Training phage scientists in developing countries: An interview with Prof. Martha Clokie

Issue 100 | November 6, 2020
11 min read
Capsid and Tail

One of the Phages for Global Health workshop instructors, Dr. Janet Nale of the University of Leicester, teaching participants during the 2nd Phage Workshop in Kenya in 2018 (photo credit: Dr. Tobi Nagel).

💯 It’s our 100th issue and 2nd birthday!! Thanks so much to all of you for reading and sharing Capsid & Tail; we wouldn’t have gotten this far without your support!

This week, Clément Girardot interviewed University of Leicester Professor Martha Clokie about her work as an instructor for Phages for Global Health, the non-profit organization founded by Dr. Tobi Nagel to facilitate the application of phage therapy in developing countries.

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What’s New

Adaptive Phage Therapeutics has deployed their PhageBank™ in Texas to treat COVID-19 patients suffering from life-threatening carbapenem resistant Acinetobacter baumannii (CRAB). Eight of these patients have so far received PhageBank™ therapy, with more anticipated.

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BiomX has announced the dosing of their first subject in their Phase 1a clinical study testing the safety, pharmacokinetics and oral delivery of a phage therapy candidate for treatment of Inflammatory Bowel Disease. Results are expected in early 2021.

Biotech newsClinical TrialPhage Therapy

Jiawei Wang (Monash University) and colleagues published a new paper in Nucleic Acids Research describing AcrHub: an integrative hub for investigating, predicting and mapping anti-CRISPR proteins.

BioinformaticsResearch paper

Jolene Ramsey (Texas A&M University) and colleagues published a new paper in PLoS Computational Biology describing Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation. Researchers can use the multi-purpose platform the Center for Phage Technology has developed to easily and accurately annotate an entire phage genome.

BioinformaticsResearch paper

Katie Bodner (Stanford University) and colleagues published a new paper in STAR Protocols showing how to engineer phages for live-cell imaging of prophage induction inside mammalian cells.

Phage methodsResearch paper

Yu Lin (University of Sydney) and colleagues published a new paper in the International Journal of Pharmaceutics showing storage stability of phage-ciprofloxacin combination powders against Pseudomonas aeruginosa respiratory infections. They show that this combination powder is stable to store for a year!

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Latest Jobs

Post Doc
The Levin lab at Emory University (Atlanta, Georgia) is hiring a postdoctoral research associate to do jointly theoretical and experimental research on the population and evolutionary biology of bacteria and bacteriophage. To inquire, please write to Bruce Levin at [email protected].
CRISPRPhD project
The Fineran lab (University of Otago, New Zealand) has openings for PhD students to study phages and CRISPR. Due to border restrictions, applicants must already be in New Zealand.
Phage Biologist
General Dynamics Information Technology (Silver Spring, Maryland) has openings for a phage immunologist, a phage biologist, and a phage molecular biologist to work on a phage therapy project for the Wound Infections Department of the Walter Reed Army Institute of Research.
Post Doc
Sandia National Laboratories (Albuquerque, New Mexico) is hiring a postdoctoral scientist to study the interaction of bacteria with noble gases, to use phage-assisted continuous evolution to evolve proteins for biosensing applications, and to engineer and characterize algal strains for biofuel applications.

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Anyone can post a message to the phage community — and it could be anything from collaboration requests, post-doc searches, sequencing help — just ask!

The third iVoM event will be Thursday, November 19, 4pm GMT, and the theme will be “Virus-host interaction: overcoming cell barriers”.

It will feature talks by:
Martin J. Loessner (ETH Zurich, Zurich, Switzerland)
Carlos São-José (Universidade de Lisboa, Portugal)
Sigal Ben-Yehuda (Hebrew University-Hadassah Medical School)

Madalena Pimentel (Universidade de Lisboa, Portugal)
Ry Young (Texas A&M University, College Station, TX, USA)

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PHAVES #10 will be a seminar by Dr. Paul Jaschke, Assistant Professor at Macquarie University, Australia, on Nov. 10, 5:30 PM Eastern Time (GMT-4) / Nov. 11 at 9:30 AM AEST. His talk is entitled “Learning How to Engineer Genomes by Building Phage”, which will cover research stories about highly engineered øX174 phage created in his group and lessons learned about genome engineering in general and phage engineering in particular. Small group networking to follow!

Register here.

PHAVESVirtual Event

Training phage scientists in developing countries: An interview with Prof. Martha Clokie

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Freelance journalist

Clément Girardot is a French freelance reporter who writes mainly in-depth stories on the Caucasus region and Turkey. His work is inspired by forgotten territories, borders and those who break them, stories of memory and resistance, by innovation and endeavor. His writing has appeared in Le Monde Magazine, The Guardian, Le Temps, L’Obs, Mediapart, Eurasianet, Days Japan, Amnesty International magazine, Die Wochenzeitung…

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Martha Clokie PhD, MSc
Clokie Lab (PI), University of Leicester, Leicester, United Kingdom

Molecular Biology, Phage Therapy, Phage isolation, Biotechnology, Bioinformatics, Machine Learning / AI, Teaching

I am a Professor of Microbiology at the University of Leicester where I lead a group of post-doctoral assistants and PhD students working on different aspects of therapeutic development of phages that target human and animal pathogens. I have a good grounding in all aspects of phage therapy development – from unravelling fundamental biology to product development, and commercialisation. Three three patents have been filed from my work. In addition to teaching Leicester undergraduate and post-graduate students, I helped develop a course, and work with the non-profit organisation ‘Phages for Global Health’ course to teach phage biology to academics worldwide. I am open to collaborations where I can provide specific phage expertise.

