because we are talking about the doctors’s laboratories using the latest technology — which is great.” The unintended consequence is that essential information, needed to further identify the source of an outbreak, often does not make its way to the CDC.

The second challenge currently facing PulseNet is also related to technology, but has a clearer resolution. The labs that make up PulseNet are moving from a technology called pulsed-field gel electrophoresis (PFGE) to the newer and more precise technology of whole genome sequencing (WGS). WGS allows scientists to examine the full genome of the bacteria — allowing experts to understand if outbreaks in different places may or may not be linked — rather than a smaller piece of it.

The outbreak of illness related to Blue Bell Creameries’ ice cream a couple of years ago demonstrated the importance of WGS technology in tracking foodborne illnesses. In 2015, the CDC was investigating a listeria outbreak that appeared to be linked to Blue Bell’s products. The company recalled the products that were associated with the outbreak, which were single-serve ice cream scoops and milkshakes. Eventually, Blue Bell Creameries chose to take all of its products off of the market and all four plants underwent a cleaning and sanitizing regime. All employees received related training.

Though it is quite uncommon for listeria to grow in ice cream due to the temperature at which it’s made and stored, around the same time as Blue Bell’s outbreak, listeria was detected in products from another ice cream manufacturer, Jeni’s Splendid Ice Creams. Investigators were able to determine, via WGS testing, that Jeni’s outbreak was not related to Blue Bell’s; these were two separate strains of bacteria.

“Looking at it with the older technology, it was not clear that there was more than one source for that particular outbreak,” Kyriacopoulos says. “But then when they did the genetic sequencing, they discovered there was, in fact, a distinct difference in the illness that people had from eating Blue Bell and the illness people had from eating something that ultimately turned out to be Jeni’s.”

The transition from PFGE to WSG is well underway. According to Shea, the newer technology is available in 46 states and the CDC’s plan to drop the older technology by the end of 2018 is on track. Kyriacopoulos adds that states that do not currently have the technology in place have at least secured funding, and “it’s winding its way through their state procurement process.”

Finally, as with any publicly funded program, an on-going threat to PulseNet is funding. The efforts to repeal the ACA have been hair-raising for those who work in public health laboratories. When most people think of the ACA, they think about the individual insurance market. But when it was passed in 2010, the law also increased funding for public health activities.

Specifically, the ACA added to the budget of a program called the Epidemiology and Laboratory Capacity for Infectious Diseases Cooperative Agreement (ELC), which provides funding to the public health laboratories that make up PulseNet. The ACA added a total of $40 million per year to the budget of the ELC through the Prevention and Public Health Fund (PPHF), which is the only mandatory public health funding program in the country.

Kyriacopoulos says the ELC “had been getting somewhere around $50 million a year,” so the PPHF nearly doubled the budget available. In addition to it being more money, he says, “that additional money was much more flexible for our member laboratories.” The flexibility allowed the labs to hire more people, and importantly, allowed for those people to be cross trained. Kyriacopoulos explains that the money in the base amount is tied pretty precisely to particular activities. “The food money had to be spent on food, the vector money had to be spent on West Nile,” he says. “But this new money wasn’t constrained like that, so that meant there were a lot of folks who could move into any of those other categories as the need came up.”

Although a recent effort to repeal the ACA failed, the Trump administration and Senate Republicans continue to talk about their desire to revoke the law. For the moment, public health laboratories have the necessary funding to continue protecting diners. Hopefully, for the sake of diners across the country, any future efforts to repeal and replace the ACA will take public health funding into consideration.

Dava Stewart is a contributor that writes about healthcare, technology, and genomics.
Editor: Daniela Galarza

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