Phage training reaches East Africa

Issue 54 | November 28, 2019
11 min read
Capsid and Tail

“A pair of mischievous monkeys at Macushla House, Nairobi, Kenya” — David Clode. Photo by David Clode on Unsplash

This week, Dr. Atunga Nyachieo and Ivy Mutai of the Institute of Primate Research in Nairobi, Kenya tell us about how phage research training began at their institute in 2017, how it continues to grow, and the impact it’s had so far.

Also in this issue: phages and the antimicrobial development pipeline, chimeric lysins to treat poultry, compassionate phage therapy in Germany, an upcoming Phage Futures conference in DC, research positions into the gut and infant phageomes, and more!

What’s New

Phage Futures Congress 2020 is happening Feb 5-6, 2020 in Washington, DC. Early bird pricing ends Dec 6. Use discount code ‘PHAGEDIRECTORY’ for an extra 10% off! Hope to see you there!

phage futures 2020

ConferencePhage TherapyBiotechSponsor

John Rex, MD (Chief Medical Officer for Wellcome Trust) has written a blog post about a new paper published by Ursula Theuretzbacher and colleagues on the global pre-clinical pipeline for antibacterials. It shows that as of May 2019, 33/407 preclinical projects were focused on phages or phage-derived therapeutics. Rex mentions that non-traditional antibacterials (like phages) will face substantial hurdles, and describes in a new paper how non-traditional antibacterial development programs should be designed.

Perspective

Steven Swift (Beltsville Agricultural Research Center) and colleagues have engineered a chimeric phage lysin that lyses Clostridium perfringens, an important poultry pathogen. They fused the cell wall binding domain of a C. perfringens phage lysin to the enzymatic domain of a Geobacillus phage lysin (a deep-sea thermophilic phage). This resulted in a thermostable C. perfringens-specific lysin that may be able to be added to poultry feed to control this pathogen.

ResearchLysinsAgriculture

Several new phage therapy reviews are out: one on the pharmacological limitations of phage therapy by Anders Nilsson, one on promises and pitfalls of in vivo evolution to improve phage therapy by James Bull and colleagues, and one on exploring standard operating procedures for phage therapy by Zelin Cui and colleagues.

ReviewPhage Therapy

Phages were successfully used to treat a 41-year old’s cardiac infection, which involved a cardiac implantable electronic device and aortic graft, at the German Heart Center Berlin in Berlin, Germany.

ResearchPhage Therapy

Congratulations to Dr. Minmin Yen, CEO of PhagePro, a company developing a phage cocktail as a household cholera prophylactic — she just won $10,000 in the 2019 TropMed pitch competition hosted by the American Society for Tropical Medicine and Hygiene!

Pitch CompetitionBiotechPhage Therapy

Latest Jobs

PhD student position: Interaction of phages and the microbiome at the preterm infant gut mucosal interface

Dr. A. Nelson, Northumbria University,
Newcastle, UK

Breast milk from mothers who deliver preterm is nutritionally distinct from term breast milk and contains a microbiome that has higher numbers of Coagulase negative Staphylococcus. Little is known about the ‘phageome’ of preterm breast milk. Recent work from our group has identified that the presence of Staphylococcus is common in the preterm gut microbiome and that LOS may be gut mediated. We hypothesise that higher phage titre in breast milk will reduce Staphylococcal load at the mucosal surface and protect preterm infants from gut mediated LOS. To test this hypothesis we will seed enteroid models with phages isolated from preterm breast milk and examine the infection profile of Staphylococci isolated from preterm stool and blood culture. Identifying how phages infect bacteria and modulate microbiome development using a biologically relevant model will allow us to develop novel therapies to protect the immature gut of preterm infants.

PhD Project Gut PhageomePreterm infant
More Details Last day: January 24, 2020

Postdoctoral position: Gut phageomics

Prof. Colin Hill, APC Microbiome and University College Cork

It is widely recognised that the gut microbiota plays an important role in human health and has become one of the most dynamic, complex and exciting areas of research in both food and pharmaceutical arenas. The microbiota is not only a target for treatment and prevention of disease, it is a repository for functional food ingredients and even new drugs and is a source of novel biomarkers of disease risk.

