Antibacterial development is essentially a race: Researchers develop drugs, bacteria mutate their way around them. And judging by the number of multidrug-resistant infections seen in hospitals - and increasingly outside of them, too - bacteria have one leg up in the race.
But new research shows how the very evolutionary principles that make bacteria such vexing adversaries might be used against them. Bacteria are not only infectious agents, but also are subject to infection themselves, by a class of viruses known as bacteriophages. And those phages can - and do - mutate to overcome bacterial resistance.
"An antibiotic is a static entity - the bacterium can become resistant, but the antibiotic cannot change unless a chemist modifies it," Jeffery Miller, professor and chair of microbiology, immunology and molecular genetics at the University of California at Los Angeles, told BioWorld Today.
In contrast, phages have a mechanism that allows them to evolve right along with their host, keeping up the old game of cat and mouse indefinitely. That mechanism is described in the Sept. 23, 2004, issue of Nature in a paper titled "Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements." Researchers from UCLA and the University of Calgary in Alberta, Canada, collaborated on the studies.
Bordetella are a group of bacteria that cause respiratory infections. It already was known that Bordetella-infecting phages mutate to be able to bind to different receptors on the host bacterium, and that the phages switch between several forms that can either have a preference for the virulent forms of Bordetella, a preference for avirulent forms or lack such a preference altogether.
In the research reported in Nature, the scientists showed that the bacteriophage has DNA that functions to change the amino acid sequence of the protein binding to the bacterial surface. The DNA responsible for generating those changes has two key regions. One region is highly conserved and serves as a template. Part of the phage's replication cycle involves reverse transcription of that template - the generation of an RNA copy from DNA.
During that transcription process, adenines in the template's DNA sequence are uniquely vulnerable to mutagenesis. The RNA resulting from the reverse transcription in them re-transcribed into cDNA. Parts of that cDNA are incorporated into the DNA sequence of a variable region located near the template in the phage genome. It is that variable region that codes for the proteins that interact with the bacterium during infection.
The transfer of the template region does not occur by a simple cut-and-paste mechanism transferring the entire template region, with a few mutated adenosines, to the variable region. Instead, the scientists demonstrated that from one phage generation to the next, the variable region shows a mosaic of sequences derived from its parental variable and template regions. The researchers estimate that the system is capable of generating more than 1012 different sequences - enough to keep infecting bacteria for a long time to come.
"What's elegant about it is that the template never changes, because the transfer of information is unidirectional and diversity is generated in the copying mechanism," Miller said.
Miller stressed that during natural infection, the generation of successful mutations is an unlikely process.
"Most of these events are probably nonproductive; they make phages that recognize no receptor," he said. However, the overall mutation rate is low, so the total phage population does not suffer. And, as the bacteria mutate, the advantages of producing a phage that is able to infect a mutated bacterium outweighs the disadvantages of producing nonfunctional receptor-binding proteins.
The idea of using phages to treat bacterial infections is not new. It is currently being used in several countries. In fact, according to an article in the Dec. 24, 2003, issue of the Journal of the American Medical Association, at least one institute, the Eliava Institute in Tbilisi, Georgia, formerly part of the Soviet Union, "retains a flourishing practice in phage therapy."
Bacteriophage therapy also was used in the first half of the 20th century in the U.S. As a therapeutic approach it was supplanted by the availability of antibiotics; penicillin became widely available in the 1940s and was quickly followed by other antibiotics, JAMA reported. But recently, with drug resistance to those antibiotics an increasingly urgent problem, the article said, there has been interest in reviving bacteriophage therapy, bolstered by a far more sophisticated understanding of phage biology than was available earlier in the century. This new research might help in those efforts by giving the phages more specificity than was previously possible.
A new company has been founded that aims to commercialize that research. Its CEO, David Martin, told BioWorld Today that Avid Biotics, which was incorporated in Delaware in July and is living on seed funding from angel investors, has "negotiated exclusive rights from UCLA with the intent primarily of developing antibacterial therapeutics based on the technology."
Miller sees two major application areas of the research. First, "we believe we will be able to transplant this basic mechanism to diversify regions of proteins of interest to acquire desired characteristics," such as changed binding or enzymatic properties.
Second, though work needs to be done to bring such an approach to the clinic, the researchers hope to one day be able to use that mechanism to tailor phages to drug-resistant bacteria.
"Phages are an untapped resource," Miller said. "They are numerically the most abundant life form on earth. They are enormously successful, because they have learned a trick or two about diversity. Phages are already diverse, and the mechanism we have discovered allows us to engineer bacteriophages that will be efficiently able to mutate themselves to overcome resistance that develops in their host."