BACTERIOPHAGES

First World War superbug treatment could save NHS millions – but is blocked by red tape

Joe Pinkstone
Tue 29 October 2024\
THE TELEGRAPH

The use of bacteria-killing viruses known as phages to treat patients dates back to the First World War


William Stocking, 81, has spent much of the last four years in and out of hospital as an infection slowly destroys his leg.

He caught a superbug, an antimicrobial-resistant strain of Staphylococcus aureus, after going to the Royal Devon and Exeter Hospital in early 2020 with a chest infection.

Superbugs are notorious for being hard to treat because of their immunity to antibiotics. Around 52,000 people a year catch superbugs in the UK, causing around 2,000 deaths and costing the NHS around £180 million annually.

However, a little-known treatment dating back to the First World War is available, if NHS doctors are prepared to spend hundreds of hours fighting a mountain of government red tape.

Bacteriophages, known as phages, are bacteria-killing viruses that inject their own DNA into a bacteria to seize control of the cell and produce more phages until the bacteria bursts.

It is an effective killing mechanism and phages are the most abundant entity in the world.

They are highly precise with only specific strains of bacteria targeted by a certain phage, and phages can be effective against superbug infections impervious to all known medication.

Doctors are increasingly looking at phage therapy to help patients who are otherwise out of options, and Mr Stocking is a pioneering patient in the UK.

The superbug bacteria was attracted to the metal in his knee replacement which he had in the late 1980s following a career-ending injury suffered in the line of duty while a sergeant in the Hampshire Constabulary.

William Stocking and his wife Lorraine hope the treatment will allow him to walk properly again - Eddie Mulholland

“It works a bit like [the video game] Pac-Man and goes around eating the infection. It’s been a partial success so far, and time will tell,” Mr Stocking told The Telegraph from his hospital bed at the Royal National Orthopaedic Hospital (RNOH) in north-west London after receiving his third and final dose of phage therapy last week.

“I’ve had numerous pills, potions, antibiotics, transfusions and none of them worked. We have exhausted the available options and are down to phage which was raised as a last resort,” Mr Stocking said.

The cost of this bespoke and unique treatment, which was paid for and administered by the NHS, is thought to be similar to a course of the most premium and highly-preserved antibiotics, at a few thousand pounds. The procedure is a last hope for him and his wife, Lorraine, 72, also a retired police officer.

After retiring, the couple moved to a smallholding in Devon and ran a rural B&B for a decade. On Wednesday, they celebrated their 48th wedding anniversary by sharing a Mars bar in hospital.

Mr Stocking now has three sinuses on his left leg from his infection which weep constantly and need regular tending.

“It’s got more and more painful, and it’s got worse and worse to the point where I can’t walk very far and I am very unstable,” Mr Stocking said.

“It has prevented us doing lots of things we would have wanted to have done. Everything has just been put on hold,” adds Lorraine.



The couple were not put off by the therapy’s experimental nature, and hope it could allow Mr Stocking’s leg to heal enough to allow him to walk with greater ease.

“I thought it was brilliant when it was first suggested to me,” Mr Stocking said.

“It was put to me that I would be the first one to have phage for something like this and that it was an experiment that could work for a lot of people and, if it works, also help a lot of people.

“I am 81 and I can’t pioneer much more with my life so whatever I can do to be of use to anybody then let’s give it a go.

“I’m never going to win a Butlins Knobbly Knees competition, but I’d like to see my leg sufficiently well to use it and walk. Walking is the main thing, to get about for the final few years of my life.”

But the path to this point, the couple say, has been exhausting. Endless red tape has delayed treatment and made access to phage a multi-year struggle.


Phage therapy is not a licensed medicine in the UK and a phage from the UK can not be provided to an NHS patient unless it reaches Good Manufacturing Practice (GMP) standard. There is no GMP facility for phages in the UK.

However, a “GMP-like” phage from abroad can be used for compassionate use if it is approved by the Medicines and Health Products Regulatory Agency (MHRA) and imported.

Proving this, and sourcing an importer to bring an unlicensed, non-GMP medicine from a laboratory in Brussels required more than 200 hours of work from Mr Stocking’s clinical team and caused most of the delays.
‘Get on with it’

The Stocking family and the doctors both urged politicians and regulators to alter the current legislation to make it easier for other patients to access phage therapy through the NHS.

“While all the faceless bureaucracy goes on we are left 200 miles away with no answers,” said Mr Stocking.

“It’s not been a very pleasant time. Phage could be useful to a lot of people but red tape is holding it all up. It has been months and months of hanging around.

“Give it a chance, expedite it,” he urged politicians. “Money is money but lives are lives and limbs are limbs. Get on with it.”

A medic treats Mr Stocking - RNOH Images

Lorraine said phage therapy could save the NHS millions of pounds a year and help treat thousands of different people around the country who have run out of options.

“Behind the delays and red tape are mental, emotional and physical impacts,” she said.