The advertised position is within APC’s Gut Phageomics Laboratory, consisting of over 20 researchers investigating the role of the gut bacteriophages in health and disease. The Post-Doctoral Researcher will work within this lab as part of the APC’s ‘Gut Phageomics Spoke’ which is collaborating with a major multi-national pharmaceutical company to explore the role of bacteriophages in shaping the human gut microbiome.

Post Doc Gut Phageome

Community Board

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

November 25, 2019

PhD student seeking unpaid 3 month industry placement

Rebecca Quinn, University of Warwick

My name is Rebecca Quinn, I’m a PhD student at University of Warwick, researching phage genetics. I’m funded by the BBSRC, and under the direction of Dr Richard Puxty.

I have funding for a 3 month work placement/internship in Summer 2020 (there is date flexibility). The placement cannot be lab-based, but all other departments (HR, IT, marketing, etc) are suitable.

I have the right to work in the UK/EU, Canada, and the US and am location-flexible.

Please email me at rebecca.quinn@warwick.ac.uk if you know of any opportunities! Thanks.

Internship

Phage training reaches East Africa

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Chief of Research
Institute of Primate Research, Nairobi, Kenya

Dr. Atunga Nyachieo is a Senior Research Scientist and Chief of Research (scientific leader) at the Institute of Primate Research, Nairobi, Kenya. He is a well-seasoned senior researcher and an excellent student mentor. Dr. Nyachieo was attracted to phage research after reading online publications and campaigns by the Phages for Global Health foundation, showing that phages can be used for therapy. Since then he has re-focused his research and ventured into phage biology for therapy as alternative to antimicrobials. With the support of well-wishers, he has put up a phage biology team called “Phage Hunting Group” aimed at isolating phages as well as creating awareness on this novel technology. He and his team members (mainly students) have isolated and characterized phages against wound causing multidrug resistant Staphylococcus aureas (4 publications on phage biology) and E. coli and Salmonella. He strongly believes that training and research on phage therapy is the key to good and healthful life. He is currently appealing for donations to support phage training and research.

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Masters Student
Kenyatta University, Nairobi, Kenya

Miss Ivy Jepkurui Mutai is currently pursuing a Master’s degree in biochemistry at Kenyatta University and a volunteer/intern at Institute of Primate Research (IPR), Nairobi, Kenya for the past three years. During this period, she developed passion for phages with the aim of controlling the rising antimicrobial resistance. She is also the team leader and coordinator of phage training, which aims at capacity building of students and interns; create more awareness and generate more research areas in phage therapy. She is a member of a vibrant phage club (IPR Phage Hunters), which has been active through tremendous support from her phage supervisor Dr. Atunga Nyachieo. She believes with this platform, we are having hope towards combating rising anti-microbial resistance.

The escalating antimicrobial resistance (AMR) pandemic is a global public health threat with extensive health, economic and societal implications. Resistance emerges because of selection pressure from rational and indiscriminate antimicrobial use in human health as well as in the veterinary, agriculture and environmental sectors. Infections caused by resistant bacteria result in a longer duration of illness, higher mortality rates and increased costs associated with alternative treatment.

Missing phage expertise in Africa

Phage therapy is the therapeutic use of phages to treat pathogenic bacterial infections. It has many potential applications in human medicine as well as dentistry, veterinary science, and agriculture. Whereas this is a promising therapy, most experts are in Europe and America. We are thankful for the efforts of Dr. Elizabeth Kutter (USA), Dr. Tobi Nagel (USA), Dr. Ben Chan (USA), Dr. Martha Clokie (UK) and Dr. Janet Nale (UK), who have dedicated their energy to providing phage training in Africa.

Bringing phage training to Africa: the first East African phage workshop

A spark was lit during the 1st East African phage training workshop (which was run in 2017 at Makerere University, Uganda by Phages for Global Health). Since then, phage training has been going on at the Institute of Primate Research (IPR) in Nairobi, Kenya.

