A View from Emily Singer
Sequencing Killer E. Coli Reveals New Strain
New sequencing technology quickly reveals deadly traits in the microbe responsible for German outbreak.
Analysis of the genome sequence of the strain of E. coli responsible for the deadly outbreak in Germany revealed that it is “an entirely new super-toxic E. coli strain,” according to BGI-Shenzhen, a DNA sequencing center in China. Both BGI and University Medical Centre Hamburg-Eppendorf announced they had assembled a draft of the organism’s genome on Thursday, using sequencing technology from Ion Torrent, a start-up that was acquired by genomics giant Life Technologies.
Ion Torrent’s desktop sequencer, which went on the market just a few months ago, is distinguished by its speed; it can sequence a sample of DNA in a couple of hours, rather than the week or more required by most of the machines now on the market. “We were able to provide the data in record time to University Hospital Muenster,” said Life Technologies’ Simone Guenther, in a report from the company. “In previous outbreaks it would have taken much longer to reach this stage.”
According to Life Technologies, sequencing data 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 […] may provide insight into this bacterium’s aggressiveness and help prevent further outbreaks.” The EAEC 55989 E. coli strain was originally isolated in the Central African Republic and has been linked to serious diarrhea.
The new strain “has also acquired specific sequences that appear to be similar to those involved in the pathogenicity of hemorrhagic colitis and hemolytic-uremic syndrome,” according to a release from BGI. “The analysis further showed that this deadly bacterium carries several antibiotic resistance genes, including resistance to aminoglycoside, macrolides and Beta-lactam antibiotics: all of which makes antibiotic treatment extremely difficult.”
BGI and collaborators are also developing diagnostic kits to help quickly detect the deadly strain.