“His condition three-and-a-half years ago was not so bad and maybe phage would be more effective had we not been this far down the line before getting it.”

Tariq Azamgarhi, the principal antimicrobial pharmacist at RNOH, and Dr Antonia Scobie, research lead for the Bone Infection Unit at RNOH, were central in securing phage therapy for Mr Stocking.

Mr Azamgarhi said phages “fall between the cracks” of much of the existing UK regulation, and urged politicians to make changes to help doctors better access phages for compassionate use in patients with no other option.
‘Huge potential’

Dr Scobie, who is also lead for the UK Clinical Working Group for bacteriophage therapy, told The Telegraph: “We are in the camp of strongly supporting phage therapy and I think it has a huge amount of potential.

“We’re under no illusion that on its own, phage therapy is never going to be able to replace antibiotics but what it does offer is a safe treatment that can be an adjunct to our existing therapies.

“We would never dream of injecting the phage and just crossing fingers and hoping that would be enough. It needs to be used in the right way, but it’s an extra tool. I think it has huge potential and it just needs to be used in the right way.”

The RNOH team is now beginning the long-winded process again for three other superbug patients with joint infections and is helping other hospitals around the country tackle the paperwork.

“We hope that by opening various doors in the process that it may be easier for them and help the next patient,” Dr Scobie said.

A report by MPs on the science and technology committee said earlier this year that the MHRA should change its rules to allow for compassionate use in last-resort medical cases, like those of Mr Stocking.

They also urged the agency to set out new guidance for how doctors can use non-GMP phages.

The MHRA has missed some deadlines set out by the committee at the start of the year and is currently reviewing proposed guidance. It says this will be published “in due course”.

The MHRA declined to comment.

 OUR FRIEND THE BACTERIOPHAGE

Bacteria-fighting viruses team up to treat drug-resistant superbugs

UChicago Pritzker School of Molecular Engineering researchers screened a library of bacteriophages to find combinations of the viruses that can work together to fight antibiotic-resistant Klebsiella pneumoniae infections

University of Chicago

 

image: 

Researchers at the University of Chicago Pritzker School of Molecular Engineering (PME) and UChicago Medicine, including Asst. Prof. Mark Mimee (left) and research specialist Ella Rotman, have shown that a mixture of collections of bacteriophages can successfully treat antibiotic-resistant infections in mice.

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Credit: UChicago Pritzker School of Molecular Engineering / Jason Smit

Researchers have a new battle tactic to fight drug-resistant bacterial infections. Their strategy involves using collections of bacteriophages, viruses that naturally attack bacteria. In a new study, researchers at the University of Chicago Pritzker School of Molecular Engineering (PME) and UChicago Medicine have shown that a mixture of these phages can successfully treat antibiotic-resistant Klebsiella pneumoniae infections in mice.

At the same time, however, the team’s work revealed just how complex the interactions between phages and bacteria can be; the viruses predicted to be most effective in isolated culture dishes did not always work in animals. Moreover, both phages and bacteria can evolve over time – in some cases, phages evolved to be more efficient in killing bacteria while in other cases, Klebsiella evolved resistance to the phages.

“We still think phages are an incredibly promising approach to treating drug-resistant bacteria such as Klebsiella,” said Mark Mimee, assistant professor of molecular engineering and senior author of the new work, published in Cell Host & Microbe. “But phages are like a living, constantly changing antibiotic which gives them a lot of complexity.”

Klebsiella pneumoniae are common bacteria found in people’s intestines where they cause little harm. However, when the bacteria escape to other body sites, such as open wounds, the lungs, the bloodstream, or the urinary tract, they can cause more severe infections. K. pneumoniae are often spread within hospital settings, and drug-resistant strains have become common.

“In my clinic, I see patients with recurrent urinary tract infections caused by Klebsiella,” says urogynecologist Sandra Valaitis, MD, of UChicago Medicine, a co-author of the new work. “Often these bacterial strains develop resistance to oral antibiotics, leaving patients with fewer options to clear the infection. We urgently need new ways of treating these bacteria.”

Phages, for more than a century, have been known as a natural enemy of bacteria and studied for their potential to treat infections. However, phages are usually very specific for one type of bacteria and predicting these matches has been difficult.

In the new research, Ella Rotman – a scientist in the Mimee Lab – screened wastewater to isolate phages that could effectively kill 27 different Klebsiella strains, including 14 that were newly isolated from University of Chicago patients. The team identified several dozen phages with the capability of killing at least some Klebsiella strains, Then, the researchers analyzed what genetic factors in the bacteria made them most prone to being killed or weakened by each of those phages.

Based on that analysis, Rotman and her colleagues developed a mixture of five phages that each targeted different components of the bacteria. In culture dishes as well as mice, this phage cocktail made antibiotic-resistant Klebsiella bacteria more likely to be attacked by the immune system and, in some cases, more susceptible to treatment with antibiotics. However, in other cases, the bacteria became more antibiotic resistant after treatment.

