Clinical phage therapy, phages for plant pathogens & phage bioinformatics: A triple webinar recap issue!
Issue 123 |
April 23, 2021
13 min read
This week, we’ve got highlights and recordings for 3 webinars we hosted this month: An interview with Dr. Randy Fish on clinical phage therapy for diabetic foot wounds, a talk by Dr. Clara Torres-Barceló on plant pathogen phage research, and a phage bioinformatics workshop with Dr. Jason Gill!
Martin Loessner and Rob Lavigne co-edited a special issue of Current Opinion in Biotechnology dedicated to phage, entitled Nanobiotechnology — Phage Therapy. The issue is now complete: check out the 21 articles here!
Adaptive Phage Therapeutics (APT) is hiring a Curator/Bioinformatician! APT is a group of seasoned veterans coupled with crazy smart biologists and engineers working to solve the problem of antibiotic resistant infections. Each day is different and at the end of the day, you’ve made a difference in someone’s life. It’s incredibly powerful when you meet somebody whose life you impacted by going to work. The work will challenge you and reward you professionally and personally. Apply here!
Scientist
The Mayo Clinic (Rochester, Minnesota) is hiring a scientist or physician engaged in research with expertise or primary interest in phage therapy or phage basic science. The role will involve clinical and laboratory-based efforts toward phage- clinical trials, compassionate use cases, development of phage susceptibility testing, and the advancement of clinical phageomics.
Pathogenicity islandsResearch Assistant
Inviting applications for a full-time Research Fellow position (Postdoctoral Fellowship) in the laboratory of John Chen at the National University of Singapore. Research in the Chen lab focuses on bacteriophages and pathogenicity islands of the bacterial pathogen. Interested candidates, please submit a detailed curriculum vitae and the contact information of 3 references to Dr. John Chen, [email protected].
Phage-bacteria-animal interactionPhageome
The Hohenheim Center for Livestock Microbiome Research (HoLMiR) is looking for young investigators interested in the field of phage-bacteria-animal interaction. If you are an expert in the field of phages and looking for new perspectives, you are welcome to contact us and share your ideas. We can offer a starting grant, which will give the candidates the chance to apply for new projects establishing their own research group. Please send a short letter together with your CV to [email protected] using ‘phageome’ as the subject. The offer is open until 16 May 2021.
Phage displaySenior scientist
Adaptimmune (Abingdon, Oxfordshire) is hiring a senior scientist to join their Phage Display team. The role aims to deliver novel SPEAR T-cell therapies to patients with cancer. Apply now!
Anyone can post a message to the phage community — and it could be anything from collaboration requests, post-doc searches, sequencing help — just ask!
PHAVES #16 will be May 12 at 2PM Mountain time. Dr. Greg Canfield and Dr. Laura Damioli from the University of Colorado will give a joint talk entitled: Freedom from antibiotic purgatory?: Salvage phage therapy for cure of spinal hardware infection.
PHAVES #17 will be May 18, 5pm CEST (Paris time). Quentin Lamy-Besnier, a PhD student in the Debarbieux lab at the Institut Pasteur in Paris will present their team’s newly launched Viral Host Range Database, an online tool for recording, analyzing and disseminating virus-host interactions.
Come learn from Quentin how to use this much-needed new tool for the phage community! Small group networking to follow.
Dear fellow virologists,
Welcome to the first conference of the World Society for Virology (WSV), which is a global non-profit organization established in 2017, to connect virologists around the world, with no restrictions or boundaries, and without membership fees. We have 40 eminent Keynote speakers, and already several interesting abstracts submitted, covering COVID-19 the first day, and all other fields of virology, including plant, animal, fungal, human and microbe viruses, such as phages and phage therapy, the next 2 days. Please see program for details on the two phage keynote talks!
Please join us in June 16-18. 2021! All sessions are recorded for prime time viewing in all time zones!
Abstract submission and early bird registration deadline: April 30th!
Welcome!
— Yigang Tong, PhD, Professor, Dean, College of Life Science and Technology, Beijing University of Chemical Technology, China
ConferenceVirology
Thanks to everyone who attended two exciting forums we helped co-host this week! Yesterday we had ‘Phage Therapy UK: Moving toward clinical trials’, which brought tons of fruitful conversations among phage-interested medical professionals, health policy experts and phage experts from the UK and beyond! If you attended, we’d love your feedback!
And today we had the third rendition of the African Phage Forum, which began with a talk led by Dr. Jesca Nakavuma from Makerere University in Uganda, and turned into an interactive discussion about how phage researchers in Africa can progress and get funding for their work! We’ll share recordings of both seminars soon!
Whenever we can, we publish recordings of our events on our YouTube channel here — subscribe to get notified: https://phage.directory/youtube!
And if you’re part of this wonderful phage community, interested in hosting an online event or webinar series, and want someone else to take care of the technical aspects (managing registration system, event website, advertising the event, invitations, Zoom room management and tech support), Phage Directory is happy to partner with you and your team! Let Jessica or Jan know and we can chat about what you’re envisioning and how we can help.
Virtual EventPhage Directory
Clinical phage therapy, phages for plant pathogens & phage bioinformatics: A triple webinar recap issue!
