An outbreak of E. coli isn't usually the stuff of feel-good stories. Feel-bad is more like it—or even feel-organ-failure. But recent E. coli outbreaks can offer us a bit of solace. We live in the anxious age of synthetic biology, when scientists can reconstruct entire genomes from raw chemicals, and when we all fret that someone is going to use this new technology to create a monster bug and unleash a man-made plague. According to one government report, "The effects of some of these engineered biological agents could be worse than any disease known to man." But a close look at recent outbreaks of E. coli—and a closer look at the bacteria themselves—may help us to put aside our fears for the moment. Engineering plagues is harder than it looks.
In 2006, a pair of major E. coli outbreaks swept across the country. One was carried on spinach, the other on lettuce. The spinach outbreak caused 204 illnesses and three deaths. The lettuce outbreak made 71 people sick. In both outbreaks, many people had to be rushed to the hospital. Some got away with just bloody diarrhea. In other cases, the bacteria released toxins into the bloodstream that caused kidneys and other organs to shut down.
The same strain was behind both cases as well as most other recent outbreaks of E. coli. It's known as E. coli O157:H7, named for some of the molecules on its surface. It emerged in the 1980s as a nasty pathogen found mostly in tainted hamburger meat. It lives comfortably (and harmlessly) in cows and other mammals, but if it gets into a human host, it sometimes wreaks havoc. When animals shed the bacteria in their manure, the pathogen can make its way onto crops, and in recent years it has contaminated not just hamburger meat, spinach, and lettuce but apples and bean sprouts. In addition to the occasional major outbreak, it causes a steady stream of illnesses—about 75,000 a year in the United States—that attract less attention.
Scientists noticed that the most recent outbreaks were particularly brutal. The bug from 2006 sent three to four times more people than expected to the hospital. Typically, only 4 percent of people who get infected with E. coli O157:H7 suffer the worst form of the disease, in which toxins are released into the bloodstream. As many as 15 percent did in 2006.
This worrisome trend led a team of scientists based at Michigan State University to take a look at the DNA of the bacteria. The researchers compared bacteria from recent outbreaks with hundreds of others samples and published the results last Monday. The scientists drew an evolutionary tree based on the differences in the bacteria's genes. One branch of the tree—the one that caused the spinach and lettuce outbreaks in 2006—is significantly more likely to make people sick than the others. And they found that this lineage has been exploding in recent years. In 2002, it accounted for 10 percent of the E. coli cases recorded in Michigan. In 2006, it accounted for 46 percent.
To figure out what makes this new strain so vicious, the scientists selected a microbe from the 2006 spinach outbreak and sequenced its entire genome. They discovered that it is not a minor variation on the basic E. coli O157:H7 plan. It is a major overhaul. Hundreds of its genes can't be found in other strains. It has lost hundreds of others. And many of the genes it shares with its close relatives have mutated.