“It is the sprouts.”

As the death toll in Germany pushed to 31, the county’s national disease-control center Friday said a new case-control study indicates that locally grown sprouts from an organic farm in Lower Saxony touched off the massive E. coli outbreak that has sickened nearly 3,000.

Speaking at a news conference Friday, Robert Koch Institute (RKI) president Reinhard Burger said, “It is the sprouts.”

Burger said samples collected from the sprouts farm have not tested positive for the outbreak strain of E. coli O104:H4, but new interviews with case patients and controls point to the consumption of sprouts as the cause of the epidemic. He said that people who reported eating the suspect sprouts were nearly nine times more likely to have developed bloody diarrhea than those who said they did not eat them.

But there also may be direct evidence implicating the sprout farm.

The Consumer Affairs Ministry of the state of North Rhine-Westphalia reported Friday that tests on a package of sprouts found in the garbage can at the home of two case patients tested positive for the outbreak strain of E. coli. That is the first direct link to the organic farm in Bienenbüttel. The ministry injected “a small element of uncertainty” about the contamination, because the sprouts package had been opened before being discarded.

The new epidemiological evidence was gathered during a third case-control study that focused on salad ingredients.

In its initial study, the questionnaire used by investigators did not include sprouts. After the second study, RKI said it had not concluded that sprouts were suspect in part because only 28 percent of case patients had reported eating them.

For its most recent case-control study, RKI said it questioned 112 people, including 19 infected with enterohemorrhagic E. coli (EHEC), who had been in tour groups or clubs visiting the same restaurant. Several patrons of that restaurant became ill. The investigators also looked at meal orders and receipts and quizzed the staff about food preparation.

Results of the epidemiological analysis showed that people who ate sprouts at the restaurant had an 8.6-fold increased risk of EHEC/hemolytic uremic syndrome (HUS), compared to those who did not. And all of those who were ill reported having eaten sprouts.

Epidemiologists outside of Germany who have dealt with sprouts-related outbreaks say sprouts should have been “a vegetable of interest” from the beginning. Sprouts are a high-risk food susceptible to contamination — the warm, moist growing conditions for sprouts also favor the growth of bacteria — yet they’ve become such a ubiquitous garnish that case patients often don’t recall having eaten them.

German investigators got side-tracked, however, when their early epidemiology implicated cucumbers, tomatoes and lettuce, and then cucumbers imported from Spain were found to be contaminated with E. coli — although further testing revealed it was not the outbreak strain.

Earlier reports that contaminated cucumber pieces were found in the compost heap of a family who fell ill were downplayed Thursday by authorities as “not a decisive lead,” according to press accounts.

As a result of the new epidemiological evidence presented Friday, the warning was lifted against eating raw tomatoes, lettuce and cucumbers in Germany.

Work was halted at the sprout farm, in the town of Bienenbüttel, a week ago and its sprout varieties were recalled. German officials said they don’t know whether the farm’s seeds or water were contaminated.

Earlier this week, Gert Hahne, a spokesman for Lower Saxony state’s Consumer Protection Ministry, said three women who worked at the farm packaging sprouts were sick with diarrhea in May and one of the women had a confirmed E. coli infection.  Hahne said an ill worker  could have contaminated the sprouts or could have been sickened by the sprouts.

German health officials said it found illness clusters centered around four office cafeterias and three restaurants that served sprouts from the implicated farm.

Contaminated sprouts have been the source of many foodborne illness outbreaks. Last November and December in the United States, an outbreak of Salmonella that sickened 140 people in 26 states was traced to an organic sprouts farm in Illinois. U.S. Food and Drug Administration inspectors found the outbreak strain of Salmonella in an outside compost pile, and observed that workers were walking and wheeling carts between the production area and an outside compost pile without cleaning and disinfecting their boots or the cart wheels.

The largest outbreak of E. coli O157:H7 on record occurred in 1996 in Sakai, Japan, and was said to be caused by tainted sprouts.  Radish sprouts in school lunches prepared in a central kitchen were epidemiologically linked to the 12,680 illnesses among students, teachers and school staff.

Fresh sprouts are one of the few foods that the U.S. Centers for Disease Control and Prevention and FDA advise children the elderly, pregnant women and immune-compromised individuals to avoid eating.  In the U.S. there have been at least 30 reported outbreaks, mostly of Salmonella and E. coli, associated with different types of raw and lightly cooked sprouts since 1996. In many of the outbreaks, according to the public heath authorities, the sprout seeds have been the source of the harmful bacteria.

Bill Marler of the food-safety law firm Marler Clark, sponsor of Food Safety News, said, “Those that know, know not to eat sprouts. Illnesses caused by E. coli and Salmonella in local, organically sprouts can be just as deadly as mass-produced beef.”

Marler Clark recently donated $10,000 to the International Sprout Growers Association (ISGA) to be used for sprout-safety research being conducted at the Illinois Institute of Technology.

To reduce the chance of foodborne illness, sprouts need to be cooked thoroughly. The CDC suggests consumers request that raw sprouts of any kind (including alfalfa, clover, radish and mung bean sprouts) not be added to food such salads and sandwiches.

Meanwhile, in a report issued Thursday, the European Food Safety Authority (EFSA) said the outbreak strain of E. coli O104:H4 seems to share characteristics of Shiga toxin-producing E. coli (STEC) and enteroaggregative E. coli (EAEC) — although it’s not yet known if the outbreak strain is an EAEC that acquired EHEC virulence, or vice versa.

EAEC, according to the U.S. Centers for Disease Control and Prevention, is “an increasingly recognized cause of diarrhea in children in developing countries, has been particularly associated with persistent diarrhea (more than 14 days), a major cause of illness and death. Recent outbreaks implicate EAEC as a cause of foodborne illness in industrialized countries.”

EFSA said the outbreak strain in Germany is not new because infections in humans caused by similar strains have been previously reported. However, this outbreak strain is rare and until now “it has never been found to be responsible for the rate of infection and severity of disease seen during the current outbreak.”

As of Friday, the European Centre for Disease Prevention and Control (ECDC) said that EU countries have reported 2,287 E. coli cases, along with 795 cases of hemolytic uremic syndrome (HUS).

Many of the HUS patients in German hospitals are developing neurological problems, according to a report in Der Spiegel. The newspaper quotes Daniel Wertheimer, the physician-in-chief at the Center for Neurology and Neurological Early Rehabilitation at the Schön Clinic in Hamburg, who said three weeks ago he would have estimated that 15 to 20 percent of HUS cases would progress to neurological involvement, including seizures and paralysis.

But now, Wertheimer told the newspaper, about half the HUS patients have such complications — and not only the patients with “full-blown HUS, but also in those whose platelet counts have been severely reduced — a much larger group of people.”