Genomic Test Might Quickly Diagnose Any Type of Infection

November 12, 2024
Dennis Thompson HealthDay Reporter

A cutting-edge genetic test can rapidly detect and identify almost any kind of disease-causing microorganism in the human body, whether it’s a virus, bacteria, fungus or parasite, researchers say.

Doctors have been using the genetic test for more than a decade to identify pathogens in spinal fluid, after its development at the University of California-San Francisco.

And now researchers have adapted the test to identify germs in respiratory fluid that can cause pneumonia, according to a new study published Nov. 12 in the journal Nature Medicine.

The research team also has automated the test, which is called metagenomic next-generation sequencing or mNGS, the study says.

The new respiratory version of the mNGS test requires just 30 minutes of hands-on time before robots and AI take over, and can return results in time to treat dangerous infections, researchers said.

“Our goal was to have the entire process completed within 12 to 24 hours, giving a same-day or next-day result,” senior researcher Dr. Charles Chiu, a professor of laboratory medicine and infectious diseases at UCSF, said in a news release.

The mNGS test takes a bare-knuckled approach to analysis.

Rather than looking for single types of pathogen one by one, the test analyzes all RNA and DNA that are present in a sample, then separates human genetic material from those that originate in bacteria, viruses, fungi or parasites.

“Our technology is deceptively simple,” Chiu said. “By replacing multiple tests with a single test, we can take the lengthy guesswork out of diagnosing and treating infections.”

The mNGS test first made waves back in 2014 when doctors used it to save the life of then-15-year-old Joshua Osborn, who’d come down with debilitating headaches, fever, weight loss and fatigue.

Osborn, who lived in Cottage Grove, Wisc., eventually fell into a coma with life-threatening encephalitis – and still no one could figure out what was making him sick. Medical tests and a brain biopsy brought back nothing.

But once mNGS was employed, the test sussed out the cause within 48 hours.

It wound up being Leptospira santarosai, a bacterial species native to Puerto Rico. As it turns out, Osborn and his family had visited a church camp there a year before his hospitalization.

The remedy for the disease, that had plagued him for more than a year, wound up being old-fashioned penicillin.

“I’m happy to be living,” Osborn said at the time. “By the percentages, the likelihood is pretty much that I wouldn’t be. I’m thankful.”

Between 2016 and 2023, the UCSF team analyzed nearly 5,000 spinal fluid samples with the test, more than 14% of which turned out to have an infection.

Overall, the test accurately identified the pathogen in spinal fluid 86% of the time, researchers say in their new paper.

“Our mNGS test performs better than any other category of test for neurologic infections,” Chiu said, “The results support its use as a critical part of the diagnostic armamentarium for physicians who are working up patients with infectious diseases.”

Based on these results, researchers have adapted the test to serve as a rapid-response system for respiratory diseases that could become the basis of the world’s next pandemic.

The new report shows that the test can detect respiratory viruses like COVID, influenza and RSV in less than a day, even if there’s only small amounts of virus present in a sample.

The test also should be able to detect strains expected to emerge in the future.

Both the spinal fluid and respiratory droplet versions of the mNGS test have received breakthrough device designation from the U.S. Food and Drug Administration, placing them on a fast track for full approval.

More information

The American Society of Microbiology has more on metagenomic next-generation sequencing.

SOURCE: University of California-San Francisco, news release, Nov. 12, 2024

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