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Research at Boston University

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Persistent Beginnings

By Chris Berdik
Dialogues

When Boston University PhD candidate Kyle Allison started working on a potential breakthrough treatment for chronic bacterial infections, the task seemed impossible. Two people convinced him to keep trying. One was the head of his lab, biomedical engineer Jim Collins, a William Fairfield Warren Distinguished Professor. The other was James Joyce.

The year before joining Collins’s lab in 2007 as a biomedical engineering doctoral student, Allison had earned a master’s degree in English literature at the University of London. He knew he wanted to be a scientist, but he also loved literature, and he took advantage of a fellowship to follow up on that love before he came to BU. He wrote his master’s thesis on Joyce’s experimental novel, Finnegans Wake, reputedly the most difficult work of fiction in the English language. According to Allison, the challenge of Joyce’s novel, written with a mix of sentence fragments, stream of consciousness, and multilingual puns, was great preparation for biomedical research.

“Understanding that book is kind of a mad hunt,” he says. “The experience of working that hard to piece it together and figure it out was really useful when I started trying to solve the big problems being worked on in Jim’s lab.”

The big problem Collins gave Allison when he arrived at BU was finding a way to kill bacteria that evade antibiotics by hunkering down into a dormant state and essentially playing dead until the danger has passed. Known as “persisters,” these bacteria are thought to cause many hard-to-treat infections, including tuberculosis, which kills about a million people every year, staph infections that kill thousands, and other chronic infections of the urinary tract, lungs, ears, and skin that antibiotics can’t seem to touch.

After many false starts, a ton of hard work sprinkled with serendipity led to a surprisingly simple solution: a little sugar could give these dormant bacteria just enough pep to turn a previously ineffective antibiotic into a killing machine. Allison tried several combinations of antibiotics and different sugars before the team found one that wiped out persisters in both the petri dish and in mice with chronic urinary tract infections.

The findings were published in Nature in May 2011, coauthored by Collins and Mark Brynildsen—a postdoc now on the faculty at Princeton. Allison gained sudden fame for discovering this simple, inexpensive new weapon in science’s ongoing war against the microbes. In November 2011, he won the $15,000 first prize in the national Collegiate Inventors Competition. A month later, he landed on the Forbes list of the nation’s 30 most-­promising scientists under 30 years old. We sat down with Allison and Collins to talk about the potential of this new treatment and the mad hunt for its discovery.

Can you tell us a little more about bacterial persisters?

KYLE ALLISON: They are a subpopulation of bacteria that tolerate antibiotics. They’re not different from normal bacteria in the population, in that they should be killed by the antibiotic, but for some reason, they go into a state of dormancy.

So, we’re not talking about the infamous “super bugs” here?

JIM COLLINS: Right. They’re genetically identical to those bacteria that are susceptible to the antibiotics. But, they have a biological or physiological response that affords them protection. It’s the biological equivalent of ducking and covering your head.

These bacterial persisters are now thought to underlie recurring, chronic infections. This goes across the bacterial spectrum. In the past, it was thought that the person was likely getting reinfected. Now, the thought is that persisters cause these clinical conditions. Persisters are also thought to underlie biofilms, which are a major problem in hospitals, especially for any device put in the body, be it a catheter, an artificial knee or hip, a pacemaker, or a defibrillator.

“It’s the biological equivalent of ducking and covering your head.”

What was the genesis of this research?

KA: When I started working at the lab, Jim had me look into the biology of how persisters are formed. But at a certain point, Jim said to me, “You know the whole reason why we’re interested in persisters at all is to try and kill them off better.” He suggested we might leapfrog ahead and find a way to kill persisters off without fully understanding the mechanisms of their formation.

I spent some time working on it, and reading through everything that I could find. I came back and told Jim that I didn’t think it was possible at this point. And Jim said, “Well, that’s great. It sounds like an excellent project for you. Keep up the good work.”

How long did it take for you to decide it was impossible?

KA: It was probably two weeks or so. This was my first year as a graduate student, so I thought that I knew quite a bit. I’d read everything I could, and I came back and just said, “It’s impossible, there’s not enough information.” Jim said, “Just go down to the lab and get some experiments going.” That’s how people make discoveries.

OK, then what?

KA: I went back to it. The dormancy of persisters was thought to be the reason why the antibiotics weren’t effective. The thought was that maybe we could switch these dormant bacteria back into an actively dividing state. If we could just make them normal again, then we could kill them off with antibiotics.

So, that’s what I was trying to do. For a few months, I kept trying to find a way to trick the dormant bacteria into waking up. But, the things I tried weren’t very successful, and it kind of led me to start reframing the question.

After doing some reading and thinking on the problem, I thought that maybe you don’t need to completely wake these bacteria up to kill them off. Maybe I could metabolically stimulate persisters to be killed by a type of antibiotics called aminoglycosides.

