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Beyond PFGE: Genomic Mapping Pinpoints Pathogens

A team of researchers led by food scientists at Cornell University has developed a new, highly accurate approach to identifying bacteria responsible for foodborne illnesses. According to the team, it should allow scientists to identify the culprits of illness outbreaks with unmatched accuracy and eventually replace the current method of pathogen identification.

Outlined by the research team in a study in the December 2011 issue of Applied and Environmental Microbiology, the approach involves mapping the genomes of bacteria strains and retrieving enough genetic information to differentiate each one down to the arrangement of its base DNA. While the concept of DNA sequencing is hardly new, advancements in sequencing technology are continually making the technique faster and more affordable, allowing for new applications such as foodborne pathogen identification.


John David, far left, a technology services engineer with 3M, talks with staff in Professor Martin Wiedmann’s lab – Esther Fortes, foreground, Steven Warchocki and Emily Wright, right. — Photo by Stacey Shackford


The current gold standard for pathogen identification, “pulsed-field gel electrophoresis” (PFGE), involves breaking bacteria DNA into small pieces and analyzing the banding patterns. The technique works to a certain level of precision, but it can lead to inconclusive results when two strains share similar banding patterns. As a result, definitively linking a specific strain to an outbreak can sometimes get tricky.

By comparison, with genomic mapping, epidemiologists can much more confidently associate outbreaks with specific pathogen strains, said Martin Weidmann, Ph. D., food science professor at Cornell University and one of the authors of the study. The result, he said, is better, more accurate epidemiology.


“Every food company is going to be touched by this technology,” Weidmann said. “Even if they’re not responsible for an outbreak, it might help prove their innocence.”

Weidmann and his partners tested their method by mapping the genomes of 47 Salmonella samples, 20 of which were taken from human cases associated with an outbreak related to peppers in salami in 2009 and 2010, while the other 27 represented control samples from various sources. The team was able to differentiate the outbreak-related strains from the control samples with relative ease and speed.     

Epidemiologists have already been using genomic mapping to trace outbreaks in other settings such as hospitals, but this is the first application of the technique in the realm of foodborne illnesses. As technology improves and cost barriers lower, Weidmann predicts more health and government organizations will adopt the genomic approach, though he stressed that the new method will not change the basic processes of epidemiology.

“To detect foodborne illness outbreaks, you need to detect people who are sick and determine that they’re infected by the same organism, then finding what they have in common — their common link. The big bottleneck will still be figuring that out,” he said. “This method becomes relevant once we figure out the source — we can be much better at differentiating it.”

Rapid advancements in genomic  mapping technology have come from the push by the National Institute of Health and the greater medical community to map a human genomes for less than $1,000. According to Weidmann, the average bacterium’s genome is roughly 1,000 times less complex than a human’s, though the costs involved do not scale at quite the same magnitude.

“Unfortunately, you won’t be able to sequence bacteria genomes for a dollar, but they will definitely be in the range of $100,” he said.

As an example of how quickly the technology has progressed, Weidmann cited the speed with which scientists mapped the genome of the bacteria from this summer’s E. coli outbreak centered in Germany. What would have taken months a decade ago now takes days:

“If you look at the European outbreak, we went from knowing nothing to knowing everything about that bacteria in five days,” he said. “It’s actually amazingly fast. We’ve come a long, long way.”

Weidmann said he expects to see organizations first using the genomic method as an additional level of verification beyond PFGE where necessary. Eventually, however, he sees it becoming the new standard.

“Beyond the next three to five years, it has the potential to truly replace the current practice. Of course, I’m a scientist, not someone who can predict the future, but it does change the standard,” Weidmann said. “I think it’s a great example of research becoming very rapidly adopted to improve science.”

Read more in the online study abstract.


Images, including photo of Martin Weidmann, by Stacey Shackford. 

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