Jul 21, 2011 – German researchers who were the first to release the initial genome sequence of the Escherichia coli O104:H4 outbreak strain published their in-depth findings yesterday, which found that it differed from a 2001 strain found in Germany, but that both could have evolved from a common progenitor.
The group, based at the University of Munster and University Hospital Munster, published their findings in Public Library of Science (PLoS) One.
Dr Dag Harmsen, one of the coauthors, said in a Public Library of Science press release that the group's work represents the first use of a next-generation sequencing platform called the Ion Torrent PGM to assist with outbreak analysis in real-time.
The group's report describes how they compared the outbreak strain sequence with an E coli O104:H4 isolated in 2001 from a German patient who had hemolytic uremic syndrome (HUS), a serious kidney complication. They also determined that the outbreak strain didn't derive from a type isolated in Africa in the late 1990s, as initially thought.
Dr Helge Karch, senior author of the study, said in the statement, "This study underlined the great importance of the long-term storage of historical HUS isolates that were collected by us since 1996 to understand the evolution of highly-pathogenic EHEC strains."
Today's publication of the E coli genome findings is the latest turn in a race to publish sequence findings in peer-reviewed publications, Nature News reported today. Its report noted that a German group from the University of Gottingen published its genetic analysis of two outbreak isolates on Jun 28 in Archives of Microbiology. In that study, researchers compared the current outbreak strain with an African E coli O104:H4 strain from the 1990s.
Dr Mark Pallen, from the University of Birmingham in the United Kingdom, told Nature News that the findings in the two published studies don't differ much from what other scientists documented earlier through "crowd-sourcing" on public domain sites.
He said in the report that the Munster group was the first to define the outbreak strain, which allowed diagnosis and surveillance. The main competition point now is to find clues about the outbreak strain's evolution.
In other developments, a report recently posted by German's Federal Office of Consumer Protection and Food Safety (BVL) said in a task force update that as of Jun 23 lab experts have tested 10,291 food samples, and none were positive for the E coli O104:H4 outbreak strain. The BVL findings were first reported today by Food Safety News.
Germany's Federal Institute for Risk Assessment (BfR) conducted tests on seeds from the sprout producer identified earlier in the outbreak as the likely E coli source. Though none tested positive, the agency said it's possible that the contaminated seeds were no longer in stock, and that the negative tests don't rule out seeds as a possible outbreak source.
Trace-back investigation of seeds used at the farm pointed to fenugreek seeds exported from Egypt. Three infected sprout farm employees had worked with the fenugreek sprouts, and the BVL report said it's not clear if the employees contaminated the sprouts or if the sprouts sickened the employees.
The BVL's update also included a slide presentation it gave to the European Commission on Jul 21.
So far 3,923 E coli O104:H4 infections have been reported from EU countries, according to an update today from the European Centre for Disease Prevention and Control (ECDC). The total includes 770 HUS cases and 43 deaths. Since yesterday Germany and France each reported one HUS case, and Germany reported three cases without HUS. France excluded one previous E coli case.
Jul 20 PLoS One study
Jul 21 Nature News report
Jun 28 Arch Microbiol study
Jul 21 Food Safety News story
Jul 21 ECDC update