A Single Test Can Diagnose Nearly All Infections

A new genomic test detects multiple pathogens with a single analysis, showing potential for faster, more accurate disease diagnosis.

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Researchers have developed a single genomic test capable of detecting most neurological and respiratory infectious pathogens in the human body. While the test has the potential to identify all infectious pathogens, its use has so far been limited to neurological and respiratory infections.

The test has shown an 86 percent success rate in diagnosing neurological infections, according to a decade-long study at the University of California–San Francisco (UCSF), published on Nov. 12 in Nature Medicine.

It has also demonstrated greater than 90 percent accuracy in detecting respiratory viruses compared with the current gold standard diagnostic tests, which are polymerase chain reaction (PCR) tests, according to a study published the same day in Nature Communications.

This test, which recently received U.S. Food and Drug Administration (FDA) recognition, can potentially improve care for neurological infections such as meningitis and encephalitis and accelerate the detection of new viral pandemic threats.

How the Technology Works

While most other tests can only detect one or a few pathogens at a time, this new one can detect all pathogens present by analyzing the genetic material in a patient sample.

This also allows the test to look at the quantity of various pathogens in the sample to predict disease severity and help quickly narrow down the target pathogen.

The technology was first developed to analyze cerebrospinal fluid (CSF), the fluid surrounding the brain and spinal cord, using a powerful genomic sequencing technique called metagenomic next-generation sequencing (mNGS). Since then, it has been performed on thousands of patients experiencing unexplained neurological symptoms, both at UCSF and other hospitals nationwide.

In a related study published on Nov. 12 in Nature Communications, researchers described how they’ve automated the mNGS process to identify pneumonia-causing pathogens in respiratory fluid.

A 1-Test Catch-All

This innovation can be particularly important for neurological diseases, where rare or unknown pathogens pose significant diagnostic challenges. Delays in diagnosis can severely affect patient outcomes.

“Our technology is deceptively simple,” Dr. Charles Chiu, professor of laboratory medicine and infectious diseases at UCSF and senior study author, said in a press statement. “By replacing multiple tests with a single test, we can take the lengthy guesswork out of diagnosing and treating infections.”

Since its introduction, the test has demonstrated real-world impact. In one notable case, rapid results helped resolve an undiagnosed infection in a young Wisconsin boy.

Between 2016 and 2023, the UCSF team analyzed nearly 5,000 CSF samples. More than 14 percent of samples were determined to be infections, and the new test identified the pathogen 86 percent of the time.

“Our mNGS test performs better than any other category of test for neurologic infections,” Chiu stated in the press release.

Future Developments

The technology continues to evolve, particularly in respiratory testing.

While the current CSF test involves more than 100 steps and takes two to seven days to complete, the new respiratory version aims for much faster results. “Our goal was to have the entire process completed within 12 to 24 hours, giving a same-day or next-day result,” Chiu said.

The findings of both studies show that the mNGS test could detect respiratory viruses likely to cause pandemics, including SARS-CoV-2, the virus that causes COVID-19, in about one day—even with only small quantities of the virus present.

The CSF and respiratory mNGS tests have already received breakthrough device designation from the FDA. This designation allows manufacturers to work with FDA experts to address issues arising during the device’s premarket review phase.