You were already trying sugars at this point?

JC: Yes, bacteria are similar to kids. You give them sugars and they can get hyped up. Kyle tried a range of different sugars and other metabolites, and he looked at how they affected the killing efficacy of different antibiotics against the persisters. He found that the sugars were not helping at all with two different classes of antibiotics—quinolones, which include drugs like Cipro, and beta-lactams, which include things like penicillin.

KA: Right. At first, I was using the best antibiotics known to kill persisters but the sugars weren’t helping. Then, a paper came out that said persisters, although they are dormant, still make proteins, which was a really critical piece of information, because aminoglycoside antibiotics target protein synthesis, and yet they aren’t known to work against these dormant bacteria. It raises the question, why not? I thought, maybe this metabolic stimulation could potentiate aminoglycoside’s ability to kill the persisters.

I was a little bit shocked the first time I ran that combination of sugar and aminoglycosides on E. coli and staph bacteria, because it just wiped out the entire population with an antibiotic that wasn’t known to work against persisters.

Then you tried this treatment on mice?

KA: Yes. These were mice that had urinary tract infections from biofilms on surgically implanted catheters. We waited two days before starting treatment. We didn’t want to give them treatment right away, because people don’t usually know immediately that they have an infection and go to the doctor.

After two days, the mice received a standard treatment for chronic urinary tract infection, which is twice-daily treatment with intravenous aminoglycosides for three days. One group of mice just got the antibiotics. Another received aminoglycosides plus the sugar mannitol. And a third group received no treatment.

Before we get to your findings, can you give a quick primer on mannitol?

JC: Mannitol is a sugar that is actually sweeter in taste than glucose, but it’s not metabolized by the body.

KA: The selection of mannitol as our sugar was critical. We could have used glucose or fructose, but we knew that if we delivered those intravenously, the sugar would be metabolized by the mouse’s body and wouldn’t reach the infection site.

So, what were the results?

KA: We found that after the three days of treatment and one day to let the mice recover, we reduced the bacterial load on the catheters significantly, by about an order of magnitude. We also reduced the spread of the infection to the kidneys, which is a major complication associated with urinary tract infections.

What conclusions should we not jump to about this research?

KA: The most important thing is that people don’t think that they can just take sugar with their antibiotic and that’s the end of the story. When the paper came out, a lot of the press put it under the headline “A Spoonful of Sugar Helps the Medicine Go Down.” That’s a great hook, but that’s not what we’re suggesting.

We’re suggesting that we can take targeted therapies to improve existing antibiotics and some of these can be very simple and surprisingly cheap. If you take a spoonful of sugar with your medicine, you’re just going to get a sugar high. You’re not going to help clear up the infection.

What’s next for this project?

JC: So, BU is in the midst of spinning out a company. It’s going to focus on the antibiotic platforms developed in our lab, including Kyle’s work. The name of that company will be EnBiotix, and we’re working with BU Technology Development to get behind this work and champion its translation into the clinic. Hopefully, we can get it into a clinical trial within a couple years via the new start-up.

KA: In the research phase, I’m starting work on the bacterial infection that is a leading cause of death among people with cystic fibrosis. About 70,000 people worldwide have this disease, which causes mucus to build up in the lungs, creating a perfect host environment for bacteria called Pseudomonas aeruginosa. Most people with cystic fibrosis are ultimately killed by this pathogen. Their median life span is only 30 years. So there is a pressing need here. If we can possibly address that problem with the method that we developed, then we should be doing it.

There’s a lot that can be done for persistent chronic infections, and I think that this approach—where we try to understand on a mechanistic level how the antibiotics work and then fine-tune the treatments to get the drugs we already have to work better—may be a faster route to fighting these infections than trying to develop brand-new antibiotics.

Kyle, how have you adjusted to the attention that followed this discovery?

KA: It’s been quite a transition. For years of working on this problem, the only people I talked to about it were Jim and Mark Brynildsen. It was something that I thought was very important. We worked hard on it, and I thought we made great progress. But it’s an entirely different thing when people whom you didn’t tell about the research come up to you and congratulate you and talk to you about it. It’s a very different thing to be validated by people beyond your immediate peers. It’s surprising, and it’s a great feeling.

Are you going to be part of the start-up that develops this treatment for patient care?

KA: Probably not. I’m interested in going the academic route. After I finish up here, I want to transition to working on ­tuberculosis.

My passion really is basic-level research. Industry is a good place to be if you want to work on translating new ideas into practices, but academia seems to be the best place if you want to start at the very beginning with brand-new ideas, coming up with and developing them. You know that a lot of them will fail, but eventually you’ll succeed.

Note: Kyle Allison graduated with his PhD in bioengineering in May 2012. He is currently pursuing research at the Albert Einstein ­College of Medicine in New York City.

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