Capsid and Tail

a weekly phage periodical
Issue 19: What's it like to help with phage crowdsourcing?
February 28, 2019

What's it like to help with phage crowdsourcing?

To understand what it's like to take part in phage crowdsourcing, we interviewed five labs who've contributed phages on behalf of a patient.

Back in November, we told you about a phage crowdsourcing effort on behalf of a patient in Helsinki, Finland. This effort is still ongoing, and excitingly, several phages have so far been found that work on the isolate.

This week, we want to delve into what it was like for those labs that sent phages.

What's New

The World Health Organization wants to better understand the current pre-clinical antibacterial R&D landscape! Companies, institutions and individuals doing pre-clinical work targeting any of the WHO Priority Pathogens, TB and/or C. difficile, submit your data here by March 18, 2019!

WHOCall for data

A new NIH funding announcement involving phages: exploratory/developmental research into microbial-based cancer therapy (“Bugs as Drugs”). Excerpt: “Utilizing bacteria, archaebacteria, bacteriophages and other non-virus microorganisms, this initiative will support research projects designed to study the underlying mechanisms of the complex interactions between microorganisms, tumor, and immune system.” Open date: May 5, 2019.

Grant FundingBugs as drugsNIH

The University of Pittsburgh has established the Roger W. Hendrix Fund to honor a giant in the phage field who was lost too soon. Please consider contributing to this endowed fund to support and encourage future generations of scientists and advance science. Contact Tom Golightly at [email protected] if you have questions.

Endowment

Dr. Ellie Jameson’s lab at Warwick University is now offering reproducible, standardized tests to investigate phages as targeted bactericidal agents. Also available: optimized phage methods to investigate interactions with other antimicrobials and phage, dose, toxicity gene screening, host-range, robustness and virulence.

Phage services

Dr. Benjamin Chan of Yale University continues his treatment of patients in need with phages. Most recently, his phages were administered to a 26-year-old woman named Ella Balasa from Richmond, Virginia, who traveled to Yale for treatment. Article: The State; Video: Associated Press.

Phage TherapyNews

The Perfect Predator came out this week! Expect a lot of new mainstream press for phages over the coming weeks/months! This week has already brought coverage from Wired and People, and tomorrow morning at 9 AM, Steffanie Strathdee and Tom Patterson will be on The Today Show! Get your copy of the book here!.

BookNews

Check out our new paper on sourcing phages for compassionate use, which was published in the journal Microbiology Australia last week!

OpinionPhage Therapy

Latest Jobs

Postdoctoral position: Mobile, phage-related staphylococcal pathogenicity islands
NYU School of Medicine, New York, NY
Dr. Richard Novick

The Novick lab at the NYU School of Medicine is seeking a post-doctoral trainee. The project involves studying conversion of highly mobile, phage-related staphylococcal pathogenicity islands into antibacterial agents. Work involves gene cloning, preparation and purification of phage-like particles, followed by testing for function in vitro and for treatment of experimental infections in mice. The project is described in the following article.

Post Doc Mobile genetic elements
Research technician: Mobile, phage-related staphylococcal pathogenicity islands
NYU School of Medicine, New York, NY
Dr. Richard Novick

The Novick lab at the NYU School of Medicine is seeking a research technician to perform laboratory experiments such as bacterial cultures, strain isolation, genetic tests, experiments with mice; manage lab - order supplies, maintain inventory, maintain equipment. Lab project: Conversion of highly mobile phage related staphylococcal pathogenicity islands into antibacterial agents. The project is described in the following article.

Research Technician Mobile genetic elements
Director of Research and Development, CARB-X
CARB-X, Boston University School of Law, Boston, MA

CARB-X, a Boston University Global Partnership, has an exciting opportunity for a talented individual to join our core team at Boston University in the role of Director of Research & Development. CARB-X is a new organization located at the BU School of Law, focused on accelerating the pre-clinical development of drugs, vaccines and diagnostics to address antibiotic resistance. The Director of R&D will take responsibility for the planning, review, awarding and monitoring of novel R&D projects addressing the antimicrobial resistance issue on a global basis. *Note: CARB-X is one of the current funding possibilities for phage research and development, so we are posting this here!

