The epidemic of E. coli O104:H4 centered in Northern Germany was 2011’s most important food safety story. The top story of the year involved a rare serotype of dangerous bacteria that in May and June killed at least 50 and sickened more than 4,000, including 852 who developed kidney-damaging hemolytic uremic syndrome (HUS).

In terms of HUS, it was the largest outbreak ever described worldwide.

Hamburg, Germany was the epicenter of the epidemic, which strained the region’s medical resources, filling intensive care units and prompting calls for blood donors. And while most of those stricken were in Germany, 16 countries reported cases of infection associated with the epidemic. Six Americans who had travelled in Germany were affected and one died after returning home to Arizona.

After the first illnesses were reported in May, Europe’s epidemiologists honed in on fresh salad vegetables as the prime suspects. But outbreak patients tended to recall eating salad items such as cucumbers, forgetting they had also eaten sprouts. When lab tests detected pathogenic E. coli on Spanish cucumbers, they were misidentified as the possible outbreak source until further tests confirmed the bacteria was not the outbreak strain.

The Spanish produce industry said it lost millions as a result.

European health officials tested more than 10,000 samples of food but never found any contaminated with the O104 outbreak strain. Cafeteria billing information eventually helped crack the case, showing that all the ill subjects who had eaten at two company cafeterias had been served sprouts supplied by an organic farm in Lower Saxony.

Then a cluster of E. coli O104:H4 illnesses turned up in France, where sprouts served during an open house at a children’s community center in Bordeaux sickened nearly a dozen people.

The link between the German sprouts and the French sprouts was a single lot of fenugreek seeds from an Egyptian exporter, the European Food Safety Authority (EFSA) announced in early July. The European Commission put import restrictions on the Egyptian seeds and sprouts that is to continue until the end of March.

Data from the genome sequencing of the unusual E. coli serotype O104 were instantly released via the Internet to researchers around the world, which resulted in some preliminary analyses outside the standard peer-reviewed science publication route.

It was what one researched called the first “open source” analysis of a microbial genome, an unprecedented turnaround in the amount of information that was made available to healthcare providers and public health authorities while they were still fighting the outbreak.

Although some early news stories described the outbreak strain of E. coli as a new and contagious superbug — a hybrid — the international team of investigators that worked collaboratively to unlock its secrets later said no. In a paper published in the New England Journal of Medicine on the completed genome mapping, they said O104 is likely a common strain that acquired an especially virulent trait.

They said E. coli O104:H4 had in fact been identified before, and although the pathogen can be easily transmitted, it isn’t more transmissible than other similar strains of harmful E. coli.

The pathogen does have unusual traits, such as an ability to stick together in a stacked-brick pattern and cling to intestinal tracts, inducing heavy mucus that protects it from a host’s immune system while it releases toxin into the bloodstream. The huge toll of illnesses in Germany indicates it is notably more virulent than most of its Shiga-toxin producing cousins. 

The lessons learned from this catastrophic outbreak are still being tallied. One is to underline the need for outbreak investigators to take into account food items, like sprouts, that are typically overlooked when case subjects try to recall what they’ve eaten. And using information sources — such as menus, meal or grocery receipts, shopper loyalty cards — independent of individual memory can be a useful way to track an outbreak source.

Another consideration is the need to screen for E. coli serotypes like O104 when patients arrive at the hospital with bloody diarrhea. Antibiotics typically are not used to treat E. coli O157:H7 infections, because there is evidence that antibiotics make the illness worse.

Some fear that because German doctors could not have known to screen for E. coli O104, they may have prescribed antibiotics after ruling out the more typical E. coli O157. That may have contributed to the unusually high number of HUS cases in Germany.

Most of all, the outbreak and the new findings should serve as a reminder that although the E coli O104:H4 epidemic is over, the world needs to be better prepared to deal with the next large outbreak of foodborne illness.