This week, we’re going over a recently-published phage therapy case report.

What was the patient dealing with?

A patient in Israel (a 42 year old male who’d been in a motor vehicle accident) sustained open fractures in his legs, and contracted an antibiotic-resistant, poly-microbial bone infection.

His leg was colonized with both extensively antibiotic-resistant Acinetobacter baumannii and multi-drug resistant Klebsiella pneumoniae.

Normally, this would necessitate amputation of the leg. However, the patient refused.

What was done?

After seven months of in-hospital treatment with surgeries and antibiotics, personalized phage therapy was combined with antibiotics to treat the wounds.

What’s personalized phage therapy again?

Personalized phage therapy involves selecting one or more phages for treatment based on their demonstrated ability to kill the patient’s exact strain of bacteria.

What was the outcome?

The patient’s infection was cleared, his wounds healed, and his leg did not have to be amputated.

The nitty gritty: How was this done?

Identifying the bacteria

The medical team at the Hadassah Hebrew University Medical Center cultured the bacteria from the patient’s leg wound, identified the bacteria (A. baumannii and K. pneumoniae), and tested them for antibiotic susceptibility.

Choosing and preparing the phages

• Adaptive Phage Therapeutics (APT) tested the patient’s bacteria for phage susceptibility against the US Navy’s large library of phages.
• One anti-Acinetobacter phage and one anti-Klebsiella phage was selected based on their ability to effectively kill the patient’s isolates.
• The phages were propagated and clinical-grade phages were produced for the patient.

Tracking phage resistance

Ronen Hazan’s lab at the Hebrew University of Jerusalem tracked emergence of phage-resistant mutants over time by culturing phage and bacteria together.

How were the phages administered?

• The two phages were given intravenously (IV) in combination with the antibiotics meropenem and colistin.
• Dose: 1 mL of around 10^7 PFU/mL each, three times a day for 5 days.
• Endotoxin levels: between 5 and 35 EU/mL

How did the patient respond to phage therapy?

• For the first day, phage therapy was done in the intensive care unit in case of adverse reactions, but none were observed.
• After the first course of treatment, A. baumannii was still isolated from the leg wound, so a second course was administered.
• After a few days, the wound began to heal and the patient’s pain diminished. The patient was discharged.

What was observed long-term?

• Over the next eight months, no more positive A. baumannii and K. pneumoniae cultures were obtained from the patient. The wounds closed, and the pain disappeared.
• Methicillin-sensitive Staphylococcus aureus was isolated in the leg three months after phage therapy, but it was successfully cleared with antibiotics.

Where did the phages end up?

No active phages were found in the patient’s blood, urine, stool or saliva.

Was phage resistance an issue?

Phage resistant A. baumannii cells grew in the lab. However, within a few weeks, Dr. Hazan’s team isolated a new phage (from sewage) that could kill the phage-resistant mutant. Comparison of the genomes of the phage-resistant mutant and the parent strain showed differences in 37 genes!

Fortunately, although phage resistance was seen in the lab, it was never observed in the patient, so the new phage didn’t need to be used.

Interesting note: combinations matter

The patient’s Klebsiella isolate wasn’t resistant to meropenem unless it was co-cultured alongside the (meropenem-resistant) Acinetobacter isolate.

When grown together, the two bacteria could only be inhibited by the antibiotics if the phages were also present.

What was the process of getting approval to try phage therapy?

The teams involved got their experimental treatment protocol and informed consent agreement approved by both the hospital’s ethics committee and the Israeli Ministry of Health. The patient then gave his informed consent, and the treatment was administered.

Conclusions

This was clearly a success story for the patient. As well, this case brings us several useful insights about personalized phage therapy:

• It can be effective in clearing a poly-microbial limb-threatening bone infection.
• It can be done to combat two bacterial pathogens at once.
• It can be adaptable in the face of phage resistance.

Of note, this was the first case of phage therapy in Israel.

Further reading

• Learn how Adaptive Phage Therapeutics’ high-throughput phage susceptibility testing system works: APT website / Paper describing the technology.
• Learn more about the phage therapy work Ronen Hazan’s lab is doing at the Hebrew University of Jerusalem. Also, check out his lab’s major focus on student mentorship—we love how he celebrates the work of his students!

Main source for this issue:

Nir-Paz, R., Gelman, D., Khouri, A., Sisson, B. M., Fackler, J., Alkalay-Oren, S., … Hazan, R. (2019). Successful treatment of antibiotic resistant poly-microbial bone infection with bacteriophages and antibiotics combination. Clinical Infectious Diseases. doi:10.1093/cid/ciz222