This week, Clément Girardot interviewed University of Leicester Professor Martha Clokie about her work as an instructor for Phages for Global Health, the non-profit organization founded by Dr. Tobi Nagel to facilitate the application of phage therapy in developing countries.

Clément: Why did you decide to join Phages for Global Health as an instructor?

Martha: When Tobi asked me to be an instructor and provide academic input developing the course content for Phages for Global Health (PGH) I barely hesitated before accepting her offer. My reason for being so pleased to join the PGH endeavour is that I think it’s such a good idea to take ‘State-of-the-art’ phage knowledge to people who need it. AMR is a global problem and in particular it is predicted to kill millions of people in Africa unless something is done about it. I think phages will be useful globally but most countries in Africa do not have a strong background in phage biology.

Tobi was cleverly putting together an infrastructure to provide this and I was very happy to input into this. I have worked on phages for nearly two decades – and like the idea of imparting the knowledge I have gained from this to help researchers from developing countries to do their own phage work. I like to impart the skills to allow them to find phages for, and carry out work on whichever bacteria they are interested in treating.

C: What are the specific needs of developing countries regarding phage therapy?

M: There are specific needs in terms of particular targets (having specific bacteria that are a nuisance); in some countries there is a real need for TB phages, and specific bacteria associated with AMR, such as those associated with respiratory or gut diseases such as Klebsiella or E. coli. Even common bacterial infections will have their own ‘strains’ associated with specific countries, so for example Salmonella food poisoning is a problem worldwide, but each African country will likely have different strains of the bacteria and therefore need specific phages.

One of the very useful things about phage research is that once people know the basics, they can then adapt and apply them to whichever system they are interested in. Some researchers are interested in human clinical applications, others in animal work and others in crops. It’s really nice teaching these mixed communities of researchers and we cover the different practical applications in our course. Often people won’t know exactly which phages they want to focus on, but through collaborations with their colleagues they can use phages to solve a range of bacterial problems.

Even in my own research I am constantly evolving which groups of phages I focus on. For example, in my human clinical phage work – it’s clear there is a need for a better map between clinical need and access to phages – in order to focus on bacteria which are particularly problematic and resistant to existing antibiotics. Therefore, I am increasingly working on bacteria such as those that cause multiple drug resistant UTIs – although I’ve only worked on these for about 3 years, I can apply my general phage knowledge to isolate, characterise and develop these phages.

In the same vein, we aim to teach folks from developing countries how to find and isolate phages from bacteria where it is relatively easy to do so – and therefore we can teach them what to do practically – they can then apply this to whatever they wish and need to.

There are country specific needs for all aspects of phages, such as to treat crop pathogens for plants and animals that are commonly grown and consumed in developing countries such as bananas or tilapia.

Furthermore, there is a need to prevent the rotting of crops to reduce food wastage. Most developing countries are hot and humid, and therefore bacteria grow readily, so foods such as meat are particularly susceptible to pathogenic bacterial growth. Often developing countries don’t have good access to reliable cold-chains for food transportation. Thus, preventing food from rotting during transportation and storage is highly desirable.

C: Each workshop lasts around two weeks, it’s quite a long time, I guess it’s more than sharing knowledge, can you tell us more about the time you share with the trainees?

M: We very much didn’t want to ‘fly in’ and ‘fly out’ and just dryly deliver lectures in a kind of ‘we are telling you’ way – we wanted to develop communities of phage researchers and this takes time. It is a significant time commitment for us all, but our team is aware that it takes time and energy to develop relationships to impart and exchange knowledge, not just delivering academic content. The participants appreciate this aspect very much and often comment on it. They like that we eat all our meals with them, sleep in the same accommodation and are there for them the whole time we are on the course.

I think that often the most important conversations are held over lunch or dinner, or walking from our accommodation to the labs. The students are not intimidated here and can ask whatever they wish.

We teach an enormous amount in two weeks, and we see it very much as a starting point for future relations and helping folks establish themselves.

We have active ‘WhatsApp’ groups for all our workshop participant cohorts, and it is enormously satisfying to see them develop their own research programmes. Because we get to know them so well, students feel confident to ask us even a couple of years later if they need help with anything.

C: What is the impact of the workshop in terms of new local research on phages done by former trainees? Do you see many interesting research projects coming up?

M: Yes! We know that projects have been and are being developed for TB phages, banana phages, pathogens of aquaculture phages. There are ongoing projects on using phages to treat bovine mastitis and for crop pathogens. There are also many projects I am aware of for bacteria which are multidrug resistant, such as E. coli, Klebsiella and Pseudomonas. Often, we (our PGH team) act as unofficial mentors to help the participants seek funding, and thus we are aware of the different streams and projects that they are applying for. Just like the course, it is wonderfully diverse.

Further reading

Read more from Clément Girardot on Phages for Global Health in his September 2020 piece for The Guardian here!

Learn more about Phages for Global Health’s mission and activities, including how you can donate and sign up for their newsletter here!

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