Bacterial Viruses Boost Antibiotic Action

When it comes to fighting bacterial infections, doctors are running out of drugs that work. At the same time, replacement drugs are slow in coming.

But new work from HMS and Boston University researchers may help on both counts. Their approach takes a natural enemy of bacteria—viruses that attack bacteria called bacteriophages—and reengineers them to put the punch back into antibiotics. The work, reported in the March 24 issue of Proceedings of the National Academy of Sciences, has the potential to make existing antibiotics more effective and may prevent bacteria from developing resistance in the first place.

HMS MD candidate and first author Timothy Lu likens the engineered phage to a Trojan horse. It is a delivery vehicle that carries a payload designed to weaken the bacterium it invades. Once debilitated, the bacterial cell becomes more vulnerable to attack from the main force, the antibiotic drug.

The idea to construct an engineered phage came after senior author James Collins, a Howard Hughes investigator and professor of biomedical engineering at BU, and his lab discovered that many antibiotics lethal to bacterial cells kill them by causing DNA damage. Collins reasoned that shutting off the DNA repair system in bacteria, a system called the SOS response, would give antibiotics a helping hand. All he needed was a way to do it.

He considered screening for a small molecule that would interfere with the proteins that construct the SOS response. But since outside efforts to find one had fallen short, Collins and Lu, who recently earned a PhD from the Harvard–MIT Division of Health Sciences and Technology, focused instead on proteins that suppress the SOS response. What they needed was a way to insert them into a bacterium. The two had engineered bacteriophages to carry enzymes that break up biofilms in 2007 and thought a similar approach could solve this problem, too.

By definition, bacteriophages have the right tools for the job—they inject DNA into bacterial cells, then hijack the cells’ machinery to turn up production of the coded proteins. All the researchers needed to do was modify a phage to inject the right DNA. “Then you’ve got delivery of the drugs”—in this case, proteins—“right where you want them,” said Collins.

The technique, which involved inserting the lexA3 SOS-suppressing gene into the phage genome, worked. Therapy combining engineered phage with the antibiotic quinolone had approximately 30,000 times more killing power than the antibiotic alone. “We were very surprised when we got these results,” said Lu.

This big boost in efficacy inspired them to run tests with other antibiotics and with antibiotic-resistant bacteria, all of which showed similar results. Not only did the engineered phage renew the effectiveness of antibiotics that had become defunct due to resistance, experiments also showed that the phage reduced the likelihood that resistance would emerge.

Since crippling DNA repair is not the only way to weaken bacterial cells, Collins and Lu look at this synthetic organism as one page out of a volume of possible phage designs. To test this idea, they rigged phage to inject two other genes, one coding a protein that suppresses a bacterium’s ability to create a biofilm and another that opens up pores allowing antibiotics to enter the cell. Both magnified the killing power of the antibiotics the investigators tested.

Collins plans to create libraries of engineered phage, with each synthetic organism injecting different DNA and targeting different strains of bacteria. Some of this work will likely happen at Harvard’s Wyss Institute for Biologically Inspired Engineering, where Collins is a founding core faculty member. Creating a library of phage is “essentially an engineering task,” said Collins. That is, it does not involve time-consuming scientific discovery. He and George Church, HMS professor of genetics, plan to put Church’s DNA synthesis technology to work filling out this library of engineered phage.

For Lu and Collins, this library represents a new way of thinking about rolling out novel therapeutics. Today, every possible incarnation of engineered phage must be approved independently. If antibiotic resistance keeps growing, said Lu, “eventually there will be some kind of paradigm shift.” A future approval process might treat the delivery vehicle differently from the payload. In this hypothetical model, if resistance to antibiotics emerges, the DNA payload could be tweaked to beat the superbug, then fast-tracked through the approval process. Bypassing reapproval of the delivery vehicle could bring new therapies to patients more quickly.

For now, however, Lu and Collins have shown only that their combination therapy is effective in mice. Engineered phage plus antibiotics saved 80 percent of mice infected with Escherichia coli, while antibiotics alone saved only 20 percent.

Lu has spun off a start-up company called Novophage to begin translating this research for the clinic. He and his partners have already raised seed money by winning a business plan competition sponsored by the University of San Francisco. As finalists in four other contests, more funding may be on the way.

“We’re thinking of targeting MRSA first,” said Lu of Novophage’s plans. MRSA is a resistant form of staph infection that according to the Centers for Disease Control and Prevention causes 19,000 deaths per year in the United States. “If we demonstrate that we can bring back defunct antibiotics against it, people will be more willing to support developing engineered phage against other pathogens.”

Though doctors used to use phage therapy to treat bacterial infections, the treatment went out of vogue after the discovery of penicillin. “Antibiotics worked like magic in the ’40s,” said Sankar Adhya, chief of the developmental genetics section at the National Cancer Institute. But antibiotics have since faltered, and phage science has progressed. According to Adhya, who has engineered phage to rapidly identify bacterial infections, “phage has a huge future.”

At the same time, clinicians are clamoring for new ideas. “We need help,” said Robert Rubin, the Gordon and Marjorie Osborn professor of health sciences and technology at Brigham and Women’s Hospital. According to Rubin, a patient in intensive care fares no better in a fight against bacterial infections today than in the 1960s. And with MRSA as an example, the outlook is getting worse. If this new approach turns out to be safe and effective, said Rubin, “we’ll use it as quickly as we can get it on board.”

Students may contact James Collins at jcollins@bu.edu for more information.

Conflict Disclosure: The researchers have patented this work and are licensing it through the BU and MIT technology transfer offices.

Funding Sources: The National Institutes of Health, the National Science Foundation and the Howard Hughes Medical Institute; Timothy Lu received support from an HHMI Predoctoral Fellowship and an HST Medical Engineering/Medical Physics Fellowship; the content of the work is the responsibility solely of the authors