Director of R&D Antimicrobial resistanceDrug Development
PhD student position: Infection mechanisms of archaeal viruses
University of Freiburg, Freiburg im Breisgau, Germany
Dr. Tessa Quax

Studying the infection mechanisms of archaeal viruses can provide insight into the evolutionary history of viruses and help to understand adaptation to extreme environments. In the framework of a recently awarded Emmy Noether grant, we offer an excellent opportunity to engage into an exciting PhD project that combines microbiology, genetics, microscopy and biochemical tools in the context of a dynamic and enthusiastic work environment, with state-of-the-art equipment and various chances for national and international scientific collaborations.

PhD Archael viruses
Postdoctoral position: Infection mechanisms of archaeal viruses
University of Freiburg, Freiburg im Breisgau, Germany
Dr. Tessa Quax

Studying the infection mechanisms of archaeal viruses can provide insight into the evolutionary history of viruses and help to understand adaptation to extreme environments. In the framework of a recently awarded Emmy Noether grant, we offer an excellent opportunity to engage into an exciting post-doc project that combines microbiology, genetics, microscopy and biochemical tools in the context of a dynamic and enthusiastic work environment, with state-of-the-art equipment and various chances for national and international scientific collaborations.

Post Doc Archael viruses

Community Board

Have a question or request for the phage community? Post it here and reach > 300 phage enthusiasts spanning academia, industry, medicine, and beyond. Feel free to be creative about what you might ask! (e.g. collaborations, advice, seeking opportunities). Find the week’s new requests here in Capsid & Tail, or find a list of all active requests here.

The community board is empty this week. Be the first to post something for next week!

What’s it like to help with phage crowdsourcing?

Recap: where are we at with this effort?

Back in November, we told you about a phage crowdsourcing effort on behalf of a patient in Helsinki, Finland. So far, a total of around 200 Klebsiella phages have been contributed on behalf of this patient. Most of these were tested on the patient’s strain by Mikael Skurnik’s lab at the University of Helsinki. Excitingly, several phages have been found that plaque on the isolate.

The next step will be deciding if and when to administer them (this depends on the patient’s health and need, and will be the doctor’s decision). For now, phages found to be effective on the patient’s strain are currently undergoing propagation and purification, in anticipation that they will be needed.

Learning from labs who sent phages

To enlighten others about what it’s like to contribute phages to a crowdsourcing effort like this one, we’ve interviewed five researchers whose labs contributed phages for this patient (four academic labs and one biotech company). Four of these labs mailed phages to the Skurnik lab, while one lab elected to receive the strain and test their phages in-house before sending.

In the future, we hope to bring you more perspectives, such as what it’s like to be on the receiving end of all of these phages!

How did it go? (What went well, what was challenging?)

“The process went smoothly. My main problem was with the FedEx shipping, there were delays at customs and getting the package delivered. I felt protective of my samples until they arrived safely. There was good communication with Mikael Skurnik which helped me feel reassured and I felt well informed during the process.” - Dr. Ellie Jameson, University of Warwick (@ellie__jameson on Twitter; lab website)

“It was very easy for us - we had filtered, phage-containing supernatants ready to go and just had to aliquot them.” - Dr. Daria Van Tyne, University of Pittsburgh (@vantynelab on Twitter; lab website)

“It was very easy to send our phages. We just had to package them and put them in the mail.” - Dr. Julianne Grose, Brigham Young University (lab website)

“We were sending phages that were already identified by our company, so when we received the request all we had to do was choose which ones we think would be most suitable. The part that took more time was the preparation of the documents (the Material Transfer Agreement) to help us be sure that our knowledge is well protected.” - Michal Habusha, BiomX (@BiomX_Ltd on Twitter; company website)

“We got the announcement of Capsid and Tail and responded to it in assent. Pretty quickly, Mikael Skurnik from University of Helsinki got in touch with us and sent us his Klebsiella pneunmoniae strain. Initially, we screened the 4 phages we already have and, in parallel, validated its antibiotic resistant profile. Indeed, the bacteria was found to be fully resistant to both antibiotics and phages. We discussed it in our group meeting and my students decided to have a “phage hunting” competition where they, individually or in teams, would try to isolate a phage against the strain, using various strategies. So far, they have not succeeded*, but still the competition is ongoing. We feel that this is important challenge also to our perhaps naïve assumption that given the time and effort, we can find a lytic phage to every bacteria.” *UPDATE: “Just to update that a student of mine, Ortal Yerushalmi succeeded to isolate a phage for the bacteria.” - Dr. Ronen Hazan, Hebrew University (@RonenHazan on Twitter; lab website)

Would you do it again? (Why/why not?)

