Phages for musculoskeletal infections

Issue 48 | October 17, 2019
14 min read
Capsid and Tail

Image by Dr. Manuel González Reyes from Pixabay

This week we highlight a recent paper on using phage therapy to treat severe musculoskeletal infections (osteomyelitis). A multidisciplinary group in Belgium made up of surgeons, infectious disease physicians, pharmacists, microbiologists and phage scientists treated four patients with phages, and in the process the team came up with a set of standards for treating this type of infection with phages.

Also in this issue: new insights into our gut phages, prophages altering evolution of social strategies, new jobs in infant gut phages, machine learning, teaching, and more!

What’s New

It’s Capsid & Tail’s one-year anniversary this week! We sent out our first issue on Oct 18, 2018. Since then, we’ve published 48 issues, including 13 guest articles (authored by 23 guest authors). We’ve grown to over 600 subscribers, with a handful of new people joining us each week. We’ve sent out 62 messages on our phage community board, and we’ve highlighted 68 phage jobs.

Thank you all so much for reading, suggesting Capsid & Tail to others, and for offering feedback and cheering us on throughout the year! And thank you VERY much to all of our stellar guest writers. It’s been great fun to put this together each week!

In our second year, we hope to see more guest articles (sign up here!), more collaborations sparked through the community board (post here!), and to find more new ways we can experiment with Capsid & Tail each week. And don’t forget, you can find past issues here and post jobs for free here.

Phage DirectoryAnniversary!

We’ve been talking about NIAID’s new request for applications for phage research; here’s the complete funding opportunity announcement. This is an R21 grant mechanism (no clinical trials allowed). NIAID intends to commit $2.5 million in FY 2021 to fund 6-8 awards. Submit between Feb 18, 2020 and March 18, 2020. And thanks to those who’ve identified yourselves as being interested in finding collaborators to apply for these funds; we will reach out to you soon to introduce you to each other.

Grant FundingFunding Opportunity Announcement

New research by Andrey Shkoporov and colleagues at APC Microbiome in Ireland has shown using longitudinal metagenomics that the human gut virome is actually very stable in individuals, but that each individual tested had their own unique virome. Plus, they identified several groups of crAss-like and Microviridae phages as the most stable human gut colonizers, and were able to find connections between stable viral communities and gut bacteria using CRISPR-based prediction. Paper | News article

ResearchHuman gut virome

Siobhán O’Brien of the University of Liverpool and colleagues published a paper showing how transposable prophages lead to P. aeruginosa adaptation. They alter iron availability to show that transposable prophages cause P. aeruginosa to evolve toward extreme siderophore production phenotypes. Their work suggests that prophages can mediate evolutionary divergence of social strategies, which wasn’t clear before.

ResearchProphage biologyPhage-host interactions

Check out this new podcast interview (The Life Scientific, by BBC Radio 4) with Martha Clokie, a University of Leicester phage professor. She talks about how her interests in botany as a child turned into interests in phages. This is a great listen, and really gets into how Martha’s research has progressed over the years (including how hard it was to find C. difficile phages, the strange places she looked, and her thought process throughout).

PodcastCareer talk

Scientific American magazine just published a nice feature on where phage therapy is at today: great storytelling, nice visuals, plus input from several phage researchers on where phage therapy is going.

Popular sciencePhage Therapy

Latest Jobs

PhD position: Phages in the infant gut: good, bad or neutral?

Quadram Institute,
Norwich, UK

Dr. Evelien Adriaenssens

We are recruiting a student at the Quadram Institute Bioscience (QIB) on the role phages play in the establishment of the gut microbiota, particularly focused on beneficial bifidobacteria. The student will join the team of Dr Evelien Adriaenssens, an expert in phage biology, and that of Dr Lindsay Hall, an expert in the infant gut microbiome. In this project, the student will use established methods to discover new bacteriophages against bifidobacteria and investigate their effects on natural bacterial communities in the infant gut through model systems and next-generation sequencing.

