Reflecting back on 2022

Issue 205 | December 16, 2022
18 min read
Capsid and Tail

We’re at the end of the year again, and what a whirlwind of a 2022 it’s been! Here’s our annual end-of-year reflection on what we’re most proud of, what we’ve accomplished, & those who’ve helped us along the way!

What’s New

Fixed Phage, a biotechnology company based in Glasgow, has secured £1.5 million in funding to further develop and commercialize its phage technology.

Biotech newsFunding news

The Phage Australia Clinical Network has published the STAMP Protocol for phage therapy. This is an open-label, single-arm trial investigating a standardised treatment and monitoring protocol for phage therapy. The aim is to recruit 50–100 patients over 5 years, from any public or private hospitals in Australia. The primary outcome is safety at day 29. Secondary outcomes include long-term safety (6 months+ following phage therapy), and feasibility, measured as the proportion of participants with >80% of minimum data available for analysis.

Phage TherapyClinical trial

In a new study published in Frontiers in Cellular and Infection Microbiology, Sheetal Patpatia (University of Helsinki) and colleagues describe how they set up a rapid hydrogel-based liquid phage susceptibility assay (PST) for the selection of phages for therapeutic use and how they established a “ready-to-screen” plate concept, where phages are readily stored in hydrogel as small droplets in microtiter plate wells.

Research paperHydrogelPhage susceptibility testing

In this study, a novel Pseudomonas phage, vB_PaeS_VL1 (VL1), was isolated from urban sewage. Phylogenetic analyses revealed that VL1 is a novel species in the genus Litunavirus of subfamily Migulavirinae. The VL1 is a virulent phage as no genes encoding lysogeny, toxins or antibiotic resistance were identified. The therapeutic potential of phage VL1 was investigated and revealed that approximately 56% (34/60 strains) of MDR P. aeruginosa strains could be lysed by VL1.

Phage TherapyPhage characterizationResearch paper

In this paper, Nale et al. review current progress in Clostridioides difficile phage research. They discuss tested strategies of isolating C. difficile phages directly, and via enrichment methods from various sample types and through antibiotic induction to mediate prophage release.

C. difficileResearch paper

Latest Jobs

Assistant or Associate Professor of Microbiology
The Department of Microbiology & Molecular Genetics at the University of California Irvine, School of Medicine invites applications for an Assistant/Associate Professor of Microbiology. All areas of microbial science involving medically relevant bacterial, fungal and parasite pathogens are of interest, including (but not limited to) molecular mechanisms of pathogenesis, host-pathogen interactions, vector-pathogen interactions, microbiomes, antibiotic resistance, & innate immunity to microbes.
BiophysicsPost Doc
The Institute of Translational Medicine for Health Care Systems at MSB Medical School Berlin is looking to fill a postdoc position in biophysics of bacteriophage infection.
PhD projectPhage TherapyPost Doc
The Hall and Deng labs at the Technical University of Munich are looking for a PhD student or Postdoc to work on developing phage therapeutics against necrotising enterocolitis (NEC).

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!

From Phase Genomics via Twitter: Milestone alert! We’re celebrating 150+ papers published using our tech. And there’s a lot to share: our clients made breakthroughs in a broad range of fields from metagenomics to oncology. Here’s a look at the highlights from 2022 (See thread)

Want a reminder about what Phase Genomics is up to? Read COO Kayla Young’s C&T blog post on how they’re mapping phage-host interactions here.

MilestonesPhage Twitter

Reflecting back on 2022

Profile Image
Product designer and co-founder of Phage Directory
Co-founderProduct Designer
Twitter @yawnxyz
Skills

Bioinformatics, Data Science, UX Design, Full-stack Engineering

I am a co-founder of Phage Directory, and have a Master of Human-Computer Interaction degree from Carnegie Mellon University and a computer science and psychology background from UMBC.

For Phage Directory, I take care of the product design, full-stack engineering, and business / operations aspects.

