Study Demonstrates Value of Genomics to Improve the Diagnosis of Infectious Diseases
The peer-reviewed journal Nature Microbiology has published a study validating the Karius® Test for detecting pathogens and showing that the test identifies pathogens potentially faster than standard testing.
Culture-based tests have been the standard diagnostic method to detect infections. Yet only a fraction of pathogens known to infect humans are readily identifiable using existing diagnostic methods like blood cultures or other forms of microbiological testing. The Karius Test is a non-invasive blood test based on next-generation sequencing of microbial cell-free DNA (cfDNA) that can identify over 1,000 clinically relevant bacteria, DNA viruses, fungi, and parasites.
This study demonstrates the value of genomics to help clinicians improve the diagnosis of infectious diseases to save lives.
This prospective, observational study is the first and most comprehensive study to validate the Karius Test as a metagenomic, infectious-disease diagnostic tool. It demonstrates the technology's power beyond the lab to help doctors treat some of the most critically ill patients. The test's clinical performance was evaluated in 350 patients with suspected sepsis, which can be caused by a wide range of pathogens that cultures often miss.
"Currently, clinicians mainly rely on cultures when diagnosing patients with suspected sepsis, which can miss many pathogens because of a limited range of detection or pretreatment with antibiotics," said Dr. Samuel Yang, Associate Professor of Emergency Medicine at Stanford University Medical Center and the study's lead author. "The Karius Test offers a complement to the standard diagnostic approaches. A more accurate diagnosis is important, as it can ultimately improve patient outcomes."
Key clinical findings:
- The Karius Test outperformed other microbiological tests in diagnostic yield. The rate of pathogen identification was about three times higher than blood culture and 28 percent higher than all microbiological testing combined.
- There was high agreement between the Karius Test and existing diagnostic tests. The rate of agreement was 93.7 percent with blood culture and 92.9 percent with the composite reference standard.
- The Karius Test's "time to diagnosis" was potentially shorter than standard-of-care testing. The median time from blood draw to test result for the first 2,000 samples was 53 hours.
"The Karius Test is a giant leap in the field of infectious diseases," said Dr. Laila Woc-Colburn, Associate Professor of Infectious Diseases at Baylor College of Medicine. "It's opening a new area in diagnostics and clinical microbiology. We typically use the Karius Test in the diagnosis of infections in patients with fever of unknown origins, endocarditis, culture negative cases, and transplant patients to help optimize therapy management."
The study announced today also assessed the analytical performance of its microbial cfDNA sequencing test using hundreds of clinical samples with known infection status, hundreds more contrived infections to model the most challenging or rare infection scenarios, and thousands of simulated data sets to evaluate performance of its custom bioinformatics pipeline.
The Karius Test proved to be highly accurate, with greater than 95 percent analytical sensitivity for organisms contributing as little as 50 fragments of cfDNA per microliter of plasma, and greater than 99.99 percent analytical specificity per pathogen.
The quantitative measurement of cfDNA concentration in plasma was linear over five orders of magnitude, with less than 25 percent standard error for all organisms across multiple measurements over several days. Application of the Karius Test to asymptomatic adults showed no significant levels of microbial cfDNA in most, with low levels of known human microbiome components detected in the remaining samples.
The study's analytical validation section identifies key challenges to developing a clinical-grade test in the field of metagenomics and evaluates test performance in light of these challenges.
"Clinical metagenomics has the potential to revolutionize how physicians diagnose infectious disease," said Dr. Tim Blauwkamp, Chief Scientific Officer and co-founder of Karius. "There are, however, inherent challenges to achieving clinical-grade quality. This is an opportunity to share what we have learned about these challenges, as well as our framework for evaluating performance in light of these new considerations. My hope is that this study will not only demonstrate the quality of our own test but clear the path for others to capture the power of clinical-grade metagenomics."
Analysis of Karius Test results from 2,000 patient samples processed in real-time through the Karius CLIA-certified and CAP-accredited lab showed that more than 98% of tests produced a valid result, with more than 85% of test results returned to the ordering physician the day after sample receipt.
The study, available online at https://www.nature.com/articles/s41564-018-0349-6, sets an industry precedent for accountability and data robustness when it comes to clinical-grade metagenomics testing that directly impacts patients.
Date Published: 5th March 2019
Source article link: Karius, Inc.
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