The treatment of sepsis requires an assessment as to whether the cause is bacterial (bacteremia). Conventional blood-culture methods take up to five days to confirm this and the delay can result in an incorrect treatment being administered, such as the wrong antimicrobial being given, and the wrong call can lead to patient death.
To overcome this, scientists from the Fraunhofer Institute have developed a method based on next-generation sequencing technology to make a rapid diagnosis of sepsis. The method sequences DNA extracted from a sample of blood plasma, and this indicates whether the cause of the sepsis is bacterial or fungal in origin (when an organism dies its DNA (Circulating Nucleic Acids in Plasma and Serum) will continue to circulate in the blood of the patient).
Discussing the platform with Laboratory Roots, Dr. Kai Sohn explains: “as a result of the direct sequencing of the DNA of a blood sample, the time-consuming step of cultivating the microorganisms in the lab is no longer necessary. In this way we can also identify those pathogens that are more difficult to grow under laboratory conditions.”
Trials of the new method have taken place in Germany, at Heidelberg University Hospital. To verify the method, DNA sequencing results were compared with blood cultures. A high level of accuracy was reported for viruses, bacteria and for fungi. The results were obtained in less than 30 hours, which compares favorably with the blood culture results, which took five days.
The DNA sequencing results were analysed using bespoke bioinformatics algorithms; this approach was able to differentiate human DNA from microbial DNA, and to match the microbial DNA to a database of bacterial, fungal and viral sequences. The algorithm was also able to differentiate between the DNA from microorganisms not typically associated with infection and those associated with infections. This was made possible by using a control sample of blood from a healthy person.
The platform is described in the journal Genome Medicine, in a paper headed “Next-generation sequencing diagnostics of bacteremia in septic patients.”
