A new preprint by Dr. Aleksandra Petrovic Fabijan and colleagues at the Westmead Institute for Medical Research in Sydney, Australia and AmpliPhi Biosciences provides much-awaited data from their IV phage therapy treatment of 13 patients with severe Staphylococcus aureus infections. They saw no adverse effects, bacterial burden and inflammation was reduced, and no phage-resistant S. aureus were isolated. Please comment on / discuss their preprint here!
Phage genomes can be hard to annotate, especially with tools that aren’t designed with phages in mind. Fortunately, Katelyn McNair and colleagues in Rob Edwards’ lab have published a paper describing their new phage gene caller, PHANOTATE. They annotated >2000 phage genomes alongside the three other most popular gene callers, and found that all four agreed on 82% predicted genes, but PHANOTATE predicted more genes than the other three. Paper | Github
Here’s our favourite #phagetwitter conversation from the week: John Beaulaurier of Oxford Nanopore describes a new preprint on using single-molecule nanopore sequencing to avoid assembling phage genomes. Without assembling, they got >1400 whole, polished phage genomes out of seawater samples using one MinION flow cell.
A new phage product is now on the market! OmniLytics, Inc. and Certis USA have released AgriPhage™, which fights fire blight (Erwinia amylovora) in apple and pear crops. This is the first phage product approved for use against fire blight.
Micreos, a Dutch phage biotech company, secured 30 million Euro last month for its phage lysin technology. The company plans to use the funds for lysin development, and to launch its over-the-counter Gladskin product (anti-Staph aureus lysin product for treating eczema, acne and rosacea) in the US.
The Taylor group is studying the structure and mechanism of biological molecular machines using cryo-electron microscopy. We are especially interested in resolving structural and functional pathways of bacteriophages and human membrane proteins. We are seeking a research assistant to work within the areas of cloning, cell culture, recombinant expression, and protein purification of soluble and membrane proteins and complexes.
Mike Barer and Martha Clokie of the University of Leicester are hiring a PhD student researcher to study the detection of pathogen-specific bacteriophages in face-mask samples to distinguish colonisation from infection in exacerbations of chronic lung disease.
This week, I’ve reviewed a book: The Perfect Predator—A Scientist’s Race to Save Her Husband from a Deadly Superbug: A Memoir, by Steffanie Strathdee and Thomas Patterson, published by Hachette Books in February 2019.
I began the Perfect Predator thinking I knew the story already, and that this would be a quick read. I’ve read news articles about Steffanie and Tom for the last year and a half, and it feels like I tell almost everyone I talk to about Tom’s remarkable phage therapy treatment. However, I came away from Steffanie and Tom’s book amazed at how little I actually knew going in, and surprised at how relateable and moving the story was.
Steffanie’s account of what happened over the period of about a year, during which time her husband Tom was fighting an antibiotic resistant infection, was vivid, emotional, sometimes even funny, and overall very human. I found myself relating in particular to a time when two of my own family members were in the ICU, and yet it’s jarring to imagine that the time my family members spent there does not add up to a fraction of the time Tom was critically ill. He had an incredibly serious infection, and I don’t think I fully appreciated this prior to reading the book.
I empathized throughout the book with Steffanie’s uncertainty, fear, and coping mechanisms as she tried to navigate a life that involved showing up at the ICU in time for rounds every morning, trying to understand the medical jargon and acronyms. Thinking, “I’m a scientist, I should understand more of this, it’s biology”. Realizing how vast the differences are between what a PhD scientist learns, even one from a biomedical field, and what medical professionals learn and practice. Adoring some of the nurses, building kinship with them, and trying to get along with the ones who are frustrated with you: the ever-pestering family member who always wants to see the charts and know about the bloodwork values. I didn’t expect this when I started the book, but it paints a very real picture of what it’s like having a loved one living in the ICU. For that alone, it is a valuable account, even for people with little interest in phage therapy.
As for the phage therapy side, I found the science and the history to be very well done: exactly enough detail for my liking. Overall it was expertly woven: a great mix of science, medicine, and of the human side of everything that happened. And (spoiler alert, but I think we all know how the story ends by now), when Tom wakes up shortly after his phage treatment, I admit even I was surprised. I knew the story, yes, but that was before I read about just how sick Tom was, how many other strategies they’d all tried, how hard it was to get him to come around. I wouldn’t have expected it, but it turns out that hearing “phage therapy worked on this man” is very different from getting the sense of going through months of illness WITH him, with his family, and with his doctors, and then reading about the effect the phages had. I didn’t think it was possible, because I spend almost all my days thinking about phages and phage therapy, but I became more convinced that this treatment needs to be made available after reading this book.
Reading this book also inspired me to believe that cross-disciplinary collaboration is more possible and more likely than I thought (and again, I spend my days thinking about this exact subject, and I’m a big believer in collaboration). But it gave me an incredible boost of hope and motivation to read about how the medical, academic, biotech, military and regulatory communities came together and took a collective leap to try something outside of every single one of their pay grades. To be honest, this book makes me want to start asking and expecting more of people—though I’m not sure that was the intention of those involved in this case! :)
Lastly, it was inspiring to read the perspective of another scientist (and a fellow Canadian, at that!), to learn about her life and career trajectory, how she became a scientist, the mountains she overcame both personally and professionally, the extremely interesting parallels she’s seen between the fields of HIV and phage/AMR, and to feel like a fly on the wall the whole way through. The writing is so inviting, and you feel like a close and trusted friend by the end.
So all in all, I fully expected to like this book. I’d been eagerly awaiting its publication for months. But I didn’t expect to keep turning the pages as quickly as I did. I didn’t expect to find such a relatable account of what it’s like as a family member in the ICU, hovering and hopeful. And I didn’t expect to come away with an even greater sense of purpose for what I am working to help build: greater access to phage therapy and a community that supports progress in this reignited field. Steffanie and Tom’s story embodies this vision, and I’m sure there will be similar gems for everyone in this treasure of a book.
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