PhD Project Gut phages
More Details Last day: November 25, 2019

PhD position: machine learning to find RNA viruses in the gut microbiome

Quadram Institute,
Norwich, UK

Dr. Evelien Adriaenssens

The Adriaenssens group at the Quadram Institute Bioscience (QIB), in collaboration with the School of Computing Sciences at the University of East Anglia, is looking to recruit a PhD student on a fully funded project. In this project, we will use machine learning approaches for the detection of RNA virus genomes in microbiome data and investigate their role in the human gut. The student will join the group of Dr Evelien Adriaenssens at QIB, specialised in gut viruses and viromics, with Dr Gavin Cawley, a specialist in machine learning, as second supervisor.

PhD Project Machine LearningGut phagesRNA viruses
More Details Last day: November 25, 2019

Biology Lab Specialist: SEA-PHAGES at Gonzaga University

Gonzaga University, Spokane, Washington

The Department of Biology at Gonzaga University invites applications for a Biology Lab Specialist to prepare laboratory facilities for the teaching of multi-section laboratory courses, to assist with the implementation of lab curricula, to teach lab sections, and to supervise teaching assistants and student workers. The labs are the first semester component of the HHMI SEA-PHAGES program (Science Education Alliance – Phage Hunters Advancing Genomics and Evolutionary Science), which is a classroom-based undergraduate research experience. Students use microbiology and molecular techniques to discover, purify, and characterize bacteriophages from soil.

Biology Lab Specialist TeachingSEA-PHAGES

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Phages for musculoskeletal infections

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Co-founder
Phage microbiologist and co-founder of Phage Directory
Phage Directory, Atlanta, GA, United States

Jessica Sacher is a co-founder of Phage Directory and has a Ph.D in Microbiology and Biotechnology from the University of Alberta.

For Phage Directory, she takes care of the science, writing, communications, and business aspects.

This week, we’re going over a new phage therapy case series report (Onsea et al. 2019). Although phage therapy to treat musculoskeletal infections (aka osteomyelitis) has historically been relatively common in Eastern Europe, most of the past studies have each been done differently, and have lacked relevant details regarding how they were done. This study aimed to take steps toward standardizing the process of phage therapy for osteomyelitis by detailing how a set of four patients were identified, treated and followed up with, along with details on the phages used.

(Here’s a previous Capsid & Tail post on how another group used phage therapy to treat this type of infection.)

The paper

The study was published last month in Viruses by Jolien Onsea of KU Leuven and the University Hospitals Leuven, alongside colleagues and collaborators at these institutes and at the Queen Astrid Military Hospital.

What are musculoskeletal infections?

Musculoskeletal infections are also referred to as osteomyelitis. Often, after implantation of orthopedic devices (e.g. prostheses), patients get infections. Often, bacteria are resistant to antibiotics, and biofilms are generally a huge problem.

What were the patients dealing with?

Four patients were found eligible for phage therapy. They were all facing poor prognoses (ie. likely amputation) because surgery and standard medical regimens had not helped. Three patients had chronic osteomyelitis of the femur. One patient had chronic osteomyelitis of the pelvis. They’d each suffered multiple infection relapses. One patient had received their diagnosis as early as 1984, another in 1995, another in 2015, and the other in 2017.

Which pathogens were cultured?

Multiple pathogens were isolated from the sites of infection. In two patients, Pseudomonas aeruginosa and Staphylococcus epidermidis were both isolated. One patient had Streptococcus agalactiae and Staphylococcus aureus, and another had Enterococcus faecalis.

Eligibility

A “multidisciplinary phage task force” (consisting of musculoskeletal surgeons, microbiologists, infectious disease specialists, plastic surgeons, and phage scientists) was assembled, and this team made the call about whether each patient was eligible for phage therapy.

To be eligible, patients had to fit the criteria declared in the Declaration of Helsinki (see our Capsid & Tail post here). This means that these patients had to have infections that weren’t being controlled by standard treatment options, and thus could qualify for unproven medical interventions (phage therapy).

Indeed, in all four cases, antibiotic therapy and surgery to remove the infected tissue had been tried, and had failed to clear the infections.

What needed to be done from an ethics standpoint?

Patients each gave their informed consent, and the hospital’s Ethical Committee gave consent for each patient to receive phage therapy.

Where did the phages come from?

Three patients received a phage cocktail called BFC1 (one S. aureus phage and two P. aeruginosa phages, all strictly lytic and well characterized) which was produced by the Queen Astrid Military Hospital. The phages in this cocktail were given a “genetic passport” by Sciensano, Belgium’s federal public health institute, as they were found not to contain toxins or antibiotic resistance genes.

