New Technique Puts DNA Profiling of E. coli on Fast Track

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Thomas Whittam, Hannah distinguished professor, has developed a new technique to test the DNA of E. coli bacteria. (view larger image)

Using new genetic techniques, MAES scientists are unlocking the secrets of how E. coli bacteria contaminate food and make people sick.

MSU has developed a new technique to test the DNA of E. coli bacteria by examining very small genetic changes called single nucleotide polymorphisms or SNPs (pronounced “snips”). Using SNPs, scientists were able to genetically analyze 96 markers—a rate never before accomplished in pathogenic bacteria.

“It used to take three months to score one gene individually,” said Thomas Whittam, MAES scientist and Hannah distinguished professor at the National Food Safety and Toxicology Center at MSU. “Now, we are working on a new, more rapid system that can do thousands of genes per day.”

In a new study released in the March 10 edition of the Proceedings of the National Academy of Sciences, “Variation in Virulence Among Clades of Escherichia coli O157:H7 Associated With Disease Outbreaks,” Whittam and his co-authors looked at the DNA of more than 500 strains of a particularly dangerous member of the E. coli family, O157:H7. In collaboration with David Alland of the University of Medicine and Dentistry of New Jersey, Whittam discovered that individual bacteria could be separated into nine major groups, called clades.

E coli makes people sick because the bacteria produce toxins, called Shiga toxins, which block protein synthesis, an essential cellular function, particularly in the kidneys. What Whittam found was that the various clades produced different kinds of Shiga toxins in varying amounts on the basis of their DNA.

“For the first time, we know why some outbreaks cause serious infections and diseases and others don’t,” Whittam said. “The different E. coli groups produce different toxins.”

Rapid genetic characterization also opens up a new world of possibilities for identifying the bacterial culprits in outbreaks and finding out where they originated.

E. coli bacteria usually come from animal waste contaminating sources of human food or water. Finding out how the bacteria entered the food source always has been a challenge, but now food safety experts can use DNA just as police use DNA at crime scenes. Scientists will be able to identify those bacteria making people sick, find out where they entered the food source and then use this information to reduce contamination.

“This is the first time anyone has been able to classify very closely related groups,” Whittam said. “This is also the first time we can tell the differences in how they cause disease.”

Whittam also has plans to use this methodology to study other bacterial strains, such as Shigella, a major cause of diarrhea around the world.

“This new equipment can be used to identify hundreds of thousands of pathogenic bacteria,” Whittam said.

The research is supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health through the Food and Waterborne Diseases Integrated Research Network.

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