Could Viruses Help in the Fight Against Antibiotic Resistance?

A study published in Nature Chemical Biology suggests that a new bacteriophage screening approach could assist scientists attempting to overcome antibiotic resistance.

The issue of resistance

The diminishing effectiveness of current antimicrobials is a result of antibiotic resistance, a serious problem causing longer hospital stays and increased mortality. Where our medicines fail however, bacteriophages may hold the key to success.

Bacteriophages are viruses that are harmless to non-bacterial cells, and have evolved to infect and kill bacteria, making them ideal medicines.

The problem presents itself when trying to determine how phages use viral proteins to kill bacteria. These proteins must be studied on an individual scale, an incredibly difficult task, as there appears to be at least one type of phage for every known strain of bacteria, with each phage evolving alongside a specific bacterial strain so that they can counter resistance traits.

Attempting to isolate a single phage from the environment and determine which microbe it targets and the mechanism used has proven to be near-impossible. Scientists are often unable to assess phage-bacteria battles based on genomic sequence alone or study them in action because many bacteria can’t be cultured in a lab.

Screening for success

Researchers in the current study set out to test an approach that could optimize this process, “We developed a high-throughput genetic screening approach that can identify the part of the bacterial cell targeted by a potent type of phage weapon called ‘single-gene lysis proteins,’” said Vivek Mutalik, a staff scientist in Berkeley Lab’s Biosciences Area. “With rising antibiotic resistance, we urgently need antibiotic alternatives. Some of the smallest phages that we know of code for single-gene lysis proteins (Sgls), also known as ‘protein antibiotics,’ to inhibit key components of bacterial cell wall production that, when disrupted, consistently kill the cell."

Mutalik and colleagues previously developed the technology required for such work, called Dual-Barcoded Shotgun Expression Library Sequencing (Dub-seq), which allows the investigation into how unknown genes work, even in complex environmental samples containing many different types of DNA – without need for cultures.

Using Dub-seq, the authors were able to identify the part of the bacterial cell wall or supporting materials targeted by each of six Sgls, “Overall, the Dub-seq genetic screen successfully uncovered high-confidence multicopy suppressors that play a role in PG [peptidoglycan] biosynthesis or are known to alleviate OM [outer membrane] stress response and provide insights into Sgl target/repair pathways at a genome-wide scale that may be challenging to obtain via traditional approaches,” the authors write.

This work confirmed that Sgl proteins have potential to be antibiotics, as they attack pathways for cell wall building used by almost all bacteria. Using fundamental and ubiquitous targets means that these proteins can kill bacteria other than the target strain.

"Phages are extraordinary innovators when it comes to destroying bacteria. We're really excited to uncover novel bacterial pathogen-targeting mechanisms that could be leveraged into therapies,” said Benjamin Adler, a postdoctoral fellow in Jennifer Doudna’s lab at UC Berkeley and first author of the study.

Now that the Dub-seq approach has been evaluated, the researchers can apply it to the thousands of single-gene lysis producing phages awaiting characterization in environmental samples that the team has collected from the ocean, soils and even the human gut.

Reference: Adler BA, Chamakura K, Carion H, et al. Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins. Nat Chem Biol. 2023:1-8. doi: 10.1038/s41589-023-01269-7.

This article is a rework of a press release issued by Lawrence Berkeley National Laboratory. Material has been edited for length and content.