Scientists explore nature’s bacterial killers

For over a century, scientists have been fascinated by bacteriophages, the tiny viruses that naturally hunt and kill bacteria. University of Otago researchers are turning to these microscopic assassins as a potentially powerful tool to fight bacterial diseases.

Under a microscope, they appear like little lunar landers, or perhaps the spindly Martian tripods from HG Wells’ The War of the Worlds.

But bacteriophages, or phages as they’re better known, are very real – and new discoveries are signalling their powerful potential against harmful bacteria.

Just as humans can be infected by viruses, so too can bacteria, and phages have been waging war on Earth’s microbes for billions of years. These tiny, oddly shaped viruses not only infect and kill bacteria, but use them to produce more phages.

With antimicrobial resistance now presenting a mounting crisis, there’s increasing focus on phages as a precise and sustainable option to combat bacteria that cause diseases, spoil food or devastate crops.

But it’s hardly new thinking, says Professor Peter Fineran, a molecular microbiologist in the University of Otago’s Faculty of Biomedical Sciences.

Their potential usefulness in beating back bacteria was recognised soon after their discovery more than a century ago, and early enthusiasm saw them trialled as treatments.

As cheap, broad-spectrum and reliable antibiotics took over medicine, phage research retreated to the sidelines. Still, they never completely disappeared from science.

Later, in the 1950s, they became central to molecular biology, helping researchers discover that DNA was the genetic material of life.

Peter says that now scientists’ attention has swung back to phages, there’s fresh appreciation of just how complex their age-old relationship with bacteria is.

That relationship might be described as an arms race: just as phages have evolved their biology to better attack bacterium, microbes have developed an array of immune systems to recognise and destroy their invaders.

Peter says the first bacterial immune systems scientists identified were what are called "restriction-modification" systems: enzymes that spot and chop up foreign DNA.

By the 1970s and 80s, the enzymes themselves were isolated and became the basis for DNA cloning. Then came CRISPR-Cas, the microbial immune system that gave rise to revolutionary new gene-editing tools.

First spotted within bacterial genomes in the 1980s, its function wasn’t understood until decades later: bacteria were storing memory of past phage invaders in their DNA, allowing them to cut up returning attackers.

“Everyone knows CRISPR-Cas9,” Peter says.

“But there are actually 30 to 40 different types of CRISPR-Cas systems in bacteria, and Cas9 is not even that common in nature.”

Beyond CRISPR, researchers have found more than 250 other bacterial defence systems. Peter’s group and other researchers have discovered that phages, in turn, have evolved ingenious countermeasures, from proteins that block CRISPR, to cloaking their DNA in sugars.

“We’re essentially discovering new things about phages and the immune systems of bacteria every day,” Peter says.

“So, even though we know a lot more now than we did 100 years ago, there are still just so many things, sitting right in front of us, that we’ve still got no idea about.”

From cherry trees to new treatments

Peter’s team is taking a fundamental approach to unlocking these mysteries and hopes to apply this knowledge to real-world problems.

On one track, they’re using what they learn about phage-bacteria interactions to develop phage therapy: the deliberate use of phages to control harmful bacteria.

With funding from the Ministry of Business, Innovation and Employment (MBIE), they’re tackling diseases that plague New Zealand’s cherry orchards.

Pseudomonas bacteria can cause losses of 20 to 50 per cent of young orchards. Growers rely on copper sprays, a blunt instrument that damages other microbes and faces rising resistance.

Peter’s group is developing phage cocktails as a more selective solution. The idea, he says, is to combine multiple phages, each with a different "key’" to unlock a bacterium’s defences. If one phage is blocked, another still gets through.

“In that way, you end up with a very robust treatment which avoids the emergence of resistance.”

Because phages are highly specific, they should leave beneficial bacteria untouched: a sharp contrast to the carpet-bombing approach of antibiotics. But the same principles apply well beyond orchards.

For example, in their recent work, Peter’s lab uncovered "jumbo phages" that build protein shells inside bacteria, creating a safe compartment where phages can replicate, untouchable by enzymes.

They’ve also studied phages that decorate their DNA with sugars, shielding themselves from CRISPR cutting. Some add one sugar, others two or three, each conferring protection against different defences.

“These types of phages would be good to have in treatments,” Peter says, pointing out that they’re naturally resistant to bacterial countermeasures.

“Pretty much all the approaches are applicable to human and animal pathogens,” he says.

On the other track, the group is fundamentally characterising unique CRISPR-Cas systems and recently how these can be exploited for new biotechnological tools.

Peter’s fellow researcher, Dr Rob Fagerlund, says that while Cas9 and its "genetic scissors" might be the best known, there are many other CRISPR variants with unique properties.

He describes one that, when activated, unleashes massive signal amplification, making it ideal for diagnostics.

“We’ve already used it for detecting small levels of RNA: it’s very specific, very sensitive, and it’s rapid.”

The potential applications range from even faster and more accurate Covid-19-style rapid tests that don’t require PCR tests, to diagnostics for invasive pests and non-transmissible human diseases.

And then there are anti-CRISPRs: molecules made by phages to sabotage bacterial CRISPR systems. Peter’s group was the first to show that some are RNAs rather than proteins, tricking CRISPR by feeding it the wrong guide.

“It just sends it off to do nothing, and then the phage can quite happily replicate.”

All this underscores how sophisticated – and surprising – phage research can be. Peter says it’s equally exciting that new technological revolutions have arrived to speed up discovery.

While artificial intelligence is now rapidly predicting protein structures to reveal new defence and anti-defence molecules, genome sequencing is exposing the vast diversity of phage and bacterial systems still uncharted.

For human health, for instance, CRISPR could go beyond editing genes to killing rogue cells outright.

Rob describes their work with experimental systems where CRISPR is programmed to detect cancer-specific mutations and trigger cell death, like a form of genetic chemotherapy.

With further research, such approaches could add precision weapons to the medical arsenal.

The use of phages to control bacterial pathogens, meanwhile, is moving from experimental to mainstream.

Western hospitals are trialling it for stubborn infections, inspired by dramatic cases where nothing else worked, and in agriculture, phage products are available. Still, Peter cautions, phages aren’t a silver bullet.

They’re likely to complement antibiotics and other approaches, rather than replace them.

“To be able to choose the right phages to get the desired outcomes, we must understand the bacterial immune systems and learn about all the ways that phages overcome these – that is why this is the focus of our core fundamental research,” Peter says.

“The added benefit is that the molecular systems we characterise – including CRISPR-Cas – may have biotechnological potential as well.”