As of Feb 2022, I’ve recently joined Jon Iredell’s group in Sydney, Australia to build informatics systems for Phage Australia. I’m helping get Phage Australia’s phage therapy system up and running here, working to streamline workflows for phage sourcing, biobanking and collection of phage/bacteria/patient matching and monitoring data, and integrating it all with Phage Directory’s phage exchange, phage alerts and phage atlas systems.

Profile Image
Phage microbiologist and co-founder of Phage Directory
Co-founderPostdoctoral Researcher
Skills

Phage characterization, Phage-host interactions, Phage Therapy, Molecular Biology

I’m a co-founder of Phage Directory and have a Ph.D in Microbiology and Biotechnology from the University of Alberta (I studied Campylobacter phage biology). For Phage Directory, I oversee community building, phage sourcing, communications, science, and our awesome team of volunteers.

As of Feb 2022, I’ve recently joined Jon Iredell’s group in Sydney, Australia as a postdoctoral research scientist for the Phage Australia project. I’m diving back into the lab to help get Phage Australia’s country-wide phage therapy system up and running here, working to streamline workflows for phage sourcing, biobanking and collection of phage/bacteria/patient matching and monitoring data, and integrating it all with Phage Directory’s phage exchange, phage alerts and phage atlas systems. I’m also delving into phage manufacturing and quality control.

Hi phage friends,

We’re at the end of the year again, and what a whirlwind of a year it’s been! These years are just whizzing by aren’t they? It still feels like yesterday when we were making new years resolutions for what we wanted to get done in 2022.

At the end of the year, we’ve always liked to spend the last issue of Capsid to reflect on the past year, to look at all progress we’ve made and all the cool stuff we’re proud of, and to highlight our amazing collaborators and volunteers!

Setting up phage therapy in Australia

By far the biggest thing we’ve done this year was move to Sydney to help set up the Phage Australia initiative.

Some of Jessica’s proudest achievements

Helped set up a phage therapy process pipeline & started treating patients!

This year I’m especially proud of helping get Phage Australia’s phage therapy pipeline off the ground! All of this work has been done alongside Stephanie Lynch, who you all know from Phage Directory — luckily for all of us, she is also a core driver of Phage Australia! Steph is the is the master of all things screening and biobanking, as well as making sure hospitals have the right paperwork in place to treat patients, among about a million other reasons this ship wouldn’t be sailing without her…

A few specifics I’m proud of:

  • We established a system of phage biobanking, & got started banking (essentially re-isolating, titring, sequencing, labeling, & adding to a database) 300+ Iredell lab phages. We also began adding collaborators’ phages (thanks especially to Heejoon Myung, who sent us tons of phages!)
  • We screened 47 patients’ isolates, found phages against 23 of them, & produced batches of 14 of them!
  • We established a working pipeline for phage production, purification, and quality control (I blogged about each on Phage Australia’s blog, & each of these also appeared in C&T here, here & here).
  • We created a set of four reports for local hospital drug/ethics committees to approve phages that go into patients, and gotten the first three sets of documents submitted and approved (this process was initiated after conversations with the TGA, Australia’s FDA, who asked us to help them regulate phage therapy — excited to keep workshopping these docs with them in the new year)
  • We treated 3 patients at two hospitals with phages we made, purified and QC’d in-house (1 E. coli and 2 P. aeruginosa patients; each got 2-3 phages; each had multiple infecting strains; all three are doing well; first two are now culture-negative & feeling better)
  • We shipped one of our first purified phages to 4 labs (in 4 states) around Australia and had everyone titre it, as an exercise in how shipping & different hands might affect phage titres (Steph wrote a blog post about it here)
  • We created a system (mostly using Notion) to keep track of protocols, protocol templates, sample inventory, and patient cases (phage list, strain list, batch list, case list, etc)

