Harnessing Nature's Warriors: The journey of bacteriophages from nature to patient

Phage Australia, led from Westmead Institute for Medical Research (WIMR) is utilising bacteriophages to fight antimicrobial resistant (AMR) infections; including Pseudomonas infections in patients living with Cystic Fibrosis (CF). 

What are bacteriophages? 

Bacteriophages, also called phages, are tiny viruses that naturally prey on bacteria. It is the most abundant entity on earth, and they have evolved alongside bacteria for billions of years, working as natural hunters to specific bacteria. Phages kill bacteria by attaching onto the surface of bacterial cells, injecting their genetic material inside, then multiply within the bacterial host, causing it to burst open and release more phages to attack other bacteria nearby (see Figure 1). 

Figure 1. Phage attaching to a bacterial cell, amplifies itself and bursting the bacterium to release the phages. 

Searching the natural environment for the solution 

Phages are believed to be the most abundant and diverse organisms on Earth, found wherever bacteria thrive! For instance, if we need a phage to combat bacteria in water, we can gather water samples to find the right phage.  

Researchers at WIMR have been isolating phages from nature for years, suiting up in protective gear (as seen in Figure 2) and collecting samples from unconventional places like hospital sewage systems and local parks.

Figure 2. Researchers at WIMR collecting samples for phage isolation (Left to right: Dr. Aleksandra Petrovic Fabijan, Dr. Nouri Ben Zakour, Dr. Ali Khalid and Prof. Ruby Lin). 

Once collected, these samples are taken to the lab where they undergo centrifugation to remove debris, followed by filtration to eliminate bacteria, leaving behind the phages (as shown in Figure 3). These phages are then ready for use in the lab. Over the years, our team has collected hundreds of phages which are stored in a large library, allowing us the flexibility to select the most suitable phage for any given situation.

Figure 3. Processing environmental samples in the laboratory for phage isolation 

Precision Diagnostics: Tailoring phage therapy to the bacterial strain 

When someone has a bacterial infection like a lung infection caused by Pseudomonas, doctors typically seek antibiotics, which can inadvertently harm beneficial bacteria in our bodies. A key advantage of phages is their specificity, targeting only harmful bacteria. This is very useful in AMR infections where antibiotics fail to work, and the patient is getting sicker. 

At WIMR, to find the specific phage(s) for a patient's infection, we receive a bacterial sample, conduct lab tests by growing the bacteria on agar plates, and then spot our phages on top of the bacterial isolates. After incubating the plates under conditions to replicate the human body temperature (37℃) for 16 hours, we examine the plates for clearings, indicating where phages successfully killed the bacteria.

Figure 4. The process of matching the right phage to the bacterial isolate causing the infection. 

Following the identification of the most effective phage or combination of phages, known as a cocktail, they are selected for production. 

From the lab to clinic: Phage purification and Quality Control 

Phage production involves growing large volumes of the phages and then using a series of filtering processes with specific lab machines to purify the product and then we can certify that the phage is safe to be used as medicine (Figure 5). 

To produce phages, we grow large quantities of them in flasks containing broth, bacteria (the target for the phages), and the desired phages. After 16 hours, the flask yields over a billion phages along with bacterial debris and broth. To purify the product, Dr Rabeya Rahmatullah uses specialised machines to remove toxins, proteins and genetic materials, ensuring the phages are purified and safe for intravenous use in patients. 

This purified product undergoes rigorous end point quality control checks for safety (including genomic safety analysed by Dr. Nouri Ben Zakour) before being dosed into vials at the appropriate levels for patients. These vials are then sent to hospitals, where clinical teams administer the phages and monitor patients throughout the treatment period.  

We use phage under Therapeutic Goods Administration’s Special Access Scheme (STAMP protocol). Specifically, we are only able to assess referrals for phage therapy from Australian-registered infectious disease specialists. If you believe that you may be a suitable candidate for phage therapy, please see your family doctor in the first instance to discuss this and request a referral to an adult infectious disease specialist. After reviewing the case, the infectious disease specialist will be able to contact one of the clinicians in our group to discuss the case.  

Phage therapy is an experimental method that is only available when all other approaches are already optimised and only under the auspices of a special access scheme defined by the Therapeutic Goods Administration or within a clinical trial. If a TGA-approved indication exists, we follow a protocol that has been defined by consensus among expert physicians and may evolve over time as data are reviewed. If you are eligible to receive therapy, we require informed consent and a minimum data set (including blood tests) that is necessary for the monitoring of your treatment. Please refer to our website for more information about phage therapy (www.phageaustralia.org) and then seek a referral to an infectious disease specialist from your GP.

Figure 5. The overview of phage production and quality control. Featuring Dr. Rabeya Rahmatullah who runs the purification machines here at WIMR. 

Summary 

In conclusion, the groundbreaking work of Phage Australia highlights the potential of harnessing nature's own solutions to combat antimicrobial resistance. By deploying bacteriophages in targeted therapy, they offer hope for more effective treatments against AMR infections.

The Phage team here at WIMR. Left to right: Laela Bouaou, Dr. Alicia Fajardo Lubian, Dr. Aleksandra Petrovic Fabijan, Dr. Stephanie Lynch, Prof. Jonathan Iredell, Karen Swensen, Dr. Rabeya Rahmatullah, Dr. Amanda Luo, Eleni Siafakas & Carina Lauter. Missing key members, Prof. Ruby Lin, Dr. Nouri Ben Zakour, Dr. Holly Sinclair