New tool offers insights into virus-cell interactions

Bacteriophages, or phages, viruses that selectively target and infect bacteria, have drawn growing attention for their potential use in a host of biotechnological processes to benefit humankind, from diagnosing contamination in consumer products to treating antibiotic-resistant infections. 

To achieve these advances, however, scientists must first know how phages specifically attach to bacterial cells early in infection — information that until now could be obtained only through a process that is labor-intensive and that yields limited insights.

But in a recent study, Yale scientists describe a new method for quantifying the host-attachment dynamics of several phage species — including some that target key bacterial pathogens — offering a powerful tool for understanding these virus-cell interactions. 

The new method, which utilizes fluorescence microscopy and particle tracking, was described in the journal Proceedings of the National Academy of Sciences.

“We decided to measure the attachment of individual viral particles to cells by directly visualizing them under the microscope,” said Jyot Antani, an associate research scientist at Yale and lead author of the study. “Using automated particle tracking, we calculate the ‘dwell time’ — or the time that a phage spends interacting with bacterial cells — to measure phage attachment at single-virus resolution.

“Basically, we use a microscope to measure the ‘stickiness’ of phages to bacteria.”

Antani is affiliated with the labs of Paul Turner, the Rachel Carson Professor of Ecology and Evolutionary Biology, and Thierry Emonet, the Lewis B. Cullman Professor of Molecular, Cellular and Developmental Biology, both in Yale’s Faculty of Arts and Sciences as well as part of Yale’s Quantitative Biology Institute. Turner and Emonet, along with Timothy Ward, a Yale undergraduate researcher, were also co-authors of the study. 

Phages and the bacteria that they target are considered the two most abundant biological groups on the planet, so their interactions have consequences that range from ecosystem function to community dynamics at the microbiome level. First discovered more than a century ago, phages latch onto specific receptors on the surface of a bacterial cell and inject their genetic material into the cell to start the infection. Some phages, which are known as “lytic” phages, replicate themselves within host cells and destroy the cell by bursting it open, a process that helps control bacterial populations.  

Knowing how phages initiate this interaction early in the infection cycle, when the phage finds and binds to bacterial cell surface, Antani said, can help scientists predict the success of infection, improve the effectiveness of phage therapy, and guide the development of more efficient antibacterial strategies. This key initial step is called “phage attachment.”

When evaluating the relationship between phages and bacteria, scientists typically use what is known as the adsorption assay method, which calculates the rate of attachment over time. Normally, this process involves mixing bacteria and phages together and then counting number of “free” phages as they become depleted over time. 

Unfortunately, Antani said, this method requires large amounts of supplies and materials to grow the host bacteria, ample human labor, and a slow incubation process. And, even then, it yields only a population-average readout.

In the new method, a fluorescent dye is used to label different viruses, and a camera records video of their interactions with bacteria immobilized on a glass coverslip surface. Using automated particle tracking, the researchers were able to obtain X-Y trajectories of individual phages.

“We noted significant variation in these trajectories’ durations [dwell time], highlighting heterogeneity in viral particle attachment,” Antani said. “By calculating the average dwell time and comparing it with traditional adsorption rate constants, we confirmed that our single-virus measurements closely match traditional bulk measurements, thus validating our new method.”

This article was originally published on Yale University News.