This new technique uses real-time, next-generation sequencing that uses tiny amounts of microbial cell-free DNA from sepsis patients’ plasma.
Dutch publishing company Elsevier released a report from The Journal of Molecular Diagnostics detailing a new DNA sequencing technique that will drastically improve sepsis diagnosing methods. This should shorten the time it takes to diagnose sepsis dramatically, increasing positive outcomes.
Currently, a diagnostic test that is both fast and specific to provide critically important information does not exist. This new technique uses real-time, next-generation sequencing (NGS) that uses tiny amounts of microbial cell-free DNA from sepsis patients’ plasma. Previous testing utilizing NGS of micro cell-free DNA to detect blood pathogens was faster than standard cultures, but treatment still needed to be faster.
“Time-consuming, error- and contamination-prone blood cultures are still considered as the standard of care for sepsis diagnostics, frequently leading to an inappropriate and delayed targeted therapy,” said Thorsten Brenner, MD, Vice Head of the Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany.
Investigators then established a diagnostic workflow. This was based on third-gen high-throughput sequencing of microbial DNA. Typically, this sequencing is used to analyze long parts; however, microbial cell-free DNA is in small fragments and low quantities in plasma. This offers the possibility of real-time analyses during sequencing. In the end, this means the significantly reduced time needed to obtain results.
Developed by Oxford Nanopore Technologies, the nanopore sequencer, called the MinION, is a handheld device that looks a little like an old flip phone. It is the first of its kind, only portable real-time device for DNA and RNA sequencing.
“The nanopore sequencing platform sequences in real-time and has the potential to reduce time to diagnosis to only a few hours,” Brenner said.
In the study, four patients with sepsis and three healthy controls were used. The participants had been admitted to a hospital’s ICU, and samples of their DNA underwent sequencing, using both the standard NGS and the new nanopore technology. With the nanopore, within two to three hours all of the septic patients’ samples were found to be positive for relevant pathogens. With some final refining, the new technology was about to increase sequencing throughputs 3.5-fold. Pathogens were not being identified within minutes.
“With up to 50 million incident sepsis cases and 11 million sepsis-related deaths per year, sepsis represents a major cause of health loss,” Brenner said. “Reliable and early identification of the pathogen enables rapid and the most appropriate antibiotic intervention, thereby increasing the chance of better outcomes and patient survival. Currently, standard-of-care diagnostics still rely on microbiological culturing of the respective pathogens, which in most cases (70-90%), do not provide timely positive results.”
This new nanopore technology would be a potentially life-saving tool in emergency departments in helping to identify patients with sepsis, which can be life-threatening. The current mortality rate for septic shock is about 40%.
