By Bio-IT World Staff
June 2, 2011 | Researchers at BGI (formerly the Beijing Genomics Institute) in Shenzhen, China, have sequenced the strain of Escherichia coli bacterium responsible for the deadly outbreak in Germany this week that has claimed at least 17 lives and infected more than 1,000 people across Europe, with symptoms including kidney failure and bloody diarrhea.
In the wake of initial reports of fatalities, BGI collaborated with the University Medical Centre Hamburg-Eppendorf to sequence the bacterium and assess the likely health risk. BGI’s preliminary analysis of the genome sequence reveals a new “super-toxic” E. coli strain.
BGI completed the sequencing of the E. coli samples within three days, using the relatively new Ion Torrent platform (owned by Life Technologies). This third-generation sequencing platform has the advantage of speed of sequencing and relatively long read lengths, which is useful for sequencing and identifying novel bacterial strains.
Bioinformatics analysis showed that the strain at the center of the latest outbreak is highly infectious and toxic. According to the results of the draft assembly (available at ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482), the estimated genome size of this new E. coli strain is about 5.2 megabases (Mb). The bacterium is an EHEC (enterohemorrhagic) serotype O104 E. coli strain, but a new serotype that has not been previously associated with any E. coli outbreaks.
Comparative sequence analysis showed that this bacterium has 93% similarity with the EAEC (enteroaggregative) 55989 E. coli strain, previously isolated in the central Africa and linked to cases of serious diarrhea. The new European strain of E. coli also features DNA sequences related to those involved in the pathogenicity of hemorrhagic colitis and hemolytic-uremic syndrome, potentially acquired through horizontal gene transfer. The genome also carries a number of antibiotic resistance genes, including resistance to aminoglycoside, macrolides and beta-lactam antibiotics.
BGI and its collaborators are studying the bacterial virulence genes, expression profiles, drug resistance, and gene transfer mechanisms. It also hopes to develop diagnostic kits. The sequences of this new E. coli strain have been uploaded to NCBI (SRA No: SRA037315.1).
Another German group at the University Hospital Muenster, working with Life Technologies’ scientists led by Simone Guenther in Darmstadt, Germany, has also sequenced the genome of the E. coli strain using the Ion Torrent platform. Life Technologies announced that the team had identified genes found in both EAEC and EHEC E. coli.
“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 Alexander Mellmann, from the German National Consulting Laboratory for Hemolytic Uremic Syndrome (HUS) at the University Hospital Muenster.
“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,” said Guenther.
Life Technologies has shipped E. coli testing kits to European laboratories to screen food supplies that may have been contaminated. Secondary testing is performed using more specific kits. Life Technologies says it will develop custom kits to detect the hybrid E.coli strain in the next few days. The Muenster team also hopes to develop better tests to identify the bacteria in suspected patients.