A Promising Tool for Rapid Diagnosis of Unknown Infections in Body Fluids: Metagenomic Next-Generation Sequencing

Womble Bond Dickinson

Womble Bond Dickinson

[author: Pam Koenig]

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Photo by National Cancer Institute on Unsplash

Scientists at the University of California-San Francisco (UCSF) have developed a single test, Metagenomic Next-Generation Sequencing (mNGS), that can rapidly identify infectious microbes in body fluids, increasing the speed at which seriously ill patients can receive life-saving drug treatments. mNGS has the potential to reshape the way infectious diseases are diagnosed.

The current gold standard for laboratory testing for infections encompasses culture-based tests and standard PCR [polymerase chain reaction]-based DNA tests. With these conventional diagnostic tests, each body fluid sample undergoes specific handling. In addition, testing is limited to the detection of only one, or perhaps a small panel of potential pathogens in a body fluid sample. Fast and accurate pathogen identification may not always be possible because cultures take 24 hours to weeks, in some cases, to grow, and PCR testing requires some idea of which pathogen might be the source of infection. In comparison, mNGS can be used to detect any infection without special processing for each body fluid. Moreover, mNGS uses DNA sequencing technology to detect all DNA in a sample, which may be from any species, including bacterial, fungal, parasitic, or viral. Analytical software is used to compare DNA sequences in the sample to massive genomic databases containing information on all known pathogens to quickly identify the cause of an infection.

In the current study, Chiu and his UCSF colleagues developed a mNGS testing protocol using different sequencing technologies to identify pathogens from cell-free DNA across a range of different body fluid samples. The researchers found that mNGS could detect bacterial or fungal pathogens with high accuracy. Additionally, in contrast to the slow results obtained from conventional cultures using PCR, mNGS could return findings in as little as 50 minutes in some cases, with an average turn around time in a range of less than 6 hours to 24 hours, depending on the sequencing technology utilized. Furthermore, in a series of patients determined to later have an infection, the investigators found that seven patients whose body fluid samples were conventional PCR negative, actually tested positive by mNGS.

Chiu et al. plan to seek regulatory approval for their mNGS protocol from the U.S. Food and Drug Administration (FDA). mNGS has real potential to eventually replace conventional culture testing for infectious pathogens. As a single diagnostic test, mNGS has the utility of expanding the scope of conventional diagnostic testing for infection to multiple body fluid types. In addition, the rapid turn around time for mNGS testing has essential applications for the treatment for infections, such as sepsis and pneumonia, that require a rapid response and timely diagnosis. mNGS may also be beneficial in the identification of culture-negative or slow-growing pathogens, as well as in the diagnosis of rare or unusual infections.

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