“It’s one of those things where biology often doesn’t work the way you want it to,” says Mimee. “But it gives us an opportunity to study the detailed dynamics between the phages and the bacteria.”

By exposing the phage mixture to a series of isolated Klebsiella bacteria, the researchers gave the phage the opportunity to evolve. This improved the ability of the cocktail to kill Klebsiella. In mice, the mixture effectively killed or weakened Klebsiella. The researchers observed co-evolution between the bacteria and phage in the mouse intestines, where the Klebsiella evolved to evade phage attack and the phage countered to better infect the altered bacteria.

Mimee’s lab group is continuing experiments to better understand how different phage and bacteria pairs interact with each other and how the presence of other phages and bacteria – naturally found in the human body—influences that. At the same time, in collaboration with Valaitis, they are seeking approval from the Food and Drug Administration (FDA) for a small clinical trial testing the phage mixture in patients with urinary tract infections.

“This research is a positive step forward in trying to sort out the complexities of phages and move them closer to the clinic,” says Mimee.

Citation: “Rapid design of bacteriophage cocktails to suppress the burden and virulence of gutresident carbapenem-resistant Klebsiella pneumoniae,” Rotman et al, Cell Host & Microbe, October 4, 2024. DOI: https://doi.org/10.1016/j.chom.2024.09.004

Funding: National Science Foundation, National Institutes of Health, Arnold and Mabel Beckman Foundation, BRaVE Phage Foundry at Lawrence Berkeley National Laboratory.

---

Journal

Cell Host & Microbe

DOI

10.1016/j.chom.2024.09.004 

Article Title

Rapid design of bacteriophage cocktails to suppress the burden and virulence of gut-resident carbapenem-resistant Klebsiella pneumoniae

Article Publication Date

4-Oct-2024

 Harnessing bacteriophages as targeted treatments for drug-resistant bacteria

Sep 5 2024

As antibiotic resistance becomes an increasingly serious threat to our health, the scientific and medical communities are searching for new medicines to fight infections. Researchers at Gladstone Institutes have just moved closer to that goal with a novel technique for harnessing the power of bacteriophages.

Bacteriophages, or phages for short, are viruses that naturally take over and kill bacteria. Thousands of phages exist, but using them as treatments to fight specific bacteria has so far proven to be challenging. To optimize phage therapy and make it scalable to human disease, scientists need ways to engineer phages into efficient bacteria-killing machines. This would also offer an alternative way to treat bacterial infections that are resistant to standard antibiotics.

Now, Gladstone scientists have developed a technology that lets them edit the genomes of phages in a streamlined and highly effective way, giving them the ability to engineer new phages and study how the viruses can be used to target specific bacteria.

"Ultimately, if we want to use phages to save the lives of people with infections that are resistant to multiple drugs, we need a way to make and test lots of phage variants to find the best ones," says Gladstone Associate Investigator Seth Shipman, PhD, the lead author of a study published in Nature Biotechnology. "This new technique lets us successfully and rapidly introduce different edits to the phage genome so we can create numerous variants."

The new approach relies on molecules called retrons, which originate from bacterial immune systems and act like DNA-production factories inside bacterial cells. Shipman's team has found ways to program retrons so they make copies of a desired DNA sequence. When phages infect a bacterial colony containing retrons, using the technique described in the team's new study, the phages integrate the retron-produced DNA sequences into their own genomes.

The enemy of your enemy

Unlike antibiotics, which broadly kill many types of bacteria at once, phages are highly specific for individual strains of bacteria. As rates of antibiotic-resistant bacterial infections rise-;with an estimated 2.8 million such infections in the United States each year-;researchers are increasingly looking at the potential of phage therapy as an alternative to combat these infections.

"They say that the enemy of your enemy is your friend," says Shipman, who is also an associate professor in the Department of Bioengineering and Therapeutic Sciences at UCSF, as well as a Chan Zuckerberg Biohub Investigator. "Our enemies are these pathogenic bacteria, and their enemies are phages."

Already, phages have been successfully used in the clinic to treat a small number of patients with life-threatening antibiotic-resistant infections, but developing the therapies has been complex, time-consuming, and difficult to replicate at scale. Doctors must screen collections of naturally-occurring phages to test whether any could work against the specific bacteria isolated from an individual patient.

Shipman's group wanted to find a way to modify phage genomes to create larger collections of phages that can be screened for therapeutic use, as well as to collect data on what makes some phages more effective or what makes them more or less specific to bacterial targets.

"As the natural predators of bacteria, phages play an important role in shaping microbial communities," says Chloe Fishman, a former research associate at Gladstone and co-first author of the new study, now pursuing her graduate degree at Rockefeller University. "It's important to have tools to modify their genomes in order to better study them. It's also important if we want to engineer them so that we can shape microbial communities to our benefit-;to kill antibiotic-resistant bacteria, for example."

