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German authorities confirmed on Friday that bean sprouts were responsible for the deadly E. coli outbreak that has now killed 30 people.

While sprouts had been named as a possible source earlier in the week, public health authorities took back that indictment after lab tests came back negative.

But now, thanks to old-fashioned epidemiological investigation, sprouts have been definitively named the culprit. By interviewing patients and chefs at restaurants where infected people had eaten, investigators found that people who had eaten bean sprouts were nine times more likely to get infected than those who hadn’t, said Reinhard Burger, head of Germany’s disease control agency, at a news conference in Berlin on Friday.

According to a report from the Associated Press, “The breakthrough in the investigation came when a taskforce linked patients who had fallen ill to 26 restaurants and cafeterias that had received produce from the organic farm.”

Authorities also said it is now safe to eat tomatoes, cucumbers and lettuce, which had all been previously implicated in the outbreak.

Researchers in Germany and China sequenced the E. coli strain responsible for the outbreak in record time, thanks to new sequencing technology from Ion Torrent, a start-up that was acquired by genomics giant Life Technologies last year. The company then created a rapid diagnostic test designed to distinguish the deadly strain–which has caused an unusual number of serious and sometimes fatal cases of kidney failure–from more common strains of E. coli. However, tests of the sprouts came back negative, possibly because the contaminated sprouts had already been thrown away.

Researchers are still studying the sequence of the bacteria for clues to its unusual virulence. Investigations for far suggest that it evolved from a strain first identified in Münster, Germany, in 2001. According to a report in the Wall Street Journal;

The 2001 strain caused fewer than five identified cases world-wide, and scientists never did identify its natural reservoir—where a new strain of the E. coli bug can originate, such as in cattle. But the genetic analysis showed that as the 2001 bug likely swapped genetic material with other bacterial strains, some big changes occurred.

The 2011 version turns out to be resistant to eight classes of antibiotics, including penicillin, streptomycin and sulfonamide. The likely reason is that rapid evolution “resulted in the gain of more genes during the last 10 years” that conferred immunity against many more antibiotics, according to BGI.

The bug’s genome has been made publicly available, so that scientists around the world can scour it for clues. Even some non-geneticists are taking a crack interpreting it.

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Tagged: Biomedicine, sequencing, Life Technologies, Ion Torrent, e. coli, outbreak

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