Researchers Complete DNA Sequencing of E coli Strain

Nancy A. Melville

July 28, 2011

July 28, 2011 — Research teams from around the globe investigating the Germany-based Escherichia coli outbreak that has killed more than 50 and sickened thousands say that they have completed DNA sequencing to crack the genetic code of the bacteria behind the outbreak.

In 2 studies published online in the New England Journal of Medicine on July 27, research teams say an extensive sequencing of the bacteria's genome identified the E coli strain as a largely enteroaggregative E coli strain, uniquely combined with the enterohemorrhagic E coli subtype.

The culprit was an unusually virulent, Shiga toxin–producing strain that is associated with symptoms including severe diarrhea and hemolytic-uremic syndrome, and is capable of causing a worsening of symptoms when certain antibiotics are used.

"Our observation that toxin production by the O104:H4 outbreak strain is induced by a quinolone antibiotic, as previously seen with enterohemorrhagic E. coli strains, suggests that caution is warranted in the use of certain classes of antibiotics to counteract this newly emerged pathogen," write lead author David A. Rasko, PhD, from the University of Maryland School of Medicine, Baltimore, and colleagues, authors of the first report.

The team isolated the O104:H4 C227-11 strain from a 64-year-old German woman who had been hospitalized in Copenhagen with bloody diarrhea and sequenced its genome, comparing it with the genomes of 6 similar strains and 5 enteroaggregative strains.

They concluded that although the bacterium is highly unusual and not commonly seen in a single E coli organism, it is not necessarily a hybrid strain, as was reported earlier in the outbreak, which began in May.

"Early in the outbreak, scientists described the bacteria as a 'hybrid' strain. This strain is not a true hybrid, because it contains only a small amount of DNA sequence from enterohemorrhagic E. coli," explained Dr. Rasko in a press statement.

"We have not seen these kinds of unique combinations very often in the past. I expect we are going to see them increasingly, now that technology. . .has advanced to the point that we can sequence more strains very rapidly and relatively inexpensively," said Dr. Rasko, who is an assistant professor of microbiology and immunology at the University of Maryland School of Medicine and a research scientist at the Institute for Genome Sciences.

The researchers added that, though rare, the combination of strains has been seen before, but not as the cause of a major illness outbreak.

"The outbreak is not the first clinically linked instance of an enteroaggregative E. coli acquiring a Shiga-toxin encoding phage," the authors write, "but it is a clear case of such a strain causing a major outbreak of disease. Whether the current outbreak is due to a particularly virulent Shiga-toxin-positive enteroaggregative E. coli, a rare epidemiologic opportunity, or both, remains unclear."

In the second report, researchers from Germany and Beijing agreed that despite its rarity, the strain has in fact been reported in various regions of the world.

"Although this outbreak strain has surprised the general public and public health officials, related potential progenitor strains have been reported from three continents," Holger Rohde, MD, from the Institute of Medical Microbiology, Virology and Hygiene, the University Medical Center of Hamburg-Eppendorf, Hamburg, Germany, and colleagues write.

A 2005 outbreak of the O104:H4 strain in Korea similarly was associated with high rates of hemolytic-uremic syndrome, and strains previously seen in Germany in 2001 and in the Central African Republic in the late 1990s also had similarities.

A report from the European Food Safety Authority has stated that fenugreek seeds (Trigonella foenum-graecum) imported from Egypt and used to grow fresh bean sprouts were the most likely source of the current E coli outbreak.

The last reports of illness from the strain were reported in early July, and German officials have declared the outbreak to be officially over.

Researchers for both papers credit advances in DNA-sequencing technologies — and the ability to freely share data and collaborate with disparate groups of researchers around the world in what was dubbed the "E. coli O10:H4 Genome Analysis Crowd-Sourcing Consortium," for allowing the rapid analysis of the genome.

"Usually, science takes place in relative isolation," Dr. Rasko said. "This is the first time we've seen true 'open source' analysis of a microbial genome."

The swift sequencing bodes well for the faster understanding of such potentially dangerous, virulent pathogens in the future, he added.

"The research may be the first time that such a comprehensive scientific analysis of an emerging pathogen took place in the first days and weeks of an outbreak, "Dr. Rasko explained in the press release.

"This technology is evolving extremely rapidly, enabling us to accomplish much more accurate analysis with unprecedented speed," he added.

"It took years and millions of dollars to sequence the first E. coli genome more than a decade ago. Here we are, just months from the start of the German E. coli outbreak, and we've published a paper on it. This paper and the research it describes represent the new paradigm of outbreak investigations."

The study by Dr. Rasko and associates was supported by the National Institutes of Health, the University of Maryland internal funds, and the Danish Council for Strategic Research. The study by Dr. Rohde and colleagues was supported by grants from the State Key Development Program for Basic Research of China, the National Key Program for Infectious Diseases of China, Schenzhen Biological Industry Development Special Foundation, Shenzhen City, the European Union Microme Program, the Alexander von Homboldt Foundation, the medical faculty of the University Medical Center Hamburg-Eppendorf, and the British Biotechnology and Biological Sciences Research Council. Dr. Rohde and coauthors have disclosed no relevant financial relationships. Many of the authors of Rasko and colleagues' study report current or past employment by Pacific Biosciences, as well as receipt of stocks or stock options from this company; Eric Schadt, PhD, the corresponding author, served as the Executive Scientific Director of Merck until June 2009.

N Engl J Med. Published online July 25, 2011. Abstract for Rasko study Abstract for Rohde study

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