I am a third year PhD student from La Trobe University, Melbourne, currently isolating and researching the use of bacteriophages for skin infections in animals. I have a background in Animal & Veterinary Bioscience and hope to continue research of bacteriophages as therapeutics within the veterinary or livestock sector. I am also currently developing and optimising the use of animal-alternative models for safety and efficacy trials of phage therapy. I am always willing to chat about phage research and would like to connect with phage biotech companies as I am interested in jobs within the industry sector.
Jason begun by streaming the first training video that he has recently created, which describes the Galaxy and Apollo based platform for phage genome annotation. Check out the training video from 3.26 - 40.13 minutes.
Jason then answered questions from the audience, here are our top 3 questions and answers. Watch the whole video for more!
Q: “Is this tool restricted or limited to have a proper phage genomic structure like PHASTER or can it be used for protein annotations of phage satellites or genomic islands?”.
A: “The workflows are built around annotating phages, some blast searches are constrained to phage proteins, but the systems are really good for any prokaryotic genomes, including plasmids. The workflows are public so you can modify the workflow and change the blast parameters to be more general or bacterial-focused instead. We are hoping to develop with Apollo a more general prokaroytic system”.
Q: “Suppose a researcher has gotten their sequence data: forward + reverse sequences and fastq files, are there steps in the galaxy workflow that allow us to trim out adapters and primers to generate a contig, and proceed with downstream analysis, such as phage genome annotation?”.
A: "Our Galaxy platform does have spades for assembly, and we have QC and trimomatic, so all the programs people use for command lines. Linux command lines can be run in Galaxy. Galaxy has a tool shed with read trimming, quality assurance and assembly".
Q: "Is there a way for a group to annotate a phage together, similar to how google docs works?".
A: “*Yes, definitely yes. There is a tool in Galaxy which is a Galaxy-Apollo bridge tooling which lets you control access from the Galaxy side. Galaxy has a tool where you can share your upload with other users. Multiple users can be annotating the same genome at the same time”.
Want more phage bioinformatics? Join our Slack Community, and check out our new page!
As a companion to this series, we’ve launched a Slack channel called #phage-bioinformatics within the Phage Directory Slack. In our community, you can share your questions and work through issues together with the community.
PHAVES #14: Jack of all strains, master of none? Host range & efficacy in phages of plant bacteria with Dr. Clara Torres-Barceló (April 13, 2021)
Ralstonia solanacearum is a gram-negative pathogen spread by water bodies that causes bacterial wilt in various plant species, such as potatoes and tomatoes.
This bacterium is a significant problem in tropical areas including Reunion and Mauritius, therefore, Clara and colleagues aimed to create a phage cocktail to be applied to agricultural crops to combat bacterial wilt caused by R. solanacearum.
As described in Scientific Reports, Clara and colleagues isolated 60 phages, which resulted in 23 unique phages creating 7 new genera and 13 new species! There were a mix of temperate and virulent phages.
Upon characterising the phages host range, it was found that the isolation origin of the phage was more important at determining host range than phage phylogeny.
Interestingly, the phages isolated in Mauritius had a significant positive correlation between host range and virulent efficacy.
Next, phage cocktails are being designed and the in vivo efficacy will be tested.
Question highlight: Q: "With the temperate phages that were isolated, were they included in the phage host range?
A: “Yes, temperate phages were included. However, there was no obvious pattern between type of phages and efficiency. It is likely we need a larger phage library to determine this.”
PHAVES #15: Interview with Dr. Randy Fish on successfully treating diabetic foot wounds with phages (April 14, 2021)
In this interview, Dr. Randy Fish, a podiatrist, begun by reminding us that diabetic foot ulcers are caused by pressure sores and become a significant problem when the wound becomes infected. Which is where phages come in.
Throughout Randy’s podiatry training, he was a student of Betty Kutter, who introduced phages to Randy! Years later, Betty and Randy brought together their expertise to trial phage therapy for diabetic foot ulcers.
Randy’s success of phage therapy for diabetic foot ulcers begun with the use phages for a patient with a Staphylococcus wound infection in 2012. Phage were injected into the wound, and within 24 hours the patient already felt better and had completely healed within 2-3 weeks. This success sparked a case series of phages to treat diabetic foot infections!
Although diabetic foot ulcers are polymicrobial, Randy currently only uses commercial Staphylococcus phages (SB-1 phage from the Eliava Institute in Tbilisi, Georgia), applied to patients at a dose interval of once per week, with the dose rate depending on the size of the ulcer. Interestingly, Randy has also had success using this phage topically and applied to gauze, which was then applied to the infected area.
Importantly, the treatment of these small foot ulcers has large benefits, as successfully healing an ulcer with phage can reduce or eliminate the need for toe or even limb amputation!
Up next, Randy is working on opening a new clinic centre with access to a surgical centre, and hopes to treat more patients with phage through a clinical trial
Question highlight: Q: "Do you see non-responders after the application of phage therapy?"
A: “Fortunately, we always see some response, and so far we have had no safety issues!”.
Register for upcoming PHAVES seminars — not only do we host speakers, interviews and AMAs, but we host breakout rooms after the talks to encourage casual socializing/networking among the phage community!
Thanks to Stephanie Lynch and Atif Khan for contributing summaries for the Jobs section this week!
