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New software detects infections within minutes
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Presenting their findings in a study published in Genome Biology, researchers at the University of Utah, ARUP Laboratories and IDbyDNA have developed a software technology called Taxonomer that uses metagenomics data on cellphones and computers to diagnose viral, bacterial and fungal infections within minutes.
“As a clinician, this gives you a better idea when we identify a pathogen whether it is really the cause of the disease,” study researcher Carrie L. Byington, MD, professor of pediatrics at the University of Utah and co-director of the Center for Clinical and Translational Science, said in a press release. “This tool will also allow us to determine if the patient is responding to a bacterial or viral infection when we do not find a pathogen or when we find multiple potential causes.”
Carrie L. Byington
High-throughput sequencing has allowed for unbiased profiling of microscopic organisms and detection of all types of pathogens, the researchers wrote. However, due to its inaccuracy and the length of time required to produce results, the technology has yet to be widely adopted.
To create an efficient and accurate diagnostic, the researchers developed Taxonomer, a publicly availably web tool that uses metagenomics data to detect viral, bacterial and fungal infections within minutes. Taxonomer classifies pathogens based on nucleotides, proteins and mRNA. In addition, Taxonomer can profile a patient’s gene expression. After a patient’s pathogen sample is sequenced, the data are uploaded to the Internet and, in less than 1 minute, an inventory of all pathogens in the sample is displayed.
In a case study, the researchers used Taxonomer to detect pathogens using real-world data from ARUP Laboratories and the CDC. For patients showing Ebola symptoms in the most recent outbreak, Taxonomer detected that some of these patients instead had severe bacterial infection.
Mark Yandell
“In the realm of infectious diseases, this type of technology could be as significant as sequencing the human genome,” study researcher Mark Yandell, PhD, professor of human genetics at the University of Utah, co-director of the USTAR Center for Genetic Discovery and co-founder of IDbyDNA, told Infectious Disease News. “Very few people have inherited genetic disease. But at some point, everyone gets sick from infections.”
Figure 1. Schlaberg co-developed Taxonomer, which can simultaneously detect pathogens quickly and accurately.
Source: ARUP Laboratories
According to Robert Schlaberg, MD, MPH, study investigator and assistant professor of pathology at the University of Utah and medical director at ARUP Institute for Clinical and Experimental Pathology, preliminary analyses show that Taxonomer is between 10 and 100 times faster than similar tools. The Bill and Melinda Gates Foundation awarded a $100,000 grant to Schlaberg to use Taxonomer in resource-limited settings.
“Seeing how a host [patient] reacts is extremely valuable,” Byington said in the release. “I believe this is a paradigm shift in how we diagnose people. It is why I wanted to be involved.” – by Will Offit
Disclosures: Yandell, Schlaberg, Flygare and others report having a patent application pending for Taxonomer. Yandell and Schlaberg report owning equity in and consulting for IDbyDNA.
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