Tuesday 12 December 2017

Guest Contributor: Genome Study Yields Possible New Information on E. coli found in Sprouts in the EU

A Recent Genome Study Yields Possible New Information Regarding the E. coli Found in Sprouts in the European Union

Guest Contributior: Michael “Mick” Guerini, Microbiologist and Technical Writer

A whole-genome investigation of samples from Europe’s Escherichia coli O104:H4 outbreak linked to fenugreek sprout seeds was recently reported in the Proceedings of the National Academy of Sciences(PNAS).  Using whole-genome sequencing, a team led by researchers from Harvard School of Public Health (HSPH) and the Broad Institute traced the path of the E. coli outbreak that sickened thousands and killed over 50 people.

 “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.

European investigators, using traditional epidemiological methods, traced the outbreaks to a shipment of seeds from Egypt that arrived in Germany in December 2009. Based on conventional molecular epidemiological analysis, the E. coli strains from the outbreaks in Germany and France appear identical.  This finding by the research team is important because it highlights the need for combining epidemiological work with molecular analysis.

However, by harnessing the Broad Institute’s expertise in whole-genome sequencing and analysis, the researchers were able to determine that there were small, but measurable, differences among the isolates. They made two surprising findings: All the strains connected to the larger German outbreak were found to be nearly identical, while the strains in France showed greater diversity; and the German isolates appeared to be a subset of the diversity seen in the French isolates.

“If genomes have fewer differences than we expect, like the German outbreak, it suggests that the outbreak might have passed through a bottleneck. A bottleneck might be something like disinfection procedures that killed most but not all of the bugs, or maybe passage through a single infected individual,” said Hanage.  Another hypothesis offered by the researchers is that there was uneven distribution of diversity in the original shipment of contaminated seeds.

As costs for genomic sequencing decline, these tools, combined with traditional epidemiological techniques, can provide greater insight into the emergence and spread of infectious diseases and will help guide: food safety testing guidelines, food safety regulations, food processing and manufacturing as well as preventive public health measures.

Paper cited — “Genomic Epidemiology of the Escherichia coli O104:H4 Outbreaks in Europe, 2011,” Yonatan H. Grad, Marc Lipsitch, Michael Feldgarden, Harindra M. Arachchi, Gustavo C. Cerqueira, Michael FitzGerald, Paul Godfrey, Brian J. Haas, Cheryl Murphy, Carsetn Russ, Sean Sykes, Bruce J. Walker, Jennifer R. Wortman, Sarah Young, Qiandong Zeng, Amr Abouelleil, James  Bochicchio, Sara Chauvin, Timothy DeSmet, Sharvari Gujja, Caryn McCowan, Anna Montmayeur, Scott Stellman, Jakob Frimodt-Moller, Andreas M. Petersen, Carsten Struve, Karen A. Krogfelt, Edouard Bingen, Francois-Xavier Weill, Eric S. Lander, Chad Nusbaum, Bruce W. Birren, Deborah T. Hung, William P. Hanage, Proceedings of the National Academy of Sciences, online February 6, 2012

(Source of Information — Harvard School of Public Health, February 6, 2012 Press release)

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