Continuous phage editing

To precisely engineer phage genomes, the scientists turned to retrons. In recent years, Shipman and his group pioneered the development and use of retrons to edit the DNA of human cells, yeast, and other organisms.

Shipman and his colleagues began by creating retrons that produce DNA sequences specifically designed to edit invading phages-;a system the team dubbed "recombitrons." Then, they put those retrons into colonies of bacteria. Finally, they let phages infect the bacterial colonies. As the phages infected bacteria after bacteria, they continuously acquired and integrated the new DNA from the recombitrons, editing their own genome as they went along.

The research team showed that the longer they let phages infect a recombitron-containing bacterial colony, the greater the number of phage genomes were edited. Moreover, the researchers could program different bacteria within the colony with different recombitrons, and the phages would acquire multiple edits as they infected the colony.

As a phage is bouncing from bacterium to bacterium, it picks up different edits. Making multiple edits in phages is something that was previously incredibly hard to do; so much so that, most of the time, scientists simply didn't do it. Now, you basically throw some phages into these cultures, wait a while, and get your multiple-edited phages."

Seth Shipman, PhD, lead author

A platform to screen phages

If scientists already knew exactly what edits they wanted to make to a given phage to optimize its therapeutic potential, the new platform would let them easily and effectively carry out those edits. However, before researchers can predict the consequence of a genetic change, they first need to better understand what makes phages work and how variations to their genomes impact their effectiveness. The recombitron system helps makes progress here, too.

If multiple recombitrons are put into a bacterial colony, and phages are allowed to infect the colony for only a short time, different phages will acquire different combinations of edits. Such diverse collections of phages could then be compared.

"Scientists now have a way to edit multiple genes at once if they want to study how these genes interact or introduce modifications that could make the phage a more potent bacterial killer," says Kate Crawford, a graduate student in the Shipman lab and co-first author of the new study.

Shipman's team is working on increasing the number of different recombitrons that can be put into a single bacterial colony-;and then passed along to phages. They expect that eventually, millions of combinations of edits could be introduced to phages to make huge screening libraries.

"We want to scale this high enough, with enough phage variants, that we can start to predict which phage variants will work against what bacterial infections," says Shipman.

Source:

Gladstone Institutes

Journal reference:

Fishman, C. B., et al. (2024). Continuous multiplexed phage genome editing using recombitrons. Nature Biotechnology. doi.org/10.1038/s41587-024-02370-5.

  

Personalized phage therapy heals resistant wounds-squeaks makes full recovery

THE HEBREW UNIVERSITY OF JERUSALEM

 

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RELAXING AFTER FULL RECOVERY

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CREDIT: MILAT AND LARRY BERKLEY

A new study demonstrates an advance in treating antibiotic-resistant infections in animals through personalized phage therapy. The treatment combined a specific anti-P. aeruginosa phage applied topically with ceftazidime administered intramuscularly, resulting in the complete healing of a persistent surgical wound after fourteen weeks. This highlights the potential of phage therapy as a practical and effective solution for antibiotic-resistant infections in veterinary practice, with implications for human medicine as well.

 

Link to pictures: https://drive.google.com/drive/folders/12ntfvgd_ZdpEYtMsgkZRjS9vB89ps5XM?usp=sharing

A new study led by Prof. Ronen Hazan and his team, from the Faculty of Dental Medicine at the Hebrew University of Jerusalem, in collaboration with the team of Vet Holim, JVMV -Veterinary medical center in Kiryat -Anavim, Israel, has shown an advance in the treatment of antibiotic-resistant infections in animals. This research, focusing on a five-year-old Siamese cat Squeaks  with a multidrug-resistant Pseudomonas aeruginosa infection post-arthrodesis surgery, marks the first published documented application of personalized phage therapy in veterinary medicine.

Squeaks, initially treated at the JVMV for injuries sustained from a high-rise fall, developed a severe infection in the right hind leg following multiple surgeries. This infection persisted despite various antibiotic treatments over four months. Facing a potential implant-replacement surgery, the team turned to the new treatment which involved a meticulously designed combination of a specific anti-P. aeruginosa phage, a virus that kills bacteria, applied topically to the surgical wound and ceftazidime administered intramuscularly. Moreover, the owners of the cat, after short demonstration, provides most of the treatment doses of phages and antibiotics at their home.

The integration of phage therapy with antibiotics was aimed at targeting the pathogen effectively and directly at the site of infection, leveraging the phage’s ability to be applied topically, which simplifies administration and maximizes its concentration at the infection site. This approach allowed the surgical wound, which had remained open for five months, to fully heal after to fourteen weeks of treatment.

The successful outcome of this case underscores the critical need for novel therapeutics like phage therapy to address the growing concern of antibiotic-resistant infections, which affect up to 8.5% of surgical sites following orthopedic surgeries in companion animals. These infections not only pose significant health risks to the animals but also increase the morbidity, mortality, and costs associated with these procedures.

