Using whole-genome sequencing, a team led by researchers from Harvard School of Public Health (HSPH) and the Broad Institute has traced the path of the E. coli outbreak that sickened thousands and killed over 50 people in Germany in summer 2011 and also caused a smaller outbreak in France. It is one of the first uses of genome sequencing to study the dynamics of a food-borne outbreak and provides further evidence that genomic tools can be used to investigate future outbreaks and provide greater insight into the emergence and spread of infectious diseases.

The study, conducted in collaboration with groups at the Pasteur Institute in France, Assistance Publique-Hôpitaux de Paris, and Statens Serum Institut in Denmark, appears on February 6, 2012 in an advance online edition of Proceedings of the National Academy of Sciences.

“A genome contains the record of a strain’s evolutionary history, so by looking at the differences between the genomes of multiple bacteria from an outbreak we can get really useful clues about what happened in the outbreak. In this way, tracking outbreaks is like detective work, and this approach will be a powerful tool in trying to understand future outbreaks,” said lead author Yonatan Grad, a research fellow in the Center for Communicable Disease Dynamics, Department of Epidemiology at HSPH and infectious disease physician at Brigham and Women’s Hospital in Boston.

“This work is a testament to the power of genome sequencing and analysis to shed light on the mechanisms that drive disease outbreaks,” said co-senior author Deborah Hung, a core faculty member at the Broad Institute, an assistant professor at Massachusetts General Hospital and Harvard Medical School, and an infectious disease physician at Brigham and Women’s Hospital. “We can see things that we simply couldn’t see before, and that holds promise for improving public health.”

The outbreak in Germany, which was caused by the strain E. coli O104:H4, led to around 4,000 cases of bloody diarrhea, 850 cases of hemolytic uremic syndrome (HUS), which can lead to kidney failure, and over 50 deaths. The source of the outbreak was traced to sprouts from an organic farm in Germany. In France, where 15 people were sickened with bloody diarrhea that progressed to HUS in nine people, the source of the outbreak was sprouts, germinated from seeds purchased at a garden retailer, that were served at a children’s community center buffet. European investigators, using traditional epidemiological methods, traced the outbreaks to a shipment of seeds from Egypt that arrived in Germany in December 2009.