SAN FRANCISCO, July 14 (Xinhua) -- A genome sequencing test developed at the University of California, San Francisco, that can rapidly pinpoint the cause of a bacterial, viral, fungal or parasitic infection from among a huge range of possibilities is now available across the United States.
The next-gen precision diagnostics is expected to help physicians diagnose mysterious cases of neurological infection in acutely ill patients.
Researchers at UCSF have used the test on a trial basis to diagnose a number of patients, including the well-known case of a 14-year-old boy who was near death with swelling in his brain. The boy had undergone months of unsuccessful attempts to identify the cause of his illness with conventional lab tests, expensive imaging technologies, and invasive procedures, including a brain biopsy.
By sequencing his cerebrospinal fluid (CSF), UCSF researchers found that the boy had a bacterial infection called leptospirosis, and he rapidly recovered after receiving targeted treatment with penicillin.
The test is now approved for clinical use.
UCSF physicians and researchers have examined the utility of the test using CSF collected from more than 200 patients enrolled in a nationwide study. All of these patients suffered from acute neurological illnesses, including meningitis, namely inflammation of the coverings around the brain and spinal cord; encephalitis, or inflammation of the brain; and myelitism, which is the inflammation of the spinal cord. Doctors often have trouble figuring out why these tissues become inflamed, as these conditions can have many causes, including infection, cancer, and autoimmune disease. This can lead to inappropriate treatment.
The new sequencing test can help overcome the uncertainly by pinpointing the genomic signatures of a wide range of pathogens, including fungi, bacteria, viruses, and parasites, all at once. If no pathogen is detected using this comprehensive test, doctors can be more confident in pursuing other non-infectious causes of the illness. While the test does not always establish the cause of inflammation, it has the potential to speed up the diagnostic process significantly, and to spare patients from having to undergo a large number of diagnostic tests and invasive procedures.
The technique, known as metagenomic next-generation sequencing, or mNGS, is a "shotgun" approach in which all of the deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) in a clinical sample are sequenced at very high depth, with the generation of 10 to 20 million reads per sample.
"Too many patients die or suffer unnecessarily because the cause of their illness cannot be determined in a timely fashion," Charles Chiu, an associate professor of laboratory medicine at UCSF and principal investigator of the mNGS study, was quoted as saying in a news release. "We now have a single diagnostic tool that can be used to comprehensively diagnose or exclude infections in hospitalized patients with mysterious illnesses."