“I would be happy to do it again. I would really appreciate the opportunity to share my work and see my research efforts and phages applied in the real world. (I would make sure that I had more working stocks before sending phage off in future).” - Ellie Jameson

“Yes!” - Daria Van Tyne

“Of course. We would be so happy if our phages ended up saving a life.” - Julianne Grose

“We would be glad to send our phages again. We believe that phages are a powerful solution for treating, among others, antibiotic resistant bacteria, which can save lives in extreme cases.” - Michal Habusha

“Yes, absolutely. I think that the idea of a phage-labs network is a great idea, and we will help as much as we can. I am certain that one day we will come across a bacterial strain which we will not have an answer for, and we will be glad to know that the consortium will be there to help us with this. Our vision for the future is that there will be a world bank with phages from labs the world over that will be able to screen any bacteria and send the phages. The problem of creating such a bank may obviously be the IP rights, but if this will be solved it would surely be for the benefit of humanity.” - Ronen Hazan

What would make the process easier? (more info/support?)

“More information on how best to send the phage samples (e.g. volumes, tube, etc) and how to label the phage samples would be great.” - Ellie Jameson

“Not sure, it was already super easy for us.” - Daria Van Tyne

“More support on appropriate MTAs (examples).” - Julianne Grose

“We believe next time the process would be easier for us, as we already have the required documents.” - Michal Habusha

“I don’t see how the process can be easier than it is currently. It was really smooth.” - Ronen Hazan

How much time did it take (and how many people in your lab worked on this?)

“It was simple to aliquot, package and send the phage, but aliquoting and labelling a lot of tubes is more time consuming than I first anticipated! The phage which was effective against the patient’s Klebsiella strain had not been characterised, so I had to bring in more help. I was well supported in this by my technician @E_Townsend_36 and @milja001 research group, primarily @SMichniewski who routinely sequences phages.” - Ellie Jameson

“Probably 30 minutes to aliquot and prep for shipment, and 10 more minutes to walk the package to FedEx. My technician Daniel Evans, who isolated the phages originally, is the one that prepped them for shipment.” - Daria Van Tyne

“1 hour - 2 people (myself and a master’s student)” - Julianne Grose

“Sending the phages took around one month from receiving of the request. Three people were working to facilitate the shipment: a phage scientist, our chief business officer and our Patent Attorney.” - Michal Habusha

“The bacteria arrived within a week and about 10 of my students, including high school students from the Alpha program (gifted high school students taking part in university-level research), got involved in a “phage hunting” competition, as I mentioned above. In fact, this is the second time we performed such a competition. The first competition occurred after we treated a patient in Israel with phages for the first time in May 2018. Together with Prof. Ran Nir-Paz from the Department of Clinical Microbiology and Infectious Disease of Hadassah Medical Center and our colleagues from APT, we managed to isolate in-vitro a mutant of the patients’ A. baumannii which was resistant to the treating phage from APT. We announced a competition to find a phage against it and one of our talented, motivated students, Amit Rimon, indeed isolated one.” - Ronen Hazan

How many Klebsiella phages did you send? How many did you not send?

“I sent all the phage I had, 50 in total. These were at various different stages of characterisation. I wanted to make sure that if I had anything that could help, it would get tested.” - Ellie Jameson

“We sent 8 phages, which is all that we had at the time.” - Daria Van Tyne

“We sent 15. We didn’t send 3 that were newly isolated and were not prepared as a high titer.” - Julianne Grose

“We have dozens of phages that were isolated in our labs. We sent 4 phages which were found to cover a broad host range of the examined bacterial strains.” - Michal Habusha

“A student of mine, Ortal Yerushalmi, succeeded to isolate a phage for the bacteria. […] We sent the phage” - Ronen Hazan

How did you determine whether or not to send phages, or to send some and not others?

