This week at the annual meeting of the Association of Public Health Laboratories in Seattle, officials from the Centers for Disease Control and Prevention – which operates PulseNet – explained the crucial role this pathogen database plays in outbreak detection and the challenges that must be met in order for it to remain effective.   

In December of 2010, 8 people in 3 different states came down with E. coli infections that were eventually linked to hazelnuts from an Oregon distributor. Fifteen years ago these cases most likely would not have been connected, and the outbreak would have gone undiscovered.



But thanks to PulseNet, the government database that tracks DNA information for foodborne pathogens, the pieces of this outbreak puzzle and thousands of others have been put together since the system was launched in 1996. 

Of the 10 largest outbreaks in the U.S. in the last decade, 8 would not have been detected had it not been for information stored in PulseNet, according to John Besser, Deputy Chief of CDC’s Enteric Diseases Laboratory Branch, who spoke Sunday at the APHL meeting.

The ability to identify a pathogen’s unique DNA fingerprint through pulsed-field gel electrophoresis, or PFGE, and to store this data in a central location, has drastically increased the number of outbreaks detected by connecting cases in different states to the same outbreak and by revealing smaller outbreaks in which only a handful of cases may have been reported. 

Beyond improving outbreak detection, PulseNet has increased accountability in the food industry. Pathogens in humans can be more easily linked to pathogens from food or environmental samples with indistinguishable DNA patterns, meaning that suppliers, grocery stores or restaurants responsible for contamination are more likely to be pinpointed. 

“We’ve seen major changes from industry itself through the pressure of outbreaks, recalls and lawsuits,” said Besser. “We’re having continuous feedback to industry and regulatory agencies on the effectiveness of our control programs.”

Future Challenges

But PulseNet – like many government-funded programs – faces uncertainty over how much funding it will receive from year to year. Though 87 public health laboratories currently contribute specimen data to the system, there is still a backlog of samples waiting to be analyzed that can lead to delays in test results. 


CDC was allotted $4 million for PulseNet for the 2012 fiscal year, but it is still waiting on a decision from Congress on its 2013 budget. 

Some state labs also receive supplemental funding in the form of CDC’s FoodNet and FoodCORE programs. States supported by these programs have been able to boost lab capacity but those lacking this funding remain behind in their ability to process samples as quickly as they come in, according to Dale Morse, Senior Advisor at CDC’s Division of 

Foodborne, Waterborne, & Environmental Diseases. 

“By focusing on certain activities they’ve seen dramatic improvements, but the amount of money has still been fairly small in those states,” he told Food Safety News in an interview at the APHL conference.

Another challenge faced by PulseNet is the development of new pathogen tests that don’t depend on cultures, meaning that they can be done rapidly without isolating and growing bacteria or viruses before analyzing them. While these culture-independent tests can be fast, the results they produce aren’t always as accurate as PFGE, and they produce a different characterization of a pathogen from the type recognized by PulseNet.

“One thing we can say for sure is that these tests provide different types of data than the ones we’re used to,” he said, addressing  APHL meeting attendees. “We know how to interpret culture; we don’t necessarily know how to interpret some of the data that is going to be coming our way.” 

The task, Besser says, is to figure out how to adapt case definitions to be able to use information from these new tests while making sure PulseNet is still a universal system.

Several committees are working on redefining case definitions and better understanding the performance of these new tests, he says.  

If PulseNet can evolve to accommodate these new types of information, the process of pathogen identification could potentially be sped up.

“As we all know, culture takes time,” Besser noted. “The whole process is very lengthy and depending on how we do this we can chop days or weeks off of the whole process.”

Another advantage of incorporating results of culture-independent tests is that they could provide better insight into how closely pathogens are related.

“PFGE is not a cladistics test that allows us to assess relatedness,” Besser explained. “There’s some real power in having variable case definitions to increase the power of our analyses.”  

Whatever happens with PulseNet adopting culture-independent tests, it must be decided on in a coordinated effort with input from experts worldwide, notes Besser. And PulseNet must adapt, he says. 

“The technology that will replace PFGE is not yet clear, but a change of technology to one that is not dependent on culture-derived isolates is essential for the continued existence of PulseNet,” he said in an e-mailed statement to Food Safety News.

The reason the German E. coli outbreak linked to sprouts in the spring of 2011 was so devastating was that Germany lacked the coherent pathogen surveillance system that the U.S. has, he says.

Instead the country was relying on a series of new, different tests that made linking pathogens much more difficult.

That’s why Besser says these new analyses must be addressed in a systematic way.

“This issue of culture-independent diagnostics is a high probability, high-impact issue,” he said. “The risks of doing nothing are very high but the benefits of doing something are also very high.” 


PFGE images and charts from the Centers for Disease Control and Prevention