Within days of the E.coli outbreak in Germany that officially ended this week, scientists at the University of Maryland Institute for Genome Sciences began cracking the genomic code of the bacteria responsible for infecting thousands and killing dozens.
Information about all the genes that make up the bacteria from these scientists and others around the globe was soon offered online at no cost to doctors treating those infected, possibly saving lives, as well as to epidemiologists looking for the source of the pathogen.
It may have been the fastest turnaround of genomic data for wide diagnostic use, and now some of those involved believe this "open source" method of conveying data will become more routine, and the use of genomics as a diagnostic tool the norm.
"This technology is evolving extremely rapidly, enabling us to accomplish much more accurate analysis with unprecedented speed," said David A. Rasko, assistant professor in the University of Maryland School of Medicine and the research scientist at the Institute for Genome Sciences who led the investigation. "This is truly the model of how genomics will get a foot in door from a diagnostic standpoint."
Rasko had helped U.S. food investigators on the E.coli outbreak in spinach in 2006 and the FBI on the anthrax attacks in 2001, but said the work cost millions and took months. The data were not of immediate use to doctors on the front lines.
The work on E.coli led by the Maryland researchers for this outbreak cost $500,000 and began producing data within days. The funding came from the National Institutes of Health and the state of Maryland. The collaboration included scientists from Pacific Biosciences of California Inc., Denmark's Statens Serum Institute, Harvard and the University of Virginia.
Other collaborations formed in Germany and elsewhere, and they all offered their findings on websites such as plosone.org an open-access journal for peer-reviewed scientific and medical research. Others such as Beijing Genomics Institute, which partnered with a university in Hamburg, Germany, to sequence the bacterium, also posted results on their own websites.
The outbreak officially ended this week because no cases have emerged in the past three weeks, according to German authorities, and the source was identified as sprouts from seeds that came from Egypt. In all, more than 4,000 were sickened and more than 50 died, including one American who had visited Germany.
The number of dead could have been higher if not for the research done by each of the groups on samples taken from infected Germans, said Rasko, who described the work in the July 27 issue of the New England Journal of Medicine.
The scientists found that in this outbreak the E.coli was an unusual combination of types of the bacteria and was unusually virulent. It was both resistant to roughly 10 different antibiotics and contained a gene that produced the Shiga toxin, which is made worse by other antibiotics. The medication actually causes more toxin to be produced, so the information was crucial for doctors, Rasko said.
According to the U.S. Centers for Disease Control and Prevention, there are an estimated 265,000 cases of Shiga toxin-producing E.coli a year in this country, though not all are reported. Up to 10 percent develop a potentially life-threatening complication called hemolytic uremic syndrome that damages the kidney and was responsible for most of the deaths in Germany.