Texas A&M biologists sequence drug-resistant bacteria in pioneering U.S. phage therapy case

The full genome of nine different bacteriophages used in one of the first modern applications of phage therapy t in the United States was published last month. Also published were the genomes of three strains of the multidrug-resistant bacteria, Acinetobacter baumannii, that the phages targeted.

The newly sequenced phages had been isolated five years earlier during an emergency mobilization of specialists and laboratories from around the world to treat a 68-year-old man suffering from a multidrug-resistant infection.

Bacteriophages are viruses that kill bacteria. They are present everywhere in the environment and are often harvested from sewage. Unlike antibiotics, phages are very specific to the bacteria they target and must be specially prepared for each use.

First understood and named in 1916 by French-Canadian biologist Félix d’Hérelle at the Pasteur Institute in Paris, they were the first modern antibacterial agent. 

By the early 1920s, d’Hérelle had demonstrated the effectiveness of phages against human infections of dysentery, cholera, and plague.

The development of penicillin and other antibiotic therapies during and just after World War II led to a waning of interest in bacteriophages in the West, with some exception in France, while they continued in widespread use in the Soviet bloc until its unraveling in 1989. 

The West’s ignoring of bacteriophage therapies began to change in the early 2000s when outbreaks of Methicillin-resistant Staphylococcus aureus (MRSA) became more common, soon followed by the appearance of other superbugs resistant to drug treatment. 

How phages came to be used in USA

This modern use of bacteriophages to treat the multidrug-resistant A. baumanii bacteria came about through an emergency collaboration of physicians and U.S. phage researchers in 2016. 

In December 2015, Thomas Patterson, a professor of psychiatry at the University of California San Diego, was losing a battle with an Acinetobacter baumanii infection that he probably had contracted on a vacation in Egypt. 

When she learned that there was no hope with any conventional treatment, his wife, Steffanie Strathdee, herself an infectious disease epidemiologist at UC San Diego, began a search for novel cures. She soon came upon bacteriophages. 

Strathdee’s Internet searches had led her to the Center for Phage Technology at Texas A&M University. Its director, Ryland Young, responded to her call for help and started her on the process of obtaining emergency approval. In order to find the appropriate phages, he would need a sample of the specific bacterial strain her husband was infected with. Even to ship it from California to Texas would require emergency approval. 

Strathdee found help from a family friend, Dr. Robert Schooley, an infectious disease specialist at UCSD. She also was able to organize a rapid collaboration between legal and regulatory representatives at her university and their counterparts at Texas A&M, succeeding in getting the emergency approvals in days rather than months.

Meanwhile Young at the Center for Phage Technology mobilized lab researchers in a race to find the right phages. He also enlisted support from the Biological Defense Research Directorate in Frederick, Maryland, which had a good collection of Acinetobacter baumanii strains and experience working with phages. Infections with the drug-resistant bacteria had become so common among soldiers in Iraq that it had acquired the nickname "Iraqi-bacter."

Soon colleagues of Young's at San Diego State University joined in the action with their expertise in fast, safe methods for cleaning phages of contaminants. 

By March 15, 2016, a collection of phages appropriate for treatment was in the hands of Schooley. By then his patient was in a deep coma, his heart, lungs and kidneys all failing. He first introduced the phages by an existing catheter into Patterson’s abdominal cavity. Two days later the phages were introduced directly into his bloodstream, a risky process because of the danger of sepsis from the killed bacteria. A few days later, Patterson woke up from his coma and began the long haul toward full recovery. 

The genome study

Phages work by attaching to bacterium and then injecting their DNA, which hijacks the bacterial cell. This shuts down the ability of the bacterium to reproduce and instead uses the cell metabolism to replicate many copies of the phage. As the newly formed phages are released from the cell, the bacterium is destroyed in a process called lysis. 

Due to the emergency nature of the treatment, there was not time to thoroughly characterize the phages used in treating Patterson.

The new study, posted online by bioRxiv on Dec. 16, 2021, reveals previously unknown information about the phages used and the bacteria causing the infection.

As a result of the new comparative genomic study, it is now known that eight of the phages used in the initial treatment were a group of closely related T4-like myophages. Myophages are a type of lytic phage that uses a contraction wave in its tail to break through the cell wall of the bacterial host. 

The ninth phage was an unrelated Fri1-like podophage. Fri1 is a recently designated variety of phage infecting Acinetobacter baumanii bacteria. 

The study also examined 19 isolates of A. baumanii collected before and during the phage treatment of Patterson. These showed that resistance to the T4-like myophages appeared as early as two days following the start of treatment,” according to the paper. The treating physician, Schooley, was aware of some phage resistance by the eighth day of treatment. During the course of treatment phages and their bacterial hosts replicate and evolve, possibly losing some potency, yet may still remain effective. 

Three of the bacterial strains were sequenced to closure “and all contained a 3.9 Mb chromosome of sequence type 570 with a KL116 capsule locus,” the study reports. 

In one strain phage-insensitive mutants were generated in vitro. The paper reports that “the majority of identified mutations were located in the bacterial capsule locus.” 

This is significant, the authors conclude, as “the presence of the same mutation in both the in vitro mutants and in phage-insensitive isolates . . . which evolved in vivo during phage treatment, indicate that in vitro investigations can produce results that are relevant and predictive for the in vivo environment."

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A. Hernandez et al., Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy, bioRxiv preprint (2021). DOI: https://doi.org/10.1101/2021.12.14.472731  

Elena Watts, "Center for Phage Technology spearheads the battle against ‘superbugs,’" Texas A&M Today (2019). 

Tom Parfitt, "Georgia: an unlikely stronghold for bacteriophage therapy," The Lancet (June 25, 2005). 

Lawrence Osborne, "A Stalinist Antibiotic Alternative," New York Times Magazine (Feb. 6, 2000).