In the battle to combat antimicrobial resistance, better and more rapid diagnostic tests are urgently needed to detect potential pathogens so that the most appropriate treatment can be prescribed.
Justin O’Grady from the Quadram Institute and the University of East Anglia on the Norwich Research Park leads a research group harnessing modern genomic techniques to deliver these tests in clinical and food sectors.
Rapid diagnostics are needed as current techniques are based on culturing microbes, which take days to produce results. Responding to this need, many research groups across the globe are engaged in finding new faster ways of identifying pathogens and resistance.
In a opinion piece on a new paper published in the journal Nature Microbiology, Justin has reviewed a new test developed by Timothy Blauwkamp and colleagues at Karius, Inc. in California. The Karius test identifies up to 1,250 clinically-relevant bacteria from fragments of partially degraded bacterial DNA that can be found circulating in human plasma. In the new paper the researchers validate their test for the clinical diagnosis of infection.
The non-invasive test encompasses purification and metagenomic sequencing of the cfDNA from human plasma and then computational analysis of the data. It provides an extremely wide coverage of pathogens and is highly sensitive. More refinements are needed to improve specificity, turnaround time and to reduce the cost of the Karius test, but it’s clear that the approach of using metagenomics has great potential in clinical diagnostics.
As Justin points out, the era of clinical metagenomic diagnostics is still in its infancy and the perfect test may not yet be developed, but they do represent an advance over current testing protocols and, once validated, their adoption in clinical settings should be encouraged.