Spoke about our phage therapy process and pipeline

  • Bioprocessing Network (Sydney, Australia): I gave a talk on some of our challenges on the manufacturing side
  • Australasian Virology Society (Gold Coast, Australia): I presented a poster & Steph gave a talk (which won an award for Best Talk in Clinical Virology!!)
  • I gave a talk to AMMI Canada (Association of Medical Microbiology and Infectious Disease Canada) about our ‘Four Reports’ system for demonstrating phage safety, & how we might expand this to other countries ready to consider implementing it, like Canada
  • Westmead Institute for Medical Research (Meet the Researcher) — where Jon Iredell and I did a brief Q&A for the public about Phage Australia and a bit about Phage Directory too

Some of Jan’s proudest achievements:

This year I’ve spent a lot of time brushing up on a lot of technical subjects, like handling bucket storage, edge workers, API-first development, and exploring database ideas like graph and event-driven databases and architectures like the triple entity-attribute-value model. I built a bunch of API-driven primitives (which I’ll be writing about and sharing next year!), and put up an awesome website and design for Phage Australia (phageaustralia.org) that runs on top of Notion for blog and text content, and aggregates across Google Sheets for the phage and bacterial data.

  • Building our own “Phage therapy operating system on top of actual data and actual cases. This is something I’ve been very keen to do since we devised the concept a couple of years ago. Instead of building and design around others’ workflows, we’re now designing and building it around our own. As part of Atlas, we’ve been building a data aggregation system, designed a massive phage and bacteria biobanking schema, and an API to ingest lots of data (from CSVs to plaque assay images to genomics files), and lots of other primitives. Don’t worry — we’re still hoping for a public release at some point!

  • Getting a data collection system put in place: From computation (DUG) to setting up a shared data storage system (Cloudflare R2) to using Google Sheets to coordinate and aggregate data across labs and efforts — pieces are coming together

  • Designed and built a “mostly dynamic” patient data collection system on top of REDCap to its limits, by programmatically generating REDCap using a new programming language called CUE

All in all, we’ve been productive, but have also enjoyed the heck out of Sydney! We’ve only had “a few” run-ins with Huntsman spiders, and still haven’t seen any wild drop bears or kangas, but overall we’ve loved our time here so far. We might also have picked up some slang along the way…

Over 200 issues of Capsid & Tail!

It’s hard to believe we’ve published more than 200 issues of Capsid & Tail (including 47 this year)! This year’s issues have been our strongest ever. It’s been really exciting to share more our process of building up a scalable phage therapy treatment pipeline, both from a wet lab and dry lab perspective.

This year has been brimming with great posts, and we had trouble choosing our absolute favorite ones (of course, we might be biased, since we wrote so many ourselves!).

Some of our favourite guest-authored posts (22/47 articles this year were guest-authored!!):

Jessica’s favourite posts to write

These were my favourites to write because they marked my first attempt at actually writing about my personal experiences (and decision making processes) in the lab. It was much scarier than recapping a webinar or summarizing someone else’s work… but these posts garnered WAY more discussions and feedback and emails, including new ideas and suggestions for collaborations! So I want to do more of these next year for sure!

Jan’s favorite posts to write

Contribute a post to Capsid & Tail in 2023!

We would absolutely love more technical, nitty gritty posts on setting up the wet lab and dry lab processes for phage therapy next year. If you’re up for sharing some of your insights, don’t be afraid to write something for Capsid!

It’s still hard to believe, but every week, we have around ~700 phage enthusiasts read Capsid & Tail!

Oh, and Phage Directory is going strong!

Phage Alerts

We’ve handled a total of 44 Phage Alerts since we started, with 11 alerts sent this year.

