A genomic test developed at UC San Francisco to rapidly detect almost any kind of pathogen - virus, bacteria, fungus or parasite - has proved successful after a decade of use.
The test has the potential to vastly improve care for neurological infections that cause diseases like meningitis and encephalitis, as well as speed up the detection of new viral pandemic threats. It uses a powerful genomic sequencing technique, called metagenomic next-generation sequencing (mNGS).
Rather than looking for one type of pathogen at a time, mNGS analyzes all the nucleic acids, RNA and DNA, that are present in a sample.
"Our technology is deceptively simple," said Charles Chiu , MD, PhD, professor of laboratory medicine and infectious diseases at UCSF and senior author of the study. "By replacing multiple tests with a single test, we can take the lengthy guesswork out of diagnosing and treating infections."
The researchers originally developed a clinical mNGS test to analyze cerebrospinal fluid (CSF), the pristine liquid that bathes the brain and spinal cord.
The test has now been performed on thousands of patients with unexplained neurological symptoms, both at UCSF and other hospitals across the country.
In a paper that appears Nov. 12 in Nature Medicine , the team demonstrated that the mNGS test correctly identified 86% of neurological infections.
In a companion study published the same day in Nature Communications , the team also used mNGS to identify pathogens in respiratory fluid that can cause pneumonia, and automated it to get results faster.
They expect that the automated test will be able to detect novel viral pathogens that could cause respiratory pandemics like COVID-19.
