Metagenomics Tool Could Change How Infectious Diseases are Diagnosed

Infectious disease still remains a significant problem in medicine. For instance, the vast majority of upper respiratory infections - which can led to difficulty breathing, fever and hospitalizations - are undiagnosed, meaning many patients may not receive appropriate treatment. On a global scale, infectious disease is one of the leading causes of death often because the cause of illness either is not diagnosed, or is not diagnosed quickly enough.

But it’s difficult for cryptic infectious pathogens to hide when their genetic material is laid bare. Taxonomer represents a new era of infectious disease diagnosis, driven by sophisticated genomic analysis and computational technologies. All genetic material in patient samples are sequenced, then the data are uploaded via the internet to Taxonomer. In less than a minute, the tool displays an unbiased inventory of all pathogens in the sample - including viral, bacterial, fungal - with species names fanned out in an interactive display.

“Taxonomer provides a critical step forward. It is extremely fast, accurate, and easy enough to use for implementation in diagnostic laboratories,” says Robert Schlaberg, M.D., Dr Med, MPH, a medical director at ARUP Laboratories who co-developed Taxonomer with Mark Yandell, Ph.D in collaboration with Gabor Marth, D.Sc., who developed the tool’s web interface. Yandell and Marth are professors of human genetics and co-directors of the USTAR Center for Genetic Discovery.

TaxonomerIn contrast to current diagnostic methods, the major advantage of Taxonomer is that clinicians won’t have to guess what is infecting the patient before testing (ie. culturing for strep, or a PCR test for meningitis), eliminating the quandary of what to do when a test returns negative. At the same time, Taxonomer analyzes the patient’s own genetic material - in this case mRNA that shows which genes are turned on - documenting their immune response. Is the body mounting a fight against virus or bacteria? In combination, the readouts make it easier to spot the most likely cause of illness.

“The computational power that allows Taxonomer to run is enormous, but what the user sees is an almost immediate response and immediate results,” says Marth. “Taxonomer gives the user an intuitive view of the take home message of the data.”

In real-world case studies, Taxonomer revealed that a patient suspected of being infected with ebola virus had a range of infections - including a massive bacterial infection - the treatment for which is vastly different. In another patient, Taxonomer revealed a never-before catalogued virus, showing the tool’s potential for discovering new causes of illness. Taxonomer is under development for deployment in the clinic.

“At some point everyone gets sick from infections. The potential of Taxonomer is huge,” says Yandell. “In the realm of infectious diseases, this type of technology could be as significant as sequencing the human genome.”

Learn more:

A genomics-based, catch-all test for infectious disease