SEA-PHAGES: from educational project to treatment prospect – an interview with Graham Hatfull

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Phages have been a huge area of interest in the past few years, particularly as an alternative treatment for drug-resistant infections with the increasing threat of antimicrobial resistance. Graham Hatfull (University of Pittsburgh, PA, USA) speaks about heading up the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) project and the role this has played in understanding phage diversity and evolution, in addition to commenting on a recent case where a phage cocktail was used to treat a case of Mycobacterium abscessus. Read on to find out more.

First can you just introduce yourself, tell me a bit about background?

Currently, I am a Professor of Biological Sciences at the University of Pittsburgh. I grew up in England and was an undergraduate in London and a graduate student at the University of Edinburgh (both UK) and then I did postdoctoral work both in Cambridge at the MRC Labs (UK) and at Yale University (CT, USA) and I have been at the University of Pittsburgh since 1988.

Could you give us an introduction to the SEA-PHAGES project and the rationale behind it?

Since I moved to Pittsburgh we have been interested in bacteriophage biology, diversity and evolution. Then in the early 2000s we realized that in order to expand our efforts and understand phage diversity we would need to isolate new phages from the environment, purify them and sequence them to help to address our questions.

In 2002, I was fortunate to get an award from the Howard Hughes Medical Institute (HHMI; MD, USA) that provided support for science education innovations and we used those resources to develop a platform where students could become engaged in authentic research isolating new phages from the environment, characterizing them, naming them, sequencing them and characterizing the genomes in order to understand questions of viral diversity and evolution. We initially developed that program locally in Pittsburgh with students working in my lab, then in 2008 together with HHMI, we developed the SEA-PHAGES program, which was the same scientific idea packaged into a course for first-year undergraduate students at institutions, community colleges and universities across the USA – so that’s how the SEA-PHAGES program started!

Initially in 2008 we had 12 schools and it has grown each year, with a really good retention of schools, now involving a total of around 130 schools and in the fall it is going to be close to 150 schools primarily in the USA. This past year has seen approximately 5,500 students participate and overall, we’ve had over 25,000 students that have been through the program. The data suggests it has been very productive in terms of getting students engaged and interested in science and it has been enormously productive from a scientific perspective, I think there has been more than 100 peer-review publications that have come out of the program.

Do you think there is a problem in retaining students in science and do you think projects like this help?

In the USA, there has been a huge problem with student persistence in the sciences and overall –only about 40% of students that begin a science program actually obtain a degree in that subject, 60% drop out.

It is a really severe problem and as a community of academics, we have done a really lousy job of getting students excited about studying and understanding the sciences. That’s part of why we are excited about the SEA-PHAGES program because rather than focusing on very particular content areas we give students a chance to actually become scientists and to appreciate the excitement of discovering new stuff and doing science. After all, there will be plenty of time and plenty of opportunities for students to learn more about very specific content later on.

Moreover, I think what is really interesting about the SEA-PHAGES program is that because it is offered to first-year students there are no criteria – you don’t have to be a ‘gifted’ student or have excelled academically – so, opportunities to do research  are offered to every student who has any curiosity and that’s all they need.

Finally, I think that projects like this are relatively low risk. Some students will get really excited by doing science and may not have realized that they have an aptitude for it, but there will be other students who realize that they don’t have the aptitude and I think that that’s equally important. If students don’t have a particular interest in doing research, it is much better to find that out early and use the opportunities to explore other things you might be interested in rather than discovering you don’t enjoy it further down the road. I think that providing students opportunities to find out what they have an aptitude for and what they are interested in is important and in many ways that is what university should be all about.

Some phages from the program were used to treat case of M. abscessus quite recently. And do you think other phages in the collection could have therapeutic usage? Is that something you are working on?

Yes, absolutely. It has been an interesting foray into an area of science that we hadn’t been particularly involved in previously. We received a couple of strains of M. abscessus from the Great Ormond Street Hospital in London (UK) and our search for phages that infected those strains was of a research interest to us; we were keen to try to understand why phages infect some strains of bacteria and not the others.

The idea that these phages could be useful therapeutically was pretty much a hypothetical prospect at the beginning but then as we moved forward, we found that although it was hard to find phages, with substantial efforts we were able to get a cocktail of phages together that looked like it would work on at least one of the M. abscessus strains.

With regards to the case, it is not an experiment, there are no controls and we are not measuring any variables. We have one patient with a condition where we know the other patients have all died, and that’s the closest to a ‘control’ group that you can get. And in (the case) Isabel has done very well and even though I think she is not out of the woods yet, she is not completely free of the pathogen, she is on the winning side of the equation at this point.

One of the things that we have learnt just looking at M. abscessus is that there is enormous variation amongst different isolates. There’s variation between different people, different patients, but we also see it in phages, specific phages in our collection would infect some strains but not others. That’s one of the more sobering sorts of findings from this exploration is that even though we got a cocktail of three phages that worked, we clearly can’t reproduce that in all patients that have M. abscessus infections. But the question is: can we reproduce those clinical outcomes in some other patients? And can we expand the group of phages that are likely to be useful in order to use them against other patients?

