Food scares: How IT helped stop E.coli outbreaks

Computerworld - Editor's Note: You may not have seen this story during the holiday rush, but we felt it was too good for you to miss.

In September and October, 199 people in 26 states across the nation started getting sick after eating E.coli-contaminated food, and patterns quickly began to emerge in data reported to the Centers for Disease Control and Prevention (CDC) in Atlanta.

Using a software analysis tool that looks through a central database of stored DNA fingerprints from suspected disease-carrying bacteria, scientists and health officials were able to link the illnesses around the country to consumption of packaged spinach that was contaminated with E.coli 0157:H7 bacteria. Three people died from the outbreak.

Earlier this month, the same software helped find and analyze the cause of food-borne illnesses reported by 71 diners in several Taco Bell restaurants in the Northeast. That E.coli contamination was most likely caused by lettuce used by the chain, the CDC concluded.

The CDC system, called PulseNet, stores the electronic DNA fingerprints of bacteria sent by health officials around the country after severe illness cases appear in local communities. PulseNet can be accessed by health officials to look for wider patterns that link the cases, even when they occur hundreds or thousands of miles away.

"We actually noticed the increase in cases in PulseNet," said Kelley Hise, a PulseNet database team leader at the CDC. By having a centralized repository for incoming case data from sickened people across the U.S., officials were able to link the cases and find the causes of the illnesses.

The data is placed into the PulseNet system by local health authorities after they do laboratory analyses of bacteria samples taken from patients. The samples are analyzed by local officials through a process called standardized molecular subtyping, which creates a DNA fingerprint of the bacteria, according to the CDC.

The subtyping is done through a process called pulsed field gel electrophoresis (PFGE), which is used by scientists to distinguish individual strains of food-borne bacteria and organisms. Once the subtyping is completed, the data is entered into the national PulseNet system, where it can be accessed by other public health officials.

"They will type it to look for what bacteria they're dealing with," Hise said. The PFGE process takes the DNA of the organism and cuts it in certain places, creating a pattern or fingerprint that can be used to identify what it is, she said.

PulseNet uses a customized version of an off-the-shelf Windows application called BioNumerics V 4.5 from Applied Maths NV in Sint-Martens-Latem, Belgium, to conduct the comparisons and analysis of the samples in a SQL Server database, according to the CDC.