The fourth patient received the Pyo phage cocktail from the Eliava Institute in Tbilisi, Georgia (contains multiple phages against Streptococcus, Staphylococcus, Proteus, Escherichia coli, P. aeruginosa, and Enterococcus, though the exact composition is not known).

Were patient strains first tested for phage susceptibility?

Yes. Three patients had Staphylococcus that was susceptible to BFC1. At least one of these patients also had P. aeruginosa that was resistant to this cocktail, but the team proceeded with the cocktail anyway based on its anti-Staphylococcus activity.

The fourth patient didn’t receive BFC1, as the cocktail doesn’t cover Enterococcus (the pathogen cultured from that patient). However, this patient’s E. faecalis was sensitive to the Pyo phage cocktail, so this patient received this cocktail instead (it was ordered from the Eliava).

How were phages applied?

Phages were given intraoperatively, by placing a draining system in close contact with the infected bone and rinsing with phage-containing solution. A sodium bicarbonate solution was applied just prior to the phage, to decrease the local acidity.

What was the dosage?

The BFC1 cocktail (used on three patients) was used at 10^7 PFU/mL in saline. Phages were given three times per day, for 7 to 10 days. Between 10-40 mL of phage solution was used to rinse the infected bone, and the phage was allowed to contact the site for 10 min (the drain was closed during this time). Before closing the wound, a gentamicin-impregnated collagen sponge soaked in phage solution was placed on the bone.

Were antibiotics used concurrently?

Yes. During phage therapy, each patient also received antibiotics (each received a different regimen, depending on their needs). The patients received antibiotics for six weeks to three months in total, even though the phages were only applied for 7-10 of these days.

How were the patients evaluated during and after phage therapy?

Each day, the patients’ clinical status was evaluated (this meant inspecting the wound, doing blood tests, checking general health status, and radiology). Blood was taken before surgery and on days 2, 4, 7, 10, 14, 28 post-surgery. Patient health was tracked for 8-16 months following phage therapy.

What was the outcome for the patients?

For three patients, no signs of infection recurrence were observed, and these patients are currently infection-free! (You can check out Figure 2 of the paper for before and after images, which are quite impressive).

One patient had to have more surgeries following phage therapy, to manage a bone defect. Eight months after phage therapy, another S. epidermidis strain was isolated from this patient. This strain had different antibiotic susceptibility compared to the first S. epidermidis strain isolated from this patient, so the team sequenced both. They confirmed the strains were not clonal (>8000 SNPs), meaning a new strain had come in to replace the first. Eventually, after additional surgeries and more antibiotics, this patient was also deemed infection-free.

Did the phages provoke inflammation?

Yes. C-reactive protein (CRP) and white blood cell (WBC) levels, markers of inflammation, were tracked in each patient over time. CRP levels increased in all patients during phage therapy, and WBC levels increased in two patients, but all levels returned to normal within a month following phage therapy in all patients.

Did the phages provoke anti-phage antibody production?

No. Serum samples were tested for their capacity to neutralize the administered phages, but anti-phage antibody production was not detected in any of the patients.

Were there any side effects?

No severe side effects were observed. The patient who got the Pyo cocktail had redness and pain during rinsing after 7 days of phage treatment, which may have resulted from a response to endotoxin present in the cocktail (Pyo cocktail is not free of endotoxin).

Summary

This paper describes the safe and successful use of phage therapy as an adjunct to antibiotics to treat severe polymicrobial musculoskeletal infections in four patients. Phages were given as pre-made, multi-target, intraoperatively-applied cocktails that were verified to lyse at least one of each patient’s isolated pathogens in advance.

Going forward

The “multidisciplinary phage task force” (infectious disease specialists, pharmacists, microbiologists, surgeons and phage scientists) assembled for this effort will continue to assess patients with musculoskeletal infections for phage therapy eligibility. Treatment plans will be developed for each, and data will be collected in a registry. The hope is that analyzing this data regularly will give insight into how to use phages to treat these types of patients safely and effectively.

Further reading

Other Capsid & Tail issues we’ve written on phage therapy case reports:

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