Prior to this training, there was phage activity at IPR started by one of our passionate master’s students, Joseph Michael Ochieng, when he was doing his research project on phages under the mentorship of both Dr. Atunga Nyachieo and Dr. Ngalla Jillani. It was during this time that he met Dr. Elizabeth Kutter, through a submitted manuscript, who later visited Kenya in 2016. She was very much amazed by Joseph’s research into isolating phages. Dr. Kutter recommended that we attend the Phages for Global Health training at Makerere University, Uganda, run by Dr. Tobi Nagel, which we did in 2017. This opened our eyes, and on return to IPR, a phage hunting group and a phage club were born, and many more were trained.

Phage training begins at the Institute of Primate Research

After meeting with Dr. Kutter, phage training was born at IPR. Dr. Kutter was impressed by Joseph’s work, and promised to send some funds to build capacity at the institution. Joseph started by training three students, which kept growing and blooming with time. Three students turned into over 70 trained students. Dr. Kutter then informed Joseph of a chance to go for his Ph.D. studies in Finland. Meanwhile, the phage training at IPR still went on, and Ms. Ivy Mutai, an intern from the primate center, took the position held by Joseph.

The Primate Center phage club is born

During this period, the 2nd East Africa phage training workshop took place in Kilifi (Pwani University, Kenya, 2018) and two more of our students, including Ivy Mutai, got the chance to be selected for intensive phage training. The training made a large impact on the selected participants, and they came back home full of ideas, ready to share them with their fellow interns at the institution. It was at this very moment that the Primate Center phage club was established. The main objectives of the club are to create more awareness of phage therapy through weekly paper presentations, gap identification, phage isolation procedures, to share more knowledge on phages, and to give a weekly report on the previous week of bench work.

The growing impact of phage training at the Primate Center: 70 students trained and counting

We can attest that the phage club has yielded many fruits in terms of training. Everyone at the primate center flocks on Tuesdays for the club. This has also eased the bench work training, since students are improving their knowledge through the club sessions. We now have 65 registered members in the club, and over 70 trained students from a small initial number of three. This has also increased the number of internship applications to our institution, since the previously-trained students recommend others from their universities to join our phage training program.

With the good work that the lead trainers (Ivy Mutai and Dennis Kotti) are doing, Dr. Kutter has been so impressed, and visited Kenya once again in December 2018. She came to witness the good work that was started by Joseph and which has succeeded well. With no doubts, she was once again impressed, and made a presentation at our institution before proceeding to other universities for talks on phages. She also awarded certificates to our trained students and phage club members. With her visit, we felt humbled and mentored, and inspired to do more. We thank her for always supporting us.

Spreading the knowledge by training students from other universities

The criteria for selecting students to train include having a biological/life science background, and coming from a variety of different universities, as this impacts the passing of knowledge to various academic institutions. Many learning institutions have created a memorandum of understanding with our center, and this has made our small phage lab always flocked to by students. Many of these students go back to their schools having done research projects on phages, and some are awaiting publications. In addition, we also have master’s students in the program who are doing their research projects on the isolation of phages from various sources. We have seen huge impacts and progress from this training.

Next steps: increasing training capacities through a ‘phage week’

We are also planning to have a ‘phage week’ at the primate center once we get some funds to procure some consumables. From May-September, there is normally a huge number of students, and it is close to impossible to train all of them within the short time available. Through a ‘phage week’, Ivy Mutai and Dennis Kotti, alongside other trained students, will train over 40 students in a week through intensive bench work. We believe with this capacity-building program, a lot will be accomplished, and this will all be of a huge impact towards the use of phages against antimicrobial resistance.

Acknowledgments

We wish to thank the Director of our institution, Dr. Hastings Ozwara, for always supporting us and allowing us to do this training program and research at the primate center. To the trainers as well (Dr. Atunga Nyachieo, Dr. Ngalla Jillani, Mr. Joseph Ochieng, Ms. Ivy Mutai and Mr. Dennis Kotti), without you, this could have never progressed. We are glad you always give your best.

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