That is something that we are very much working on in the lab and there are two main directions. One is we would like to be able to find more phages, some of that will be going and digging a little bit deeper in certain pockets of diversity within the phage collection and some will be trying to isolate other phages from the environment. Second, we would like to have better methodologies, more high-throughput strategies, so that we can find the phages that may act against strains more simply. The screening currently is pretty tedious and time consuming, so we feel that if we could speed up the screening process by advancing some of the technologies, we may be able to find these strains more easily.

Read more about this story on Infectious Disease Hub here >>

The phages that were used in the treatment of this case were genetically engineered, what do you think the significance is of that?

Part of the importance is recognizing the fact that we had to genetically engineer the phages, we didn’t really have any choice because we wanted to have a cocktail. We wanted to have three phages because we were concerned that if we only used one phage the bacteria could become resistant. However, when we did the screening and we took 50–100 of our best candidates we essentially only found one that worked well, so the question was, where are we going to get others from?

While we had one phage that worked very well, we had many phages that don’t infect at all and then there was a subset of phages for which it looked as though we see some infection of the M. abscessus strain, but it is not sufficiently good that you would use it therapeutically. We were successful in taking a couple of examples where the phages didn’t work very well and engineering them so that they became a good and a useful phage – that was mostly really to convert temperate phages to lytic phages.

So, two of the phages were engineered in order to be lytic and then one of the phages we did something additional, which was isolating a host range mutant, or natural variant, that had essentially learned to efficiently infect the pathogenic M. abscessus strain. Even though the parent phage doesn’t infect very well, once we isolated this mutant it now infects perfectly well, so, in some senses, it is a process of natural evolution.

Finally, within the field about new phages you talked a bit about way you think the future is, but what are the big challenges and how do you think they will be overcome?

The therapeutic use of phages is an interesting field because I am not sure I know anything else that’s quite like this. People have been interested in using the phages therapeutically for 100 years, since they were discovered, and enthusiasm in using them therapeutically has gone in cycles. At the moment, it is one of its high points, so is it going to grow to an even higher point with even greater success or is it going to go back into another period of decline? I think that perspective helps us to think about what the challenges are.

First, it depends on how one views the application. There are two different ways in which you can use phages as a therapeutic. One way is as a personalized treatment, in other words, phages that work against a particular strain for a particular patient. There are now several well-documented cases for this, including the M. abscessus case in London. I think that although the number of cases is small, there is a pretty good suggestion that phages will be useful in treating specific patients.

The second line of application of phage therapy is broader; the doctor gives you a prescription, you take it to the pharmacy and they pull something off the shelf for the infection you have. Even though I think that there is considerable enthusiasm for the personalized approach, the broader, off-the-shelf approach really poses the greatest challenges. One of the main challenges is that for many pathogens there’s a lot of variation amongst clinical isolates and it’s challenging to identify phages that will infect all clinical isolates. In addition, there may be newly evolving strains that you don’t have phages for, so you may never be able to get deeper penetration into the strain variations.

Moreover, once you now start talking about putting 20 or 30 phages together, each manufactured under GMP specifications, together you have to start worrying about the cost. If the cost is prohibitive, then is phage therapy ever going to be more broadly used?

Looking forward, I think the first thing to do is to try to understand what kind of infections  are likely to be the best candidates for a phage intervention, and to stop thinking about phage therapies as a kind of ‘’magic bullet’ that is going to cure all of our woes with antibiotic resistance. We know, for example, that even though the strain variation issue is true for many pathogens it is not true for all pathogens, e.g., in Mycobacterium tuberculosis the strain variation is quite minimal. If you don’t have the problem with the strain variation then you could imagine designing clinical trials where you could assess if phage therapy was feasible and get a good, clear answer.

Once we’ve understood which diseases are good candidates for phage intervention we need to figure out how to do good clinical trials in order to evaluate, to measure the variables, to understand the kinds of infections, the dose, the frequency of dosage, the incidence of resistance and how we can be best tackle it, whether it is best to have cocktails or to use phages sequentially and whether the immune system and immune reactions to phages are limiting for their usage. In addition, we need to understand to what extent phages can be used together with antibiotics in order to either make the antibiotics more effective, to shorten the regimens, or to simply minimize the incidence of new antibiotic resistance.

I think that’s still a fairly ambitious set of questions and I think that what we need as a community most of all is some really good scientific evaluation. Moreover, I think that continued investment in trying to understand bacteriophage biology – how phages interact with their hosts, what the origins of the strain specificity are, what the mechanisms of resistance are, how the phages co-evolve to counter resistance – is likely to be incredibly useful for moving the field forward. For example, in the particular therapy case that we were involved in it is pretty clear we would not have had a successful intervention if it wasn’t for programs like SEA-PHAGES, which has generated this huge collection of phages, and we have spent many years understanding the biology and developing tools to be able to engineer phages so that they could be used therapeutically. The translational applications really wouldn’t have happened, and they benefited directly from all those basic biology operations. I think that investing in the core biology and appreciating that advances and investments there are likely to open new avenues for therapies is really important.

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