Creek survey uncovers bacteriophages that could combat superbugs

A survey of a waterway on Wurundjeri land has led to the discovery of new viruses that kill the superbug Klebsiella.

With estimates that superbugs will kill at least 10 million people a year across the world by 2050, the finding, led by a partnership of Traditional Owners and Monash University researchers and published in the journal, mBio, suggests that small waterways may be an untapped source of viruses with genetic variations capable of addressing the rise in drug-resistant superbugs.

Working with the Wurundjeri Woi Wurrung Cultural Heritage Aboriginal Corporation, the Monash University team led by Professor Trevor Lithgow, from the Monash Biomedicine Discovery Institute, found two versions of a bacteriophage (a virus that kills bacteria). Elders named the bacteriophage in Woi Wurrung language Merri-merri-uth nyilam marra-natj (MMNM), which translates as “Dangerous Merri lurker” in English.

Importantly, the researchers found that a single genetic difference between the two forms of MMNM was sufficient to change how well they could kill bacteria. According to Professor Lithgow, this sequence variation was then subject to further, forced evolution in the lab. “All of the various new phages that we evolved can kill Klebsiella, but some of the variant phages kill better than others,” he said.

“The finding gives hope that there are as yet undiscovered natural phage populations that have untapped genetic variations that can be leveraged into new ways to kill antibiotic resistance bacterium.”

After discussions informed with Traditional Knowledge and ecological considerations, the partnership decided on working with water from the Merri Creek in Melbourne (where the Wurundjeri Woi wurrung are its Traditional Owners). The new Klebsiella-killing bacteriophages were found in just a small area of Merri Creek, according to Professor Lithgow, “suggesting to us that there may be even more that we can find in that Creek alone,” he said.

Earlier this year, the European Centre for Disease Control and Prevention of the European Union reported a significant increase in the number of cases of hypervirulent Klebsiella pneumoniae and that these cases were resistant to even the class of antibiotics called carbapenems, which are often a “last resort” treatment for bacterial infections.

The partnership of Traditional Owners and Monash University researchers have developed a system where they can observe, through DNA sequence analysis and lab-based killing assays, how multiple small mutations in bacteriophages can be selected in the laboratory to potentially develop means to kill the constantly evolving and changing drug-resistant bacteria like Klebsiella.