Remarkable accuracy - a sepsis diagnosis tool combines genetic sequencing with analysis of patients' immune responses. According to estimates, sepsis—a condition in which the immune system overreacts to an infection—causes 20% of fatalities worldwide and somewhere between 20 and 50% of hospital de
The new technology correctly identified 99% of confirmed bacterial sepsis cases, 92% of confirmed viral sepsis cases, and predicted sepsis in 74% of clinically suspected but undiagnosed cases.
Chaz Langelier, M.D., Ph.D., an associate professor of medicine in UCSF’s Division of Infectious Diseases and a CZ Biohub Investigator, is senior author of a study describing a remarkably accurate diagnostic tool for sepsis. Credit: CZ Biohub Current sepsis diagnostics focus on detecting bacteria by growing them in culture, a process that is “essential for appropriate antibiotic therapy, which is critical for sepsis survival,” according to the researchers behind the new method. But culturing these pathogens is time-consuming and doesn’t always correctly identify the bacterium that is causing the infection.
But rather than relying on cultures to identify pathogens in these samples, a team led by CZ Biohub scientists Norma Neff, Ph.D., and Angela Pisco, Ph.D., instead used metagenomic next-generation sequencing . This method identifies all the nucleic acids or genetic data present in a sample, then compares those data to reference genomes to identify the microbial organisms present.
The researchers found that when traditional bacterial culture identified a sepsis-causing pathogen, there was usually an overabundance of genetic material from that pathogen in the corresponding plasma sample analyzed by mNGS. With that in mind, Kalantar programmed the model to identify organisms present in disproportionately high abundance compared to other microbes in the sample, and to then compare those to a reference index of well-known sepsis-causing microbes.
The team was also excited to discover that they could use this combined host-response and microbe detection method to diagnose sepsis using plasma samples, which are routinely collected from most patients as part of standard clinical care. “The fact that you can actually identify sepsis patients from this widely available, easy-to-collect sample type has big implications in terms of practical utility,” Langelier said.
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