Viruses act as decoys, study finds, helping bacteria evade the immune system

These viruses weren’t supposed to affect humans. They were supposed to ride along inside bacteria — unobtrusive hitchhikers taking advantage of another microbe’s machinery. But that wasn’t what Dr. Paul Bollyky and his colleagues saw in their lab dishes three or four years ago. The viruses seemed to be changing the behavior of human immune cells. Instead of gobbling up bacteria as they normally did, white blood cells just sat there.

“They basically don’t eat anything. They don’t move around much either,” said Bollyky, an immunologist and infectious disease specialist at Stanford University. “They would just ignore … the bacteria that were in the dish with them.”

Now, with a paper published Thursday in Science, what began as a chance observation has yielded a startling window into the inner lives of infections — one in which viruses tag-team with bacteria to trick the immune system by providing a decoy. Bollyky describes it as having someone trip the fire alarm so that the rest of the team can pull off a robbery in the chaos that ensues.

Not only has the team chronicled a strange case of collusion between viruses and bacteria, they’ve used that knowledge to make a vaccine that may help combat Pseudomonas aeruginosa, a species of bacteria that the World Health Organization classifies as a “priority pathogen” because of antibiotic resistance.

The findings are “jaw-dropping,” said University of Pittsburgh biologist Graham Hatfull, who was not involved in the study.

That’s because it brings our understanding of bacteriophages to a whole new level. Bacteriophages — or phages, for short — are viruses that colonize bacteria. Some of them do so violently: They enter a microbe, replicate themselves, and then burst out, killing their host. Those phages, which are now being used as an experimental treatment for antibiotic-resistant infections, are not the viruses that Bollyky was studying. Instead, he was interested in phages that form relationships with the bacteria they inhabit, settling comfortably inside the genome as if it were a camper van.

Scientists have known for years that these non-exploding phages can indirectly take a toll on human health. They lend toxin-producing genes to microbes, causing diphtheria and transforming everyday E. coli into some of the nastiest food poisoning agents around. But in Bollyky’s experiments, the viruses were not helping the bacteria to become more intrinsically virulent; instead, they were allowing the bacterial infection to take hold by disabling the human body’s defenses.

The discovery is long overdue. In the 1970s, Dr. Carl Merril, then at the National Institute of Mental Health, proposed that phages could carry genes into mammalian cells. He was met with ridicule. Merril’s claims were followed up by other, similar reports, “which I would put in the category of pretty wacky,” Hatfull said. “And maybe they are wacky, but clearly this paper shows that you can get significant and substantial immune modulation by some types of phages. That needs to be taken seriously.”

When Bollyky’s team punched a hole in a mouse’s skin and seeded the wound with Pseudomonas, they found a big difference between the phage-carrying microbes and their phage-less counterparts: It took significantly fewer bacteria to cause an infection when they were harboring viruses within them. In other words, Pseudomonas needs the help of phages to efficiently infect.

By making the viruses fluorescent, the team could watch them emerging from the bacteria and ending up inside immune cells. The researchers could see that when the viruses were around, these cells took in and destroyed 10 times fewer bacteria. But how were they getting in?

To figure it out, the team blocked off a number of possible cellular entrances. “We closed the window, we closed the garage, we turned off the internet connection,” said Bollyky. What remained, he said, was the everyday process of endocytosis, which cells use to bring in particles.  “It’s a backdoor for bringing in different molecules … it’s the way you bring in groceries, it’s the way that you bring in the mail — normal homeostatic stuff.”

It turned out that once the viruses had snuck inside, they were interrupting the immune signals that move from cell to cell, warning of a bacterial infection. Instead of springing into anti-bacterial action, imprisoning microbes, the immune system battened down the hatches to try to prevent more viral infiltration, explained Bollyky.

To Robert Hancock, Killam professor of microbiology and immunology at the University of British Columbia, it’s astounding to learn that Pseudomonas aeruginosa, which already targets those with weakened immune systems, has an additional weapon to break down our bodies’ defenses. “It has an extremely high rate of lethal infection,” he said. “This realization that the phage is a major player is a huge thing right up front.”

That knowledge may also help prevent such infections from becoming serious in the first place. Making vaccines against gram-negative bugs like Pseudomonas can be tricky because of their slippery outer walls. “They’re covered with slime,” Bollyky said. “Antibodies don’t stick very well.” But with the viruses emerging from all that goop, he said, suddenly there was something more stable for the immune system to grab onto — and his team capitalized on that fact to create a vaccine. By targeting proteins on the surface of the phages, the researchers were able to reduce wound infection in mice. They’re now testing the approach in pigs, Bollyky said, and are partnering with a company called Inimmune.

The Stanford team only described how a very specific kind of phage helps along Pseudomonas aeruginosa by directly changing our immune response. But other such partnerships may well be going on inside of us. Jessica Sacher, who founded the Phage Directory to connect clinicians hoping to use phage therapy with researchers who have them, said the viruses studied in this paper are very different from the bacteria-exploding kind. She doesn’t think it will dampen the excitement around phage therapy. But, as she explained in an email, “It does drive the point home that there may be totally unexpected effects of phages and their components in the human body, and we should expect to find more examples like this.”