In May 2011, a virtually unknown strain of E. coli, known as O104:H4, made worldwide headlines when an outbreak in Germany sickened approximately 4,000 people and killed 50, including one American. This event, linked to fresh sprouts, quickly became the deadliest foodborne illness outbreak in history. In the days following the first reports of illness, microbiological research laboratories around the globe began pooling resources to coordinate the world’s first “open source” analysis of a microbial genome. In turn, this spurred an unprecedented level of focused study by international collaborators that is still going on two years later. Before the German outbreak, the only reported illness associated with O104:H4 was in South Korea and involved a solitary case of hemolytic uremic syndrome, or HUS, a potentially fatal kidney disease associated with severe E. coli infections. Little to no research had focused on the rare strain leading up to its record-setting outbreak. But, as soon as it hit, O104:H4 rose in notoriety to a status reserved for E. coli O157:H7, the strain that has caused numerous deadly outbreaks in the past two decades and made E. coli a household name. Thanks to recent technological advancements in DNA sequencing, researchers around the world were able to map the genome of O104:H4 within days – a feat that would have taken months if the outbreak had happened a decade earlier. By working together to analyze the genome, researchers could more quickly determine why O104:H4 might be so particularly deadly. It became apparent rather quickly that O104:H4 stood apart from the pack because of a unique assemblage of genes, said David Rasko, Ph.D., associate professor of microbiology and immunology at the University of Maryland School of Medicine and lead author on the study mapping the genome of O104:H4. As it turned out, E. coli O104:H4 evolved from a type of E. coli known to be harmless enteroaggregative E. coli and had acquired the genes to produce Shiga toxin from more virulent strains known as enterohemorrhagic E. coli. When the outbreak struck in May 2011, medical professionals only knew to screen for enterohemorrhagic strains of E. coli, adding another layer of confusion to the initial response. Like other enteroaggregative E. coli strains, O104:H4 groups together in defensive brick patterns within a host’s intestines, inducing mucus production that both shields and feeds it. Combine that with the ability to produce Shiga toxin, and O104: H4 possesses the right cocktail of genes to become especially harmful in an outbreak. That combination of traits could also explain why the German outbreak saw such a high proportion of HUS cases. Nearly 1,000 of the 4,000 ill – or one in four – developed HUS as part of their infection. Outbreaks of other E. coli strains typically result in about one in 10 patients developing HUS, predominantly children. What’s more, the O104:H4 outbreak caused HUS in adults at the same rate it did in children. Rasko and other researchers suspect that the HUS cases were exacerbated by the early prescription of antibiotics to patients when doctors did not realize they were dealing with an E. coli outbreak. The use of antibiotics against Shiga toxin-producing E. coli has a well-established link with higher rates of HUS due to bacteria releasing additional toxin when killed. In July 2012, research from the University of New Mexico Children’s Hospital found that treating children’s E. coli infections with antibiotics tripled their risk of developing HUS. A study published by German doctors in December 2012 stated that antibiotics did not increase the risk of HUS in patients infected with O104:H4, and that they, in fact, observed fewer patients prescribed antibiotics developing HUS compared to those who did not take the antibiotics. Rasko and another E. coli expert, Alison O’Brien, Ph.D., said that everything they know about Shiga toxin-producing E. coli suggests that antibiotics increase toxin production and should not be used on E. coli patients. The thick film O104:H4 produced in the gut likely kept it around in adults long enough to make the German outbreak especially severe, said O’Brien, professor and chair of the Department of Microbiology and Immunology at the Uniformed Services University of the Health Sciences. O’Brien’s O104:H4 research has focused on studying the virulence factors of the bacteria in animal models. Her lab’s future research aims to determine how long the bacteria survive in the environment, as well as investigate the rate at which the toxin genes are transferred between E. coli strains. “Transfer of genes between bacterial strains is one of the major methods that bacteria acquire certain features, such as the capacity to produce a toxin or to resist antibiotic treatment,” O’Brien said. A team out of Michigan State University has been experimenting with those gene transfers in an attempt to transfer anti-biofilm genes back to O104:H4. Thus far, the experiments have not worked very well, said Shannon Manning, Ph.D., molecular biologist at MSU. She added that, in theory, any common anti-biofilm compound might be useful for weakening O104:H4 enough for immune systems to better defend against it. Manning said it was difficult to predict if O104:H4 could cause another outbreak on the scale of the one it caused in Germany. It might be that the pathogen and the food source met in the perfect storm and won’t likely cause such severe outbreaks in the future. “However, that is what public health officials originally thought about O157 infections, and now they are a leading cause of foodborne infections worldwide,” she noted. O’Brien said that, thanks to decades of experience with O157, public-health personnel were better equipped today to handle toxic strains of E. coli as they appear, although fresh produce continues to pose an E. coli risk. The ultimate risk, she said, is that more enteroaggregative strains may inherit toxin-producing genes in the future. One positive, O’Brien added, was that O104:H4 is a human-specific pathogen, meaning that the risk of exposure through animal sources is significantly lower compared to other E. coli strains. The bacterium likely originally evolved in the gut of a human who was infected with both O157:H7 and an enteroaggregative relative of O104:H4. Rasko said that public health is better prepared to study bacteria, but he doubted that the food system was much better equipped today to prevent a similar outbreak to the one in Germany. “You would need to have sequencing or diagnostics monitoring at every step of the food chain, which just isn’t feasible economically,” he said. Looking to the future, Manning said that her biggest concern lies in public health’s inability to predict the next unpredictable pathogen. “From a public-health perspective, the emergence of new pathogens causes the biggest problems,” Manning said. “In these cases, we don’t know what we are looking for and don’t understand how they cause clinical symptoms, let alone how to treat them.”