Recent studies suggest that phage therapy, already showing high success rates in human medicine for treating orthopedic infections and chronically infected wounds, can offer a promising solution for similar issues in veterinary practice. Moreover, the successful treatment of this cat by its owners at home highlights the practicality and efficacy of personalized phage therapy, which could be extended to treat other pets facing similar antimicrobial resistance challenges.

Interestingly, opposite to common situations, this case was performed on an animal based on the team's insights from treating humans first.

The positive reception from veterinarians and pet owners regarding phage therapy points to a growing awareness and acceptance of this treatment option. As the new treatment continues to be explored in veterinary settings, it not only improves the health and well-being of pets but also offers valuable data that contribute to the broader application of phage therapy in both animals and humans. This bridging of data can enhance treatment protocols and outcomes across a variety of bacterial infections, potentially changing the landscape of infection treatment in both veterinary and human medicine.

Treatment Process

CREDIT

Milat and Larry Berkley

JOURNAL

Veterinary Quarterly

DOI

10.1080/01652176.2024.2350661 

METHOD OF RESEARCH

Case study

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Successful phage-antibiotic therapy of P. aeruginosa implant-associated infection in a Siamese cat

Phage therapy: In-depth discussion on ethical considerations and regulatory landscape at upcoming European conference “Targeting Phage Therapy 2024”

MITOCHONDRIA-MICROBIOTA TASK FORCE

 

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BARBARA BRENNER, A LEGAL EXPERT IN MEDICAL LAW AND HUMAN RIGHTS, WILL DELIVER A TALK TITLED "REGULATORY RESTRICTIONS VS. HUMAN RIGHTS, THE HIPPOCRATIC OATH, AND THE FREEDOM OF THERAPY – THE LEGAL ASPECT OF PHAGE THERAPY" AT TARGETING PHAGE THERAPY ON JUNE 20-21, 2024

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CREDIT: TARGETING PHAGE THERAPY

The 7th World Conference on Targeting Phage Therapy 2024 is set to take place on June 20-21 at the Corinthia Palace in Malta, welcoming over 150 attendees from 30 countries and featuring more than 32 communications. This annual event showcases the latest advancements in phage research and therapy, emphasizing how these developments could revolutionize healthcare practices globally.

The Ethical Considerations and Regulatory Landscape of Phage Therapy will be highlighted

Targeting Phage Therapy 2024 will include a dedicated session on the ethical and regulatory aspects of phage therapy, particularly in Europe. Barbara Brenner, a legal expert in medical law and human rights, will deliver a talk titled "Regulatory Restrictions vs. Human Rights, the Hippocratic Oath, and the Freedom of Therapy – The Legal Aspect of Phage Therapy". Her presentation will focus on balancing regulatory frameworks with the urgent need for accessible, life-saving treatments.

Phage therapy faces significant regulatory and ethical challenges, and Brenner will address several critical points:

- Regulatory Frameworks and Human Rights: Brenner will provide an overview of EU and German legal and regulatory frameworks, highlighting the tension between the right to safe drugs and the right to life-saving treatment in emergencies, especially concerning antimicrobial-resistant (AMR) infections and non-GMP phages.

- Ethical and Legal Questions: The session will explore whether it is ethical to deny life-saving treatments for safety reasons and whether regulatory bodies like the FDA and EMA can be held liable for prohibiting non-GMP phages if GMP phages are unavailable or unaffordable. Additionally, Brenner will discuss the validity of scientific evidence derived from anecdotal sources versus the necessity of randomized controlled trials (RCTs) and whether these trials need to be redesigned. The legal status of phage therapy as "experimental" and the potential liability of clinicians who refuse phage therapy when it could save a patient will also be examined.

- Combatting Antimicrobial Resistance (AMR): The presentation will include the One Health approach, integrating human, animal, and environmental health practices. Brenner will highlight Georgia's successful model, advocating for the promotion of phages as primary interventions, reserving chemical antibiotics for situations where phages are ineffective.

 

Speakers Lineup

• Robert T. Schooley, University of California, San Diego, USA

Clinical Trials in Phage Therapeutics: Looking Under the Hood

• Ekaterina Chernevskaya, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Russia

Adaptive Phage Therapy in the Intensive Care Unit: From Science to Patients

• Jean-Paul Pirnay, Queen Astrid Military Hospital, Belgium

Magistral Phage Preparations: Is This the Model for Everyone?

