Nav: Home

New next-generation sequencing technique dramatically shortens diagnosis of sepsis

March 05, 2020

Philadelphia, March 5, 2020 - A report in the Journal of Molecular Diagnostics, published by Elsevier, describes a new technique that uses real-time next-generation sequencing (NGS) to analyze tiny amounts of microbial cell-free DNA in the plasma of patients with sepsis, offering the possibility of accurate diagnosis of sepsis-causing agents within a few hours of drawing blood. Current diagnostic tests are neither fast nor specific enough to provide timely, critically important information.

"With up to 50 million incident sepsis cases and 11 million sepsis-related deaths per year, sepsis represents a major cause of health loss," explained co-lead-investigator Thorsten Brenner, MD, vice head of the Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany. "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 to 90 percent) do not provide timely positive results."

NGS encompasses several advanced processes used to sequence the nucleotides in DNA. In previous work, the investigators described a system that utilized NGS of microbial cell-free DNA to detect blood pathogens that was highly sensitive and faster than standard blood cultures (within 28 hours). However, their ultimate goal was to develop an even faster test to expedite treatment.

To overcome this limitation the investigators established a diagnostic workflow based on 3rd generation high-throughput (nanopore) sequencing of microbial DNA. Normally, nanopore sequencing is used to analyze long fragments in sufficient amounts. However, microbial cell-free DNA occurs in small fragments and low quantities in plasma. Nanopore sequencing offers the possibility of real-time analyses during sequencing, which dramatically reduces the time needed to obtain results. "We also had to create validated, specifically adapted bioinformatic procedures to reliably identify pathogens," noted principal investigator Kai Sohn, PhD, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.

This new technique relies on the use of a handheld nanopore sequencer known as the MinION. This device is portable, can read out ultra-long reads, and immediately processes reads in real time.

In this proof-of-concept study, the investigators analyzed plasma from four septic patients and three healthy controls who were hospitalized in the ICU. Each sample's DNA underwent sequencing using both technologies: the standard NGS (Illumina) and the new nanopore NGS technology. With nanopore sequencing, all septic patient samples were found to be positive for relevant pathogens, whether bacterial, viral, or fungal.

After additional refinements, the new technique was able to achieve a 3.5-fold increase in sequencing throughput, allowing pathogen identification within minutes after sequencing began. In fact, the highest quality results were generated within 2 or 3 hours of the beginning of sequencing. In contrast, with Illumina the final results are available only after the sequencing is finished. "This new system might facilitate same-shift adaption of antibiotic intervention at the ICU, which might, in turn, improve patient outcomes significantly," commented Dr. Sohn.

The investigators also compared the probability of pathogen detection with the MinION system to the highly accurate and clinically validated Illumina NGS technique in a retrospective analysis of 239 samples taken from sepsis patients. Although the accuracy of nanopore sequencing was lower than with Illumina (approximately 85 percent vs. 99 percent), they found a strong correlation between the findings generated by MinION vs. Illumina.

"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 Prof. Dr. Brenner. "The nanopore sequencing platform sequences in real time and has the potential to reduce time to diagnosis to only a few hours."
-end-


Elsevier

Related Dna Articles:

Zigzag DNA
How the cell organizes DNA into tightly packed chromosomes. Nature publication by Delft University of Technology and EMBL Heidelberg.
Scientists now know what DNA's chaperone looks like
Researchers have discovered the structure of the FACT protein -- a mysterious protein central to the functioning of DNA.
DNA is like everything else: it's not what you have, but how you use it
A new paradigm for reading out genetic information in DNA is described by Dr.
A new spin on DNA
For decades, researchers have chased ways to study biological machines.
From face to DNA: New method aims to improve match between DNA sample and face database
Predicting what someone's face looks like based on a DNA sample remains a hard nut to crack for science.
Self-healing DNA nanostructures
DNA assembled into nanostructures such as tubes and origami-inspired shapes could someday find applications ranging from DNA computers to nanomedicine.
DNA design that anyone can do
Researchers at MIT and Arizona State University have designed a computer program that allows users to translate any free-form drawing into a two-dimensional, nanoscale structure made of DNA.
DNA find
A Queensland University of Technology-led collaboration with University of Adelaide reveals that Australia's pint-sized banded hare-wallaby is the closest living relative of the giant short-faced kangaroos which roamed the continent for millions of years, but died out about 40,000 years ago.
DNA structure impacts rate and accuracy of DNA synthesis
DNA sequences with the potential to form unusual conformations, which are frequently associated with cancer and neurological diseases, can in fact slow down or speed up the DNA synthesis process and cause more or fewer sequencing errors.
Changes in mitochondrial DNA control how nuclear DNA mutations are expressed in cardiomyopathy
Differences in the DNA within the mitochondria, the energy-producing structures within cells, can determine the severity and progression of heart disease caused by a nuclear DNA mutation.
More DNA News and DNA Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Making Amends
What makes a true apology? What does it mean to make amends for past mistakes? This hour, TED speakers explore how repairing the wrongs of the past is the first step toward healing for the future. Guests include historian and preservationist Brent Leggs, law professor Martha Minow, librarian Dawn Wacek, and playwright V (formerly Eve Ensler).
Now Playing: Science for the People

#566 Is Your Gut Leaking?
This week we're busting the human gut wide open with Dr. Alessio Fasano from the Center for Celiac Research and Treatment at Massachusetts General Hospital. Join host Anika Hazra for our discussion separating fact from fiction on the controversial topic of leaky gut syndrome. We cover everything from what causes a leaky gut to interpreting the results of a gut microbiome test! Related links: Center for Celiac Research and Treatment website and their YouTube channel
Now Playing: Radiolab

The Flag and the Fury
How do you actually make change in the world? For 126 years, Mississippi has had the Confederate battle flag on their state flag, and they were the last state in the nation where that emblem remained "officially" flying.  A few days ago, that flag came down. A few days before that, it coming down would have seemed impossible. We dive into the story behind this de-flagging: a journey involving a clash of histories, designs, families, and even cheerleading. This show is a collaboration with OSM Audio. Kiese Laymon's memoir Heavy is here. And the Hospitality Flag webpage is here.