New Genome Sequencing of 2011 E. Coli Outbreaks in Europe Provides New Clues Into Origins the of Disease
May 7, 2012 by Dian Cai
The European E.coli outbreak made headlines last summer as the death toll mounted to 50, as 4,000 suffered bloody diarrhea, and as an unprecedented number of victims suffered kidney failure.
This was the largest outbreak of foodborne E.coli illness on record, but it could have been worse. Investigators used a high-speed DNA sequencing technology to track the epidemic to its source and wrestle it to an end.
U.S. experts are impressed with how fast this tool can pinpoint the origins of an outbreak.
“Using this fast and effective high resolution tool will greatly enhance our ability to prevent future food-borne outbreak in U.S. and shape public health,” said Eric Brown, the director of the Division of Microbiology for the U.S. Food and Drug Administration.
A team led by scientists from the Harvard School of Public Health HSPH and the Broad Institute, researchers sequenced and compared samples from seven people in France and four from Germany who were sickened during the worst of the outbreak in Mayand June 2011.
Disease detectives used the genetic fingerprints of these E. coli strains to discover that the outbreak of this deadly, foodborne illness began with raw sprouts germinated from Egyptian fenugreek seeds, which arrived in Germany in December 2009. Fenugreek is an herb whose seeds are used in cooking; mature plants are grown for animal forage.
The tainted seeds would have been more difficult to find, perhaps impossible, using traditional detection methods.
“The genome sequencing technology is similar to obtaining a map and flashlight when traveling in the middle of the night,” said Ming Zhang, the associate professor of epidemiology at the University of Georgia.
“This technology allows us to look into much more detailed genetics relativeness between strains than traditional molecular epidemiological analysis. It helps to better determine which strains are an exact part of the outbreak and which are not,” said Brown.
This pioneering application of genome sequencing to a food-borne illness outbreak showed that E. coli strains from French patients were more genetically diverse than strains from patients in Germany, where the epidemic was more severe variation in the German isolates appeared to be a subset of the diversity seen in the French isolates.
The researchers say these findings are surprising because a previous study, using narrower genetic analysis, concluded that the French and German strains were identical. This points to a single source for outbreaks in both countries, which was indeed the case.
The type of whole genome sequencing done by the HSPH and Broad team costs more than traditional analysis, which examines only parts of an organism’s genetic code. Still, Brown predicts that this new tool will be widely applied three to five years from now and will improve food safety.
“I believe we will be able to apply it in real time as the technology advances to a point when the cost will no longer be the challenge like it is today,” said Brown, a microbial geneticist who has used whole-genome sequencing to study salmonella outbreaks for the FDA. “Once we know the source of a contamination by using this tool in the future, we could immediately cooperate with the food industry.”
“We could better and more effectively guide them and tell them how to process the food safely, in both market and farm areas,” he added. .
Zhang, however, believes there the technology is not ready for prime time.
“There are still many technical challenges within the data analysis aspect,” said Zhang. “Another greater challenge is the public’s lack of understanding of this novel technology and how could it be related to their own health problems.”