At the recent annual meeting of the Association of Public Health Laboratories
in Seattle, Washington, USA, officials from the Centers for Disease Control and
Prevention explained how its foodborne pathogen database, PulseNet, aids in outbreak detection as well as future challenges CDC
anticipates.
PulseNet, launched in 1996, identifies the DNA information for foodborne pathogens, including those in petfood, using pulsed-field gel electrophoresis. The pathogen DNA information is then stored in a central database, which can then link cases in different states to the same outbreak. Because PulseNet uses DNA information to link illnesses to pathogens from human food, petfood or environmental samples, the contamination source is more likely to be identified.
However, a future challenge for the PulseNet database is the variable amount of funding it is expected to receive over the years. Congress gave CDC US$4 million for PulseNet for fiscal year 2012, but has not yet received its funding allotment from Congress for 2013.
According to Dale Morse, senior advisor at CDC's Division of Foodborne, Waterborne, & Environmental Diseases, some state labs receive supplemental funding from CDC's FoodNet and FoodCORE programs, which boosts lab capacity, but also means that many states lacking funding are behind in processing samples as soon as they come in.
"By focusing on certain activities they've seen dramatic improvements, but the amount of money has still been fairly small in those states," Morse said.
Additionally, PulseNet is challenged by the development of new pathogen tests that do not depend on cultures and use different a different pathogen characterization from that recognized by PulseNet. The new pathogen tests are fast, but do not isolate or grow bacteria or viruses before analyzing them, making them less accurate than current pathogen tests, Morse said.
"One thing we can say for sure is that these tests provide different types of data than the ones we're used to," said Morse. "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."
John Besser, deputy chief of CDC's Enteric Diseases Laboratory Branch, said several committees are working to better understand the performance of the new pathogen tests and adapt case definitions to use these new tests, which could speed up the current testing process and provide a better understanding of how closely pathogens are related.
"As we all know, culture takes time. The whole process is very lengthy and depending on how we do this we can chop days or weeks off of the whole process," Besser said. "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."
PulseNet, launched in 1996, identifies the DNA information for foodborne pathogens, including those in petfood, using pulsed-field gel electrophoresis. The pathogen DNA information is then stored in a central database, which can then link cases in different states to the same outbreak. Because PulseNet uses DNA information to link illnesses to pathogens from human food, petfood or environmental samples, the contamination source is more likely to be identified.
However, a future challenge for the PulseNet database is the variable amount of funding it is expected to receive over the years. Congress gave CDC US$4 million for PulseNet for fiscal year 2012, but has not yet received its funding allotment from Congress for 2013.
According to Dale Morse, senior advisor at CDC's Division of Foodborne, Waterborne, & Environmental Diseases, some state labs receive supplemental funding from CDC's FoodNet and FoodCORE programs, which boosts lab capacity, but also means that many states lacking funding are behind in processing samples as soon as they come in.
"By focusing on certain activities they've seen dramatic improvements, but the amount of money has still been fairly small in those states," Morse said.
Additionally, PulseNet is challenged by the development of new pathogen tests that do not depend on cultures and use different a different pathogen characterization from that recognized by PulseNet. The new pathogen tests are fast, but do not isolate or grow bacteria or viruses before analyzing them, making them less accurate than current pathogen tests, Morse said.
"One thing we can say for sure is that these tests provide different types of data than the ones we're used to," said Morse. "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."
John Besser, deputy chief of CDC's Enteric Diseases Laboratory Branch, said several committees are working to better understand the performance of the new pathogen tests and adapt case definitions to use these new tests, which could speed up the current testing process and provide a better understanding of how closely pathogens are related.
"As we all know, culture takes time. The whole process is very lengthy and depending on how we do this we can chop days or weeks off of the whole process," Besser said. "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."
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