New genomic test diagnoses virtually any infection

Researchers at the University of California, San Francisco (UCSF) have developed a genomic test that can quickly detect almost any type of pathogen.

This is a test whose results are published in a journal Natural medicinecould speed up detection of future viral pandemics and improve treatment of neurological infections that cause diseases such as meningitis and encephalitis, the authors note.

The team used a powerful genomic sequencing technique called metagenomic next-generation sequencing (mNGS). “Its advantage is that instead of looking for one type of pathogen each time, it analyzes all the nucleic acids, RNA and DNA present in the sample,” he points out. Charles Chiu

professor of laboratory medicine and infectious diseases at UCSF and senior author of the study.

“Unlike other diagnostic methods, the mNGS test uses a non-targeted approach that does not require prior clinical suspicion of the cause of the infection. In addition, it can detect the entire spectrum of pathogens that cause infections in one test.” such as bacteria, fungi, viruses and parasites,” Chiu explains to SINC.

Scientists initially developed a clinical mNGS test to analyze the cerebrospinal fluid that bathes the brain and spinal cord. During the seven-year study, the test was administered to thousands of patients with unexplained neurological symptoms at both UCSF and other U.S. hospitals. In their work, the authors showed that it correctly identifies 86% of such infections.

Pathogens in respiratory fluids

In an additional study published in Natural communicationsThe team also used next-generation metagenomic sequencing to identify pathogens in respiratory fluids that can cause pneumonia, and automated it to provide faster results.

Chiu comments that “Covid-19 has accelerated the development of mNGS tests applicable to respiratory infections, with the aim of detecting viruses before they spread or assisting in pandemic response.”

This technology, he adds, “is capable of identifying new viruses even without human reference genomes due to genetic similarity to viruses from animals and other organisms.”

One of the main challenges was to automate the mNGS test so that it could be performed in a typical clinical laboratory. The goal was to reduce processing time to less than 24 hours and minimize manual intervention, simplifying the process from more than 100 steps to less than 30, explains the researcher.

Technology license

To make this technology widely available, UCSF licensed testing to a startup. Delve Bioco-founded by Charles Chiu. The goal would be to offer it as a reference test in hospitals and clinics. “In the future, we hope that simplification and automation will allow it to be used in local laboratories and health centers,” says the co-author.

Links:

Patrick Benoit et al. “Seven-Year Performance of Clinical Metagenomic Next-Generation Sequencing for the Diagnosis of Central Nervous System Infections.” Natural medicine(2024).

Jessica Kariel Tan et al. “Laboratory Validation of Clinical Metagenomic Next-Generation Sequencing for Respiratory Virus Detection and Detection.”Natural communications