Us against Them

New ways to fight antibiotic-resistant bacteria

Scottish researcher Alexander Fleming didn’t need to develop a strategy to discover penicillin. In the summer of 1928, before embarking on a 2-week holiday, he accidentally left a petri dish smeared with staphylococcus bacteria uncovered on his lab bench. While he vacationed at his family’s country home in Suffolk, England, a warm spell settled on Oxford, and the flourishing bacteria covered the dish’s gel in a thick lawn.

THE CHOSEN ONES. These plates contain growing bacteria isolated from soil that show promise for producing new antibiotics. Cubist Pharmaceuticals

Yet Fleming noticed upon his return that some tiny specks on the gel’s surface were surrounded by clear halos where bacteria had died. Spores from an obscure mold had probably drifted up from a mycology lab one floor below, landed on the gel, and secreted a bacteria-killing goo—which was later identified as an antibiotic.

Today’s researchers don’t have the luxury of waiting for new antibiotics to drop out of thin air. With the number of antibiotic-resistant bacteria rising rapidly—and once-curable infections again killing thousands of people each year—scientists are on the hunt for new antibiotics to battle toughened bacteria.

Some researchers are scouring nature to find organisms with antibiotic properties that have been overlooked. Other scientists are concentrating on enhancing natural germ-fighting chemicals to make them more effective or on creating synthetic antibiotics from scratch. One group is working to restore the effectiveness of older antibiotics by taking resistance away from bacteria.

Promising antibiotics arising from these techniques have a long way to go before reaching the pharmaceutical market—most new drugs take 10 to 20 years from when they’re discovered to when they’re sold to consumers. So, many researchers see an urgency to finding new ways to fight antibiotic-resistant bacteria. “This problem is growing. We’re not going to get away from [antibiotic resistance] anytime soon,” says Warren Jones of the National Institute of General Medical Sciences in Bethesda, Md.

Fishing trip

The majority of antibiotics currently in use originally came, as penicillin did, from natural substances secreted by fungi, bacteria, and other organisms.

“In a crowded, rough-and-tumble world, if an organism has the ability to make and release antibiotics into its environment, it can outcompete the bacteria around it,” says Jones.

Since the 1940s, when penicillin was developed into a drug, scientists have mined the natural world for new antibiotics. However, many scientists now suspect that this vein is running out, Jones says. Researchers have found fewer new natural antibiotics with each passing decade. Some scientists are working to buck that trend, either by striking out into new territory or by relentlessly reexamining fronts previously considered.

Edward Noga and his colleagues at North Carolina State University in Raleigh, for example, are searching the seas. Although oceans cover more than 70 percent of Earth, Noga says, they’ve barely been explored as sources of new drugs.

In 2001, while looking for chemicals that fish naturally produce to defend themselves against disease, Noga and his colleagues discovered a new class of antibiotics in the cells of fish gills. The team named the chemicals piscidins.

The gill cells, known as mast cells, are best known for their role in producing allergic reactions in people. However, these cells aren’t just “biological bad guys,” says Noga. Instead, the immune-system cells provide a broad response that can quickly kill many types of parasites, bacteria, and viruses.

Noga says that in the past few years, his team has also discovered piscidins in many other species of fish and has turned up other types of natural antibiotics in shellfish. The scientists have started a biotechnology company to commercialize their discoveries and plan to work with pharmaceutical companies to develop antibacterial drugs based on the natural chemicals.

With the majority of deep-ocean waters unmapped and not easily accessible, searching for new drugs from the seas could be a difficult and costly task, says Frank Tally of Cubist Pharmaceuticals, based in Lexington, Mass. Instead, he and his colleagues have developed an inexpensive way to scour land for antibiotics that have been overlooked. They’ve undertaken an unusually wide-ranging search of the world’s dirt.

Bacteria from soils have contributed many of the antibiotics currently in use. However, Tally notes that researchers have generally taken advantage of bacteria that are abundant and widespread. “All the low-hanging fruits have already been found. Now, we have to come in and find all the rare organisms,” says Tally.

Cubist has extended the search to tens of thousands of soil samples from points around the globe. When any of the company’s 310 employees go on vacations or business trips, they return to the office with tiny vials of soil from their destinations. From these samples, Cubist scientists have already discovered hundreds of new bacterial species.

Changing a decades-old paradigm of how pharmaceutical companies grow bacteria in the lab, the company’s research teams have streamlined the determination of which newly discovered bacteria produce effective antibiotics. They miniaturized the process by growing bacteria in droplets of broth and adopted robotic methods to evaluate which bacterial species produce promising new antibiotics.

From their pool of newly discovered bacterial species, Tally notes, Cubist has isolated several chemical “hits”—novel compounds shown to kill other species of bacteria. The company is analyzing each of these chemicals to determine which to pursue as new drugs.

New and improved

Although natural antibiotics have benefited their microbial producers for billions of years, medical researchers have ideas for properties that could strengthen the power of drugs modeled after natural products. According to Chaitan Khosla of Stanford University, no antibiotic on the market has all the qualities that physicians find valuable—for example, being effective in an oral dose or killing a wide range of bacteria.

“You’d like to be able to build in that quality that nature didn’t build into its own products,” says Khosla.

To make more-potent antibiotics that stay effective, he and other scientists aren’t looking in nature. Instead, they’re using the latest genetics techniques in their own labs.