• Barbara Brenner, Kanzlei BRENNER, Germany

Regulatory restrictions vs. Human Rights, the Hippocratic oath and the Freedom of therapy– The legal aspect of phage therapy

• Nannan Wu, Shanghai Public Health Clinical Center, Fudan University, China

Phage Therapy: A Glimpse into Clinical Studies Involving Over 150 Cases

• Graham F. Hatfull, University of Pittsburgh, USA

Mycobacteriophages and Their Therapeutic Potential

• Antonia P. Sagona, University of Warwick, United Kingdom

Genetic Engineering of Phages to Target Intracellular Bloodstream E.coli Infections

• Paul Turner, Yale University, USA

Leveraging Evolutionary Trade-Offs in Development of Phage Therapy

• Pieter-Jan Ceyssens, Sciensano, Belgium

Quality control of phage Active Pharmaceutical Ingredients (APIs) in Belgium

• Wolfgang Weninger, Medical University of Vienna, Austria

The Phageome in Normal and Inflamed Human Skin

• Sabrina Green, KU Leuven, Belgium

Making Antibiotics Great Again: Phage resistance in vivo correlates to resensitivity to antibiotics in pan-resistant Pseudomonas aeruginosa

• Rodrigo Ibarra Chávez, University of Copenhagen, Denmark

Phage Satellites, a Diversity of Extradimensional Symbionts and Pathways to Phage Therapy

• Domenico Frezza, University of Roma Tor Vergata, Italy

Towards efficient phage therapies: investigation of phage / bacteria equilibrium with metagenome of dark matter in natural samples

• Besarion Lasareishvili, Eliava Institute of Bacteriophage, Microbiology and Virology, Georgia

Modern Concepts of Phage Therapy: An Immunologist’s Vision

• Kilian Vogele, Invitris, Germany

Cell-Free Production of Personalized Therapeutic Phages Targeting Multidrug-Resistant Bacteria

• Frederic Bertels, Max Planck Institute for Evolutionary Biology, Germany

Improving Phages through Experimental Evolution

• Eugene V Koonin, National Institutes of Health, USA

Evolution and megataxonomy of viruses: the place of phages in the virosphere

• Federica Briani, University of Milan, Italy

Addressing Phage Resistance to Enhance the Robustness of Phage Therapy for Pseudomonas aeruginosa Infections in People with Cystic Fibrosis

• Jumpei Fujiki, University of California San Diego, USA

Phage therapy: Targeting intestinal bacterial microbiota for the treatment of liver disease

 

Targeting Phage Therapy 2024 Supporters: Cellexus, Precision Phage, Jafral.

Contributing Partner: PHAGE Therapy, Applications, and Research Journal.

Media Partner: Bacteriophage.news.

For more information, registration details, list of attendees and the program, please visit: www.phagetherapy-site.com.

SEE

https://plawiuk.blogspot.com/search?q=PHAGES

 https://plawiuk.blogspot.com/search?q=BIOPHAGES

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Zombie cells in the sea: Viruses keep the most common marine bacteria in check

MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY

 

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SUNSET OVER THE ISLAND OF HELGOLAND IN THE GERMAN BIGHT, WHERE THE RESEARCHERS FROM THE MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY OBTAINED THEIR SAMPLES.

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CREDIT: JAN BRÜWER/MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY

The ocean waters surrounding the German island of Helgoland provide an ideal setting to study spring algae blooms, a focus of research at the Max Planck Institute for Marine Microbiology since 2009. In a previous study, the Max Planck scientists observed a group of bacteria called SAR11 to grow particularly fast during these blooms. However, despite their high growth rates, the abundance of SAR11 decreased by roughly 90% over five days. This suggested that the cells were quickly decimated by predators and/or viral infections. Now, the Max Planck researchers investigated what exactly lies behind this phenomenon.

Finding the phages infecting SAR11

“We wanted to find out if the low numbers of SAR11 were caused by phages, that is viruses that specifically infect bacteria”, explains Jan Brüwer, who conducted the study as part of his doctoral thesis. “Answering this seemingly simple question was methodologically very challenging”.

How does phage infection work? Phages infect bacteria by introducing their genetic material into them. Once there, it replicates, and utilizes the bacterial ribosomes to produce the proteins it needs. Researchers from Bremen used a technology that enabled them to “follow” the phage’s genetic material inside the cell. “We can stain the specific phage genes and then see them under the microscope. Since we can also stain the genetic material of SAR11, we can simultaneously detect phage-infected SAR11 cells”, explains Jan Brüwer.

While this might seem straightforward, the low brightness and small size of the phage genes made it challenging for researches to detect them. Nonetheless, thousands of microscope images were successfully analyzed, bringing some exciting news.  

“We saw that SAR11 bacteria are under massive attack by phages”, says Jan Brüwer. “During periods of rapid growth, such as those associated with spring algae blooms, nearly 20% of the cells were infected, which explains the low cell numbers. So, phages are the missing link explaining this mystery.”

Zombie cells: A global phenomenon

To the surprise of the scientists, the images revealed even more. "We discovered that some of the phage-infected SAR11 cells no longer contained ribosomes. These cells are probably in a transitional state between life and death, thus we called them 'zombie' cells”, Brüwer explains.

Zombie cells represent a novel phenomenon observed not only in pure SAR11 cultures but also in samples collected off Helgoland. Furthermore, analysis of samples from the Atlantic, Southern Ocean, and Pacific Ocean revealed the presence of zombie cells, indicating this phenomenon occurs worldwide.