“If I had chosen not to send all my phage it would be because I did not have enough viable stocks of some phage.” - Ellie Jameson

“This exact application is what we’re working towards, so it was a no-brainer to send all the phages we had.” - Daria Van Tyne

“We sent all that we had that were purified and high lysates” - Julianne Grose

“It is difficult to predict which phages will work against a specific strain in case you don’t have previous information on the target host strain. Therefore, we provided phages that were found to be active against a relatively broad host range of K. pneumoniae strains, hoping it will also infect this desired isolate.” - Michal Habusha

How characterized were the phages you sent? (genome sequenced? tested in animal model?)

“Of the phage I sent the best characterised had genome sequences, morphology, host range, latency and burst size. While at the other end of the scale I had phage which had been recently isolated and I knew very little about.” - Ellie Jameson

“We have not yet sequenced the phages but are planning to once we have isolated more of them.” - Daria Van Tyne

“They were all at different stages. Half had their genome sequenced, half were in the process of genome sequencing. None have been tested in an animal model.” - Julianne Grose

“Their genome was sequenced, compared to known phages in the NCBI genome database and checked for virulence. Some of the phages we sent were already used in animal studies.” - Michal Habusha

Was your university/company supportive? How involved were they?

“Everyone I have talked to has been very supportive. I have also had good support from the water company Severn Trent who run the sewage works from which some of my phage were isolated.” - Ellie Jameson

“Yes - the University was supportive but concerned about having the appropriate MTA.” - Julianne Grose

“Our company was supportive. There was agreement across the company’s management to contribute to this important cause.” - Michal Habusha

“The Hebrew University, Jerusalem and Hadassah Medical Center, including their R&D departments, are highly supportive of phage therapy. Currently, our team, which consists of my lab and the Department of Infectious Disease of Hadassah, is exploring some requests for companionate use phage treatment. We envision establishing in our shared campus a phage therapy research & treatment center.” - Ronen Hazan

Any tips for people helping with phage hunts in the future?

“Take part if there is a call for phage and you can help. Make sure the phage are sterile filtered and well backed up, which is really important when working with phage in general. Check everything is backed up (again) and you have a comprehensive inventory of everything.” - Ellie Jameson

“Do it! The more researchers/labs involved, the better.” - Daria Van Tyne

“We think that it is essential that all establishments who work with phages will be coordinated and share information in order to promote the idea of phage therapy as a safe and effective treatment.” - Michal Habusha

“I think that a brain-storming session regarding sharing, yet keeping the rights of labs on their phages, needs to be done with the vision of creating international network of phage therapy centers.” - Ronen Hazan

Anything we missed?

“I really appreciate the feedback from Mikael Skurnik’s group on how well testing is going and which phage were effective against the patient’s Klebsiella. I look forward to future updates. I would love to know more on how the phage will be used to treat the infection. If they will be used topically, orally, intravenously. How many different phages will be used and how will the dose be calculated?” - Ellie Jameson

“No I think this is great!” - Daria Van Tyne

“I thank you for the initiative of “Capsid and Tail” and “Phage Directory”. I think that it is an important step towards the idea mentioned in the previous section.” - Ronen Hazan

Thank you!

We want to extend a huge thank-you to everyone who has contributed or tested phages on behalf of this effort and to the other efforts we have ongoing!

Importantly, this week’s interviewees represent only a subset of those who’ve participated so far, and we hope to shine light on everyone’s efforts in the future. For now, we hope you’ve enjoyed hearing from Ellie, Daria, Julianne, Michal and Ronen about their experiences, and we thank you five for your time in answering our questions!

Further reading:

Check out our new paper, “Sourcing phages for compassionate use”, which was published in the journal Microbiology Australia last week!

Thanks for reading!
–Jessica <>={

Jessica Sacher is a co-founder of Phage Directory and has a Ph.D in Microbiology and Biotechnology

For every issue of Capsid & Tail, we are committed to getting our facts straight, but we’re not experts in the information we’re bringing to you. If you feel that we’ve missed an important viewpoint, or if you have something to add, please reach out to us by emailing [email protected]. We’d love to hear from you, and we’d be happy to revisit topics we’ve covered (ideally with added information and viewpoints from community members like you!).

Lastly, please reach out if you’re interested in writing for us, or have suggestions for future issues!