Researchers have been tinkering with antibiotics for years by chemically changing parts of their molecules’ structures. However, notes Khosla, modern genetics research has taken this tinkering in a new direction. Rather than change an antibiotic’s composition through chemistry, his team and others are genetically reprogramming organisms that make natural antibiotics so that they produce new kinds of molecules.

“The beauty of how nature makes antibiotics is that it makes them on an assembly line,” explains Khosla. Bacteria slap together an antibiotic molecule piece by piece, with different genes or sets of genes controlling each new addition. By genetically hijacking various steps on the assembly line, Khosla’s lab has created more-effective forms of existing natural antibiotics. For example, they’ve fine-tuned erythromycin, which is frequently prescribed for respiratory infections, and rifampin, which is often used against tuberculosis.

The new molecules are missing some standard pieces and have some additions. These remodeled forms can overwhelm bacteria that have become resistant to current forms of antibiotics.

Khosla’s strategy capitalizes on researchers’ growing knowledge of bacterial genomes. Today, for many disease-causing microbes, whole catalogs of their DNA sequences with information on each gene’s probable function are available online in shared databases.

John Blanchard of the Albert Einstein College of Medicine in New York says that such catalogs have guided his lab in making synthetic compounds that target a bacterium’s Achilles’ heel—any of the proteins or other compounds required for its survival.

Both natural and synthetic antibiotics have traditionally focused on one of four major targets essential to bacterial life:

  • the cell wall, a structure found in bacteria but not animals;
  • protein production, a pivotal function for cell maintenance;
  • DNA and RNA replication, necessary for bacterial replication;
  • and folate synthesis, the creation of a necessary nutrient.

To develop new targets to which bacteria might have more difficulty developing resistance, Blanchard’s team started with the simple question, “What can bacteria do that [people] can’t?” The researchers noted that while people must obtain 10 amino acids and numerous vitamins from their diets, bacteria can make all 20 necessary amino acids and many vitamins on their own. Scans of bacterial genomes have shown that of the 200-to-400 genes absolutely necessary to support life in many microbes, about one-fifth code for processes that make amino acids and vitamins.

Bacteria employ a step-by-step process for constructing not only antibiotics but also amino acids and vitamins. Once you’ve administered chemicals that block any part of this process, Blanchard says, “you’ve stopped the organism in its tracks.”

Blanchard and his colleagues work with pathogenic bacteria, including those that cause tuberculosis. The team has identified several chemicals that disrupt the seven-step process for making L-lysine, an amino acid that the bacteria require. What’s more, bacteria use a protein precursor of L-lysine to construct their cell walls. When the scientists blocked L-lysine production early enough, the bacteria lost their cell wall component as well as L-lysine.

Blanchard’s lab has partnered with the pharmaceutical company Merck to develop the chemicals into drugs.

Resisting resistance

The threat of antibiotic resistance is the major force that drives antibiotic innovations.

Once a bacterium develops drug resistance, a genetic element that’s common in bacteria enables the newfound invulnerability to rapidly spread to other bacteria—even beyond the original species. The vehicle for that spread is a plasmid, a circular bit of DNA that bacteria routinely exchange.

Traditionally, scientists have viewed this transfer of antibiotic resistance as inevitable. However, Paul Hergenrother of the University of Illinois at Urbana-Champaign questions that assumption.

For bacteria to pass on plasmid-residing resistance genes from generation to generation, each dividing cell needs to make new copies of its plasmids to go into each of its daughter cells. “What we wanted to do was to vanquish these plasmids from the [daughter] cell so that the bacteria were sensitive to antibiotics again,” says Hergenrother.

Hergenrother’s team reported a successful proof-of-principle experiment last year. After designing and administering a chemical that halts plasmid replication, the researchers found that each Escherichia coli bacterium had only a single copy of the resistance-carrying plasmid to pass on. As each new generation had only half as many bacteria with resistance-causing plasmids as the previous generation did, colonies that received the chemical eventually lost the ability to resist antibiotics.

Hergenrother envisions giving a patient who has an antibiotic-resistant infection a dose of antibiotic combined with the chemical that halts plasmid replication. Then, as the bacteria lose the plasmid, the antibiotic will wipe them out.

Even with promising results such as Hergenrother’s, many large pharmaceutical companies have recently backed out of research programs fighting antibiotic resistance, says Steven Projan of the pharmaceuticals company Wyeth in Cambridge, Mass.

Projan notes that the field isn’t a big moneymaker for most companies—people tend to take antibiotics for the short term, but they spend far more money on chronic conditions, such as depression or diabetes. With the growing cost of clinical trials, Projan says, companies prefer to invest in drugs likely to have a substantial return.

He adds that some smaller companies that had focused on developing new antibiotics have merged with large corporations, which then reduced the infectious-disease–research programs. “Where there were probably two score or more active groups in the ’80s, there are now maybe five. By my estimate, this translates to over 4,000 fewer scientists working on antibacterial drug discovery,” Projan says.

The scientists who continue in this field have their work cut out for them. Jones says that the continuing rise of new forms of antibiotic resistance will necessitate new antibiotics far into the foreseeable future. “As soon as you develop a new [antibiotic], you start the clock running toward ineffectiveness,” he says. “It’s an unending battle.”

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