“In our study, zombie cells make up to 10% of all cells in the sea. The global occurrence of zombie cells broadens our understanding of the viral infection cycle”, Brüwer emphasizes. “We suspect that in zombie cells, the nucleic acids contained in the ribosomes are being broken down and recycled to make new phage DNA.”

Brüwer and his colleagues hypothesize that not only SAR11 bacteria, but also other bacteria, can be turned into zombies. Thus, they want to further investigate the distribution of zombie cells and their role in the viral infection cycle.

“This new finding proves that the SAR11 population, despite dividing so fast, is massively controlled and regulated by phages”, stresses Brüwer. “SAR11 is very important for global biogeochemical cycles, including the carbon cycle, therefore their role in the ocean must be redefined. Our work highlights the role of phages in the marine ecosystem and the importance of microbial interactions in the ocean”.

Infected cells and zombie cells 

Under the microscope, scientists identified SAR11 zombie cells by their distinct lack of ribosomes. In an example comparing a live, infected SAR11 cell to an infected zombie cell: blue indicates bacterial DNA, yellow shows ribosomes, and purple highlights phage genes. The live cell (upper pictures) displays all three colors, while the zombie cell (lower pictures) lacks the yellow ribosome signal. The final column of images on the right merges these colors, clearly distinguishing the two cell types.

CREDIT

Jan Brüwer/Max Planck Institute for Marine Microbiology

JOURNAL

Nature Communications

DOI

10.1038/s41467-024-48172-w 

ARTICLE TITLE

Globally occurring pelagiphage infections create ribosome-deprived cells

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CRISPR is promising to tackle antimicrobial resistance, but remember bacteria can fight back

Experts looking to use the Nobel winning technology to target resistance genes and make bacteria sensitive to first line antibiotics again; but the bacteria have ways to fight back

EUROPEAN SOCIETY OF CLINICAL MICROBIOLOGY AND INFECTIOUS DISEASES

In the second new research review on this subject, Assistant Prof. Ibrahim Bitar, Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University in Prague, Plzen, Czech Republic, will give an overview of the molecular biology of CRISPR technology in explaining how it can used to tackle antimicrobial resistance.

Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR associated genes (cas) are widespread in the genome of many bacteria and are a defence mechanism against foreign invaders such as plasmids and viruses.  The CRISPR arrays are composed of a repeated array of short sequences, each originating from and exactly matching a nucleic acid sequence that once invaded the host.

Accompanying CRISPR sequences, there are 4-10 CRISPR-associated genes (cas), which are highly conserved and encode the Cas proteins. Cas proteins conduct adaptive immunity in prokaryotes (bacteria) based on immunological memories stored in the CRISPR array. The CRISPR/Cas system integrates a small piece of foreign DNA from invaders such as plasmids and viruses into their direct repeat sequences and will recognise and degrade the same external DNA elements during future invasions.

As the CRISPR/Cas systems integrate DNA from invading pathogens in chronical order, genotyping can be used to trace the clonality and the origin of the isolates and define them as a population of strains that were subjected to the same environmental conditions including geographic location (region) and community/hospital settings and eventually further extended to track pathogenic bacteria around human society.

CRISPR/Cas systems can also be employed for developing antimicrobial agents: introduction of self-targeting crRNAs will effectively and selectively kill target bacterial populations. Due to the shortage of available effective antimicrobial agents in treating multidrug-resistant (MDR) infections, researchers started to search for alternative methods to fight MDR infections rather than going through the process of developing new antimicrobial agents which can go on for decades. As a result, the concept of CRISPR/Cas-based selective antimicrobials was first developed and demonstrated in 2014. Vectors coding Cas9 and guide RNAs targeting genomic loci of a specific bacterial strain/species can be delivered to the target strain via bacteriophages or conjugative bacterial strains. In theory, delivery of the engineered CRISPR/Cas systems specifically eliminates target strains from the bacterial population, yet it is not that simple.

While these systems can seem a target for manipulation/intervention, all bacteria are regulated by multiple pathways to ensure the bacteria retains control over the process. Therefore, there remain several major challenges in using this system as an antimicrobial agent.

Most methods require delivery of the re-sensitised system by conjugation; the vector is carried by a non-virulent lab strain bacteria that is supposed to go and share the vector/plasmid through conjugation. The conjugation process is a natural process that the bacteria do which results in sharing plasmids among each other (even with other species). The percentage of conjugated (successfully delivered) bacteria in the total bacterial population is critical to the re-sensitised efficiency. This process is governed by several complicated pathways.

Bacteria also possess built-in anti-CRISPR systems, that can repair any damage caused by CRISPR-Cas systems. Defence systems that the bacteria uses to protect itself from foreign DNA often co-localise within defence islands (genomic segments that contain genes with similar function in protecting the host from invaders)  in bacterial genomes; for example: acr (a gene that acts, with other similar variants, as a repressor of plasmid conjugative systems) often cluster with antagonists of other host defence functions (e.g., anti-restriction modification systems) and experts hypothesise that MGEs (mobile genetic elements) organise their counter defence strategies in “anti-defence” islands.

