Researchers at the University of California, San Francisco (UCSF) have developed a single genomic test that can rapidly detect nearly any type of pathogen in a patient. This allows for faster diagnosis, allowing targeted treatment to begin sooner and potentially reducing healthcare costs.
The test is based on a genome sequencing technology called metagenomic next-generation sequencing (mNGS). Rather than having a doctor observe symptoms, guess the cause, and then test, mNGS analyzes a sample for a wide range of pathogens at once and checks the results against a database. Next, identify the virus, bacteria, fungus, or parasite that is causing the patient’s illness.
Researchers led by UCSF Professor Charles Chiu tested 4,828 patient samples over a seven-year period using clinical mNGS methods. The test analyzed a sample of cerebrospinal fluid (CSF), the fluid that flows around the brain and spinal cord. In a paper published yesterday in Nature Medicine, the research team noted that the mNGS test correctly identified 86% of neurological infections.
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Chiu has been working on this testing method for about 10 years. He also co-founded Delve Bio, a company that manufactures mNGS test kits, analyzes samples and provides results within 48 hours.
This is particularly useful in diagnosing neurological diseases and central nervous system infections such as meningitis, which have rare causes and can rapidly worsen a patient’s condition.
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mNGS can help doctors diagnose and begin treatment for these serious conditions in days instead of weeks. It can also prevent prolonged hospitalization and unnecessary treatment.
In an mNGS test, a patient’s DNA and RNA are extracted from a CSF sample. It is then analyzed by processing the sequence through a computational pipeline. Millions of sequences are analyzed every minute to identify the genetic signature of potential pathogens. For reference, Delve Bio, which partners with UCSF for mNGS testing, currently uses a database of over 68,000 pathogens.
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Although mNGS testing has been demonstrated to be useful in conjunction with CSF in the diagnosis of central nervous system infections, the method has also been used to detect respiratory viruses with pandemic potential, such as SARS-CoV-2 and influenza. can. This means it can help provide early warning signs. A looming widespread health crisis.
To this end, researchers discovered a way to use respiratory fluid for mNGS testing, largely automating the process and reducing processing time from 2-7 days to 12-24 hours. This method can also detect new viruses, even if only small amounts are detected in the sample.
Chiu and his team are also working on adapting mNGS testing methods to plasma and other body fluids. As of now, the CSF and respiratory fluid versions of the mNGS test have received breakthrough device designation from the FDA and could be reviewed in the coming months.
Source: UCSF
