From mutant microbes to drug discovery

Researchers link infection with a corkscrew-shaped bacterium called Helicobacter pylori to ulcers, stomach cancer and even a type of lymphoma. The usual treatment — an antibiotic cocktail plus antacids — which patients must take for weeks at a time, is often ineffective because of drug resistance, and is impractical to administer easily in many developing countries where the infection is widespread.

But the search for better therapies may now be easier thanks to a new research tool developed by Dr. Nina Salama and colleagues. The approach allows scientists to identify genes that are essential for Helicobacter's growth or its ability to cause disease — genes that are likely to be potential targets for drugs that can effectively wipe out the infection.

The December issue of the Journal of Bacteriology features the study. Co-authors include Benjamin Shepherd, a research technician in Salama's Human Biology Division lab, and Dr. Stanley Falkow, an investigator at Stanford University School of Medicine.

Mutant library

The new resource created by Salama and colleagues is called a mutant library, which is essentially a collection of Helicobacter strains that each harbor a different mutant gene. The mutations were made by randomly inserting bits of DNA called transposons throughout the bacterial genome so that one gene was disrupted in each strain. Using a technique called microarray tracking, the researchers determined the identity of each mutant gene in the more than 5,000 mutant strains they created.

Salama said that the accomplishment is significant because until now, researchers have lacked a powerful tool for systematically testing the function of each of the microbe's genes, some of which contain the blueprints for Helicobacter's ability to cause infection.

"A byproduct of the transposon tracking experiment was identification of a class of genes that cannot be mutated because they encode genes essential to the organism's survival," she said. "We expect that some of these essential genes will be useful for developing new antimicrobial drugs. In addition, they will help us to understand a great deal about the basic biology of this organism."

Helicobacter pylori infects more than half of the world's population, although in about 90 percent of cases the bug does not cause severe disease. Scientists suspect that the infection is spread from person to person and originates in contaminated water supplies.

Once inside the human body, the microbe makes its home in the mucous-rich lining of the stomach and is associated with the vast majority of ulcers of the stomach and upper gastrointestinal tract. Long-term Helicobacter infections also significantly increase a person's risk of developing gastric (stomach) cancer and a type of cancer known as mucosal-associated-lymphoid-type lymphoma. Gastric cancer is the second most common form of cancer worldwide, with the majority of cases occurring in Asia.

Scientists do not yet understand the factors that cause Helicobacter infections to be benign in the majority of infected individuals and cause a diverse range of diseases in others. It's likely the different outcomes result from an interaction between bacterial genes, host genes and environmental factors.

Salama said that scientists are eager to develop new therapies that are highly specific for Helicobacter and that are easily deliverable, particularly in developing countries.

"People are usually treated with triple- or quadruple-therapy: two antibiotics, one of several drugs to reduce stomach acid, and sometimes bismuth," she said. "Drug doses are high and the usual regimen is to take them for two weeks."

The problem, she said, is that drug resistance has been observed for all of the antibiotics that have been used. What's more, the drug regimen is complex to administer and the antibiotics that are used can kill other naturally occurring bacteria in the body, which can cause side effects.

Promising projects

To search for additional promising drug targets, Salama's lab is focusing on several new screens of their mutant library. Postdoctoral fellow, Dr. David Baldwin leads a study that evaluates which mutant strains are unable to survive in mice. Graduate student Laura Syrcura is examining genes that determine the organism's spiral shape, which scientists have speculated is important for Helicobacter's ability to invade the mucous-rich lining of the stomach.

A third project in the lab, led by graduate student Elizabeth Lester, focuses on determining the three-dimensional structure of some of the essential Helicobacter genes identified in their recently published study. The work, a collaborative effort with Dr. Barry Stoddard, may lead to a better understanding of the function of these essential genes.

Salama said the goal for each of these projects is to identify potential targets for drugs or vaccines that might be administered alone in one or a few doses.

Research in her laboratory is funded by National Institutes of Health, the Pew Charitable Trusts and Fred Hutchinson's New Development Fund.