One test to rule them all.

Metagenomic next-generation sequencing (mNGS) can potentially diagnose all infectious agents — viruses, bacteria, fungi, and parasites — in a single test.

mNGS in a Nutshell

What is mNGS?

Metagenomic next-generation sequencing (mNGS) is a shotgun sequencing approach in which all of the nucleic acid (DNA and RNA) in a clinical sample is sequenced at a very high depth, 10-20 million sequences per sample. mNGS can be performed for any type of clinical sample, including cerebrospinal fluid, plasma, respiratory secretions, urine, stool, or tissue.  Read more about it.

How is mNGS used to diagnose infectious diseases?

A single mNGS test can detect sequence reads corresponding to all pathogens – viruses, bacteria, fungi, and parasites.  It can thus be used to identify the potential cause of a patient’s infection.

Can mNGS testing be used clinically?

Before mNGS testing can be used for patient diagnosis, it must be validated in a licensed clinical laboratory.  In the United States, all of these laboratories are CLIA-certified. At UCSF, our CLIA-certified clinical microbiology laboratory has validated mNGS testing from cerebrospinal fluid for pathogen detection in meningitis and encephalitis and from plasma samples for pathogen detection in sepsis and disseminated infections.

Clinical mNGS testing of other sample types and infections is on the horizon, but not yet available.

What is the clinical laboratory workflow for mNGS?

What is the turnaround time for analysis?

Sample processing takes about 72 hours from start to finish. Currently, our result reporting timeline is 1-2 weeks from time we receive a sample to when we can report the results.

How do you analyze millions of sequences so quickly?

We use SURPI+ (SURPI PLUS), a clinical bioinformatics software pipeline that can rapidly analyze mNGS data for pathogens.  SURPI+ is modeled after the SURPI research pipeline.