Top five organisms phages are requested for (# alerts sent out)

  • P. aeruginosa (5)
  • E. coli (4)
  • Mycobacterium avium (3)
  • Klebsiella pneumoniae (3)
  • Burkholderia cepacia (3)

For alerts we have sent out, 82% have led to at least one lab responding and offering phage screening (between 1- 20 responding labs per request)

8/44 (18%) had zero responding labs – this is the best proxy we have right now for hard-to-find phages, but of course lack of responders could be influenced by other things like timing of the alert

Organisms responsible for ‘zero response’ alerts:

  • Helicobacter pylori, Mycobacterium abscessus (2022)
  • Mycobacterium avium (2022)
  • Propionibacterium avidum (2020)
  • Streptococcus anginosus (2020)
  • Mycoplasma genitalium (2019)
  • Staphylococcus epidermidis (2018)
  • Burkholderia cepacia (2017)

Organisms responsible for low responses (0-3 responses):

  • Organisms span 23 species
  • Mycobacterium (abscessus, avium, kansasii, genitalium) - 7 alerts
  • Burkholderia (gladioli, cepacia, dolosa) - 5 alerts

Outside of that, we have gotten our most desperate requests from patients for Mycoplasma and Borrelia, but these essentially never have a doctor on board so we don’t send alerts.

Of note, for Mycobacterium we tend to send people directly to Graham Hatfull instead of doing an alert; this was a choice we made a few years back. So our Mycobacterium numbers would be underrepresented.

Community-building & phage data systems

  • We’re proud to have successfully run the iVoM series and built a lot of the underlying poster and abstract submission systems for VoM. We’re also glad that we’ve taken a break from running Zoominars (so exhausting…), but we do really miss connecting with the community in that way… (We’re also sad we couldn’t make it out to VoM Portugal this year!)
  • The Phage Directory back-end system has gone through a massive rehaul. Much of it’s not user-facing, but we now have a much more robust API-first system in the back, which means we’ll finally get to do more Phage Directory experiments next year!
  • We’ve experimented with automating the Phage Directory registration system, but know a lot more can be done, and we’re doing those things next year.
  • Instill is being rethought from ground up and ready to be launched very soon… and this time it’ll be integrated closely with Phage Directory!

Our volunteers make everything possible!

We wouldn’t be here without our army of the best volunteers! Many thanks go out to Atif Khan, Stephanie Lynch, Jessica Neubauer, Madhav Madurantakam Royam, Sayde Perry, Kyle Jackson, Katharine Muscat, and many many more! They’ve been incredible, from helping us to find job openings and news to contributing articles to Capsid & Tail to helping us tweet news to keeping our Slack fun. Here’s a breakdown of how our volunteers have helped us this year!

Also, many thanks to everyone who’s asked and answered questions on Phage Slack!

Thank you sponsors and partners!

Thank you to your continued support throughout the years, JAFRALCellexusKisaco Research: Phage Futures, and PHAGE Journal!

Also a huge shout out to VoM and ISVM. We’re really sad we couldn’t make it out out to VoM Portugal this year, but we had a lot of fun hosting iVoM and building the Abstract Portal!

Thank you to Phages for Global Health for your continued support.

A HUGE thank you to Grant for the Web for supporting Instill and our experimental ideas in push forward community-building and publishing.

Last but not least, thank you to Phage Australia, particularly Jon Iredell and Ruby Lin, for giving us a chance to build out the phage therapy pipeline of our dreams! And lastly thanks to all our amazing colleagues here at WIMR in Sydney, such as Stephanie Lynch, Ali Khalid, Nouri Ben Zakour, and many more.

What’s in store for 2023?

We’ve made the great leap to Australia, set up a phage therapy pipeline, but we’re still just getting started! We have lots of ideas for next year, including scaling up our phage therapy process, rolling out our phage data collection system, and maybe even experimenting with new Capsid formats and turning Phage Directory into something more community oriented… but we’ll get more into all of that in January. Between now and then, let’s everyone get some time off with friends and family!

Cheers, and see you in the new year!

— Jess & Jan <>={

Many thanks to Atif Khan for finding this week’s phage news, jobs and community posts, and Jessica Neubauer for tweeting & LinkedIn-ing them out!

Capsid & Tail

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We send Phage Alerts to the community when doctors require phages to treat their patient’s infections. If you need phages, please email us.

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Mary Ann Liebert PHAGE

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Leona M. and Harry B. Helmsley Charitable Trust

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