Preliminary data from DNA sequencing performed in cooperation with the University Hospital Muenster, Germany, on the Ion Personal Genome Machine (PGM) strongly suggests that the bacterium at the root of the deadly outbreak in Germany is a new hybrid type of pathogenic E. coli strains.
The data obtained from the DNA sequencer shows the presence of genes typically found in two different types of E. coli: enteroaggregative E. coli (EAEC) and enterohemorrhagic E. coli (EHEC). These results, which are being confirmed by further data analysis on the Ion PGM(TM), may provide insight into this bacterium's aggressiveness and help prevent further outbreaks.
The data gathered at Life Technologies' laboratories in Darmstadt, Germany, will be used by scientists at the University Hospital Muenster to develop better tests to positively identify the illness in people showing symptoms of the infection, which includes kidney failure and bloody diarrhea. For the first time since the outbreak, it is now possible to study in detail the basis for what makes this strain so aggressive.
"The rapid whole genome sequencing results enabled us to discover within days a unique combination of virulence traits ... and makes this German outbreak clone a unique hybrid of different E. coli pathovars," said Dr. med. Alexander Mellmann, scientist at the German National Consulting Laboratory for Hemolytic Uremic Syndrome (HUS) at the Institute of Hygiene, University Hospital Muenster.
Life Technologies' Simone Guenther, Ph.D., who carried out the sequencing work, said, "The severity of this outbreak meant that speed was of the essence. We were able to provide the data in record time to University Hospital Muenster. In previous outbreaks it would have taken much longer to reach this stage."
To help prevent further spreading of the bacterium, Life Technologies began shipping its E. coli testing kits to European laboratories to screen contaminated food thought to be at the center of the outbreak that has killed 17 people and affected more than 1,000 throughout Europe.
The kits are a first line of defense to detect the presence of pathogenic E. coli and then secondary testing is performed using more specific kits. Life Technologies will develop new customized kits specifically designed to detect the hybrid strain in Germany once the sequencing data has been fully analyzed in the next few days. The company can design custom assays in less than one week.
The kits shipped to Europe are part of a large offering of molecular tests developed by Life Technologies capable of accurately detecting most pathogens that are dangerous to humans. The Ion PGM(TM) is a DNA sequencing instrument featuring semiconductor technology that can complete a highly accurate sequence of DNA in just two hours. The DNA sample used for the sequencing work was collected from a patient with the illness.
The Ion Personal Genome Machine sequencer is for research use only and is not for use in diagnostic procedures - but you can take one with you to that organic farmer's market.