Gene Sequence Of Deadly E. Coli Reveals Surprisingly Dynamic Genome

The type of foodborne E. coli that was sequenced, designated O157:H7, is a worldwide threat to public health and has triggered scores of recent outbreaks of hemorrhagic colitis (painful, bloody diarrhea) and many fatalities from kidney failure, according to project leaders at the Genome Center of the University of Wisconsin-Madison (UW-Madison). Close to 75,000 infections caused by O157:H7 transmitted through contaminated food occur annually in the United States, and such infections are most dangerous to children under the age of 10 and the elderly. One well-known U.S. outbreak in 1982, linked to contaminated hamburger meat, led to identification of O157:H7. An outbreak last summer in Milwaukee, Wisconsin, resulted in 60 cases and the death of a 3-year-old child.

"E. coli O157:H7 is one of the most dangerous pathogens threatening our food and water supplies," says Anthony S. Fauci, M.D., director of NIAID. "Better ways to diagnose, treat and prevent E. coli O157:H7 infections are badly needed. This new information will provide important leads to scientists working to reduce the human and economic burdens of this important pathogen."

When researchers compared the more than 5,000 genes of this harmful E. coli to those of a previously sequenced and harmless laboratory strain, they found O157:H7 possessed more than 1,000 genes the other strain lacked. Many of these new genes appear to have been transferred from other bacteria by way of bacterial viruses, indicating that over evolutionary time E. coli acquires foreign genes at a much higher rate than other organisms.

"We found a whole host of unexpected differences between the two types of E. coli," says lead author Nicole T. Perna, Ph.D., of UW-Madison, "things that have never been seen before, and things we hadn't thought to look for." The genetic variability of E. coli and its close relatives may help explain the diversity of human diseases they cause.

"This bacterium is loaded with interesting genes," says UW-Madison research team leader Frederick R. Blattner, Ph.D. E. coli can obtain new genes in several ways, he explains, but the new research especially points the finger at viruses called bacteriophages that infect only bacteria. Bacteriophages insert their genetic material into bacterial DNA. Some of these viral genes, originally acquired from other bacteria in E. coli's environment, may prove advantageous. The new genes can quickly spread through an E. coli population through a process called conjugation, whereby bacteria exchange DNA directly. "We have found that the genomic pieces are constantly shuffling around so that any particular strain contains a subset of the full range available," Dr. Blattner says. "We've termed this larger pool of available genes the pathosphere."

Some of the new genes may contribute to the organism's virulence. E. coli produces two known toxins called Shiga toxins, which can cause fatal kidney damage. But initial analysis of the genome sequence shows that several new genes, probably inserted by viruses, are likely toxin-making genes as well. These genes appear similar to known toxin genes in other pathogenic organisms.

The new genes also help explain why E. coli O157:H7 infections are sometimes difficult to treat, says Guy Plunkett III, Ph.D., a geneticist at UW-Madison. The reason is that certain antibiotics used against E. coli can actually stimulate virally infected bacteria to produce more viruses and viral toxins. "The antibiotics kill the E. coli, but in their death throes the bacteria release more of these toxins," Dr. Plunkett explains. "So in the course of treating the disease, you could actually exacerbate the problem."

Another set of newly discovered E. coli genes might allow the bacteria to withstand fever, one of the body's defenses against infection, Dr. Plunkett says. Even so, nothing protects the microbe against the higher temperatures of thorough cooking.

The genome sequencing has done more than reveal how tough this organism is, however. The sequencing has given scientists a much larger number of genetic markers -- segments of DNA that can be used to identify the bacteria -- than were previously known, Dr. Perna points out. This information should allow scientists to detect the presence of E. coli more easily, whether it is in humans or potentially contaminated food.

In addition, the new genetic information should aid efforts to create an animal vaccine against this pathogen, says Dennis Lang, Ph.D., enteric diseases program officer at NIAID. Such a vaccine might reduce or eliminate E. coli in cattle or other animals, thus limiting subsequent human exposure, Dr. Lang explains. A human vaccine would be less useful but could help prevent person-to-person spread during large foodborne outbreaks, Dr. Lang says.

The researchers used a new technique called optical mapping, invented by co-author David C. Schwartz, Ph.D., also of the UW-Madison Genome Center, to help organize this E. coli gene sequence. With optical mapping, scientists use a fluorescence microscope to photograph and measure a specially prepared DNA molecule, allowing them to more quickly determine its size and structure. The National Human Genome Research Institute (NHGRI) provided funds to develop the optical mapping methods.