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.

Students from Cambridge University, in England, engineered bacteria to produce pigments in all colors of the rainbow (shown above) as part of the International Genetically Engineered Machines Competition at MIT. Credit: Mike Davies

Bioengineering students from around the world converged on MIT this weekend in what has become an annual ritual in synthetic biology--iGEM, the international genetically engineered machines competition. Among the finalists this year were "GluColi", a new generation of glue made by bacteria, a biological version of an LCD screen made of yeast, and a multicolored menagerie of bacteria that might ultimately become part of a biological system designed to change color in response to toxins or other target compounds, providing an easy-to-read warning system.

By combining snippets of DNA, dubbed biological "parts", students build microbes designed to perform useful functions, such as producing medicines or detecting toxins. Each year "parts" built for the competition are entered into a biological library, so that next year's teams can use them to build even more sophisticated machines. As iGEM co-founder and MIT bioengineer Tom Knight explained in a previous piece, "The key idea here is to develop a library of composable parts which we think of in the same way as Lego blocks. These parts can be assembled into more-complex pieces, which in many cases are functional when inserted into living cells."

Entries into previous years have included yeast designed to produce beer with the health benefits of red wine, sweet-smelling E. coli, a commonly used research bacterium with a vile odor, and probiotic bacteria, like that found in yogurt, designed to fight cavities, produce vitamins, and treat lactose intolerance.

To make multicolored microbes, students from Cambridge University, in England, mined bacterial genomes for pigment-producing genes. They then engineered those genes into the harmless strain of E. coli used in genetic research. Carotinoid enzymes co-opted from Pantoea ananatis, a bacterium that can rot onions, generated red and orange pigments. A gene for melanin, an enzyme from the soil bacterium Rhizobium etli, produces brown. Chromobacterium violacein, a soil and water dwelling microbe offered genes capable of producing shades of violet, green and blue.

UC San Diego bioengineers have created the first stable, fast, and programmable genetic clock that reliably keeps time by the blinking of fluorescent proteins inside E. coli cells. The clock's blink rate changes when the temperature, energy source, or other environmental conditions change. Shown here is a microfluidic system capable of controlling the environmental conditions of the E. coli cells with great precision--one of the keys to this advance. Credit: UC San Diego Jacobs School of Engineering

A molecular timepiece that ticks away the time with a flash of fluorescent protein could provide the basis for novel biosensors. The clock, or synthetic gene oscillator, is a feat of synthetic biology--a fledgling field in which researchers engineer novel biological "parts" into organisms.

To create the clock, scientists genetically engineered a molecular oscillator composed of multiple gene promoters, which turn genes on in the presence of certain chemicals, and genes themselves, one of which codes for a fluorescent protein. When expressed in E. coli bacteria, the feedback system turns the fluorescent gene on and off at regular intervals.

The clock's oscillations can be tuned by the temperature at which the E. coli are grown, the nutrients they are fed, and specific chemical triggers. According to a paper published today in Nature, the fastest oscillations that the scientists have recorded so far are about 13 minutes.

"The on-off frequency could potentially be used to determine the level of some toxic chemical in the environment," says Jeff Hasty, a bioengineer at UC San Diego, who led the project. "One could make simple modifications so that it responded to other chemicals or sugars."

According to a press release from UC San Diego,

One next step is to synchronize the clocks within large numbers of E. coli cells so that all the cells in a test tube would blink in unison. "This would start to look a lot like the makings of a fascinating environmental sensor," said Jeff Hasty, a UC San Diego bioengineering professor and senior author on the Nature paper. Researchers in his lab have also developed sophisticated microfluidic systems capable of controlling environmental conditions of their E. coli cells with great precision. This enables the bioengineers to track exactly what environmental conditions affect their clocks' blink rates.