Assistant Professor Bitar concludes: “In summary, this method seems very promising as an alternative way of fighting antimicrobial resistance. The method uses the concept of re-sensitising the bacteria in order to make use of already available antibiotics – in other words, removing their resistance and making them vulnerable again to first-line antibiotics. Nevertheless, the bacterial pathways are always complicated and such systems are always heavily regulated by multiple pathways. These regulated pathways must be studied in depth in order to avoid selective pressure favoring anti-CRISPR systems activation, hence prevalence of resistance in a more aggressive manner.”

 

Experts developing way to harness Nobel Prize winning CRISPR technology to deal with antimicrobial resistance (AMR)

EUROPEAN SOCIETY OF CLINICAL MICROBIOLOGY AND INFECTIOUS DISEASES

Antimicrobial resistance (AMR) is continuing to increase globally, with rates of AMR in most pathogens increasing and threatening a future in which every day medical procedures may no longer be possible and infections thought long dealt with could kill regularly again. As such, new tools to battle AMR are vitally needed.

In a new research review at this year’s ESCMID Global Congress (formerly ECCMID – Barcelona 27-30 April) shows how the latest CRISPR-Cas gene editing technology can be used to help modify and attack AMR bacteria. The presentation is by Dr Rodrigo Ibarra-Chávez, Department of Biology, University of Copenhagen, Denmark.

CRISPR-Cas gene editing technology is a groundbreaking method in molecular biology that allows for precise alterations to the genomes of living organisms. This revolutionary technique, which brought its inventors, Jennifer Doudna and Emmanuelle Charpentier, the Nobel Prize in Chemistry in 2020, enables scientists to accurately target and modify specific segments of an organism's DNA (genetic code). Functioning like molecular ‘scissors’ with the guidance of guide RNA (gRNA), CRISPR-Cas can cut the DNA at designated spots. This action facilitates either the deletion of unwanted genes or the introduction of new genetic material into an organism's cells, paving the way for advanced therapies.

Dr Ibarra-Chávez says: “Fighting fire with fire, we are using CRISPR-Cas systems (a bacterial immunity system) as an innovative strategy to induce bacterial cell-death or interfere with antibiotic resistance expression – both hold promise as novel sequence-specific targeted ‘antimicrobials’.”

One line of their work involves creating guided systems against antimicrobial resistance genes could treat infections and prevent dissemination of resistance genes.

Mobile genetic elements (MGEs) are parts of the bacterial genome that can move about to other host cells or also transfer to another species. These elements drive bacterial evolution via horizontal gene transfer.  Dr Ibarra-Chávez explains how repurposing mobile genetic elements (MGEs) and choosing the delivery mechanism involved in the antimicrobial strategy is important for reaching the target bacterium.

A phage is a virus that infects bacteria, and it is also considered MGE, as some can remain dormant in the host cell and transfer vertically. The MGEs his team is using are phage satellites, which are parasites of phages. He says: “These ‘phage satellites’ hijack parts of the viral particles of phages to ensure their transfer to host cells. In contrast to phages, satellites can infect bacteria without destroying them, offering a step-change over existing methods involving phages and thus developing an arsenal of viral particles that are safe to use for applications such as detection and modification via gene delivery. Phage particles are very stable and easy to transport and apply in medical settings. It is our task to develop safe guidelines for their application and understand the resistance mechanisms that bacteria can develop.”

Bacteria can evolve mechanisms to evade the action of the CRISPR-Cas system and delivery vectors can be vulnerable to anti-MGE defences. Thus Dr Ibarra-Chávez’s team and others are developing the use of anti-CRISPRs and defence inhibitors in the delivery payloads to counter these defences, to enable the CRISPR to arrive and attack the AMR genes in the cell.

Dr Ibarra-Chávez will also discuss how combination strategies employing CRISPR-Cas systems could promote antibiotic susceptibility in a target bacterial population. Phages have a particular selective pressure on AMR cells, which can improve the effect of some antibiotics. Similarly, using CRISPR-Cas in combination with phages and/or antibiotics, it is possible to suppress the mechanisms of resistance that infectious bacteria may develop by targeting such virulence/resistance genes, making these therapies safer.

He explains: “Bacteria are particularly good at adapting and becoming resistance. I believe we need to be cautious and try using combinatorial strategies to avoid the development of resistance, while monitoring and creating guidelines of new technologies.”

Dr Ibarra-Chávez has primarily focused on tackling resistance in Staphylococcus aureus and Escherichia coli. Now, in collaboration with Prof. Martha Clokie and Prof. Thomas Sicheritz-Pontén, his team will treat group A Streptococci necrotising soft tissue infection (flesh eating bacteria) using the combination approaches described above.

 

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ARTICLE PUBLICATION DATE

26-Apr-2024

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