Today's Clinical Lab - News, Editorial and Products for the Clinical Laboratory
Laboratory staff with blue gloves handles purple capped blood tubes in a laboratory tube rack with white laboratory equipment in the background.
The Karius Test can identify >1,000 different clinically relevant bacteria, DNA viruses, fungi, and parasites, and produce an antimicrobial resistance detection report from a patient sample.
iStock, fotostorm

Next-Generation Sequencing (NGS) Expands AMR Detection Capability

Receive pathogen and AMR marker detection from a patient sample within 48 hours with the Karius Test®

Karius
Published:Dec 18, 2023
|3 min read
Register for free to listen to this article
Listen with Speechify
0:00
5:00

Man with grey hair and black round glasses wearing a white and blue checked shirt smiles at camera in professional headshot with a grey backdrop.

Frederick (Rick) S. Nolte, PhD, D(ABMM), F(AAM), is a nationally-recognized medical microbiologist. Nolte has directed clinical microbiology programs at several world-class institutions in the US and has numerous publications on the laboratory and clinical validation of infectious disease diagnostics. Nolte is a senior director of medical affairs at Karius. 

What is the Karius Test and how does it work?

The Karius Test is the only commercially available plasma-based, culture-independent, mNGS test with antimicrobial resistance (AMR) marker detection. This is important because the sensitivity of culture-dependent methods is often limited. The Karius Test also uniquely links AMR marker detection to the pathogen identified. 

The Karius Test is an analytically and clinically validated blood test based on metagenomic next-generation sequencing (mNGS) of plasma microbial cell-free DNA (mcfDNA). As microbes replicate in the body, small fragments of their genomes are shed into the bloodstream. Since microbial cell-free DNA (mcfDNA) is 106 times less abundant than human cell-free DNA, Karius developed proprietary protocols to enrich the mcfDNA and deplete most of the human cfDNA prior to sequencing. The sequences are then mapped to >30,000 clinical-grade references to report >1,000 clinically relevant bacteria, DNA viruses, fungi, and parasites. The Karius Test is a laboratory-developed test offered in our CLIA-licensed, CAP-accredited clinical laboratory. The main diagnostic applications of The Karius Test include pneumonia, febrile neutropenia, endocarditis, invasive fungal infections, and fever of unknown origin. In particular, The Karius Test may be used to detect infections in immunocompromised patients, including those being treated for hematological malignancies or following transplant. 


How does the Karius Test support antimicrobial stewardship?

The Karius Test is a valuable adjunct to standard-of-care testing (SOCT) for diagnosing clinically adjudicated causes of infection, in some cases with a diagnostic yield higher than SOCT. The first AMR feature incorporated into Karius Test reporting in July 2019 enumerated DNA fragments derived from SCCmec, the genetic element within the Staphylococcus aureus genome harboring the mecA and mecC resistance genes that code for methicillin resistance. This year, we have developed and launched a more sensitive assay that directly targets a panel of six additional common AMR genes in 18 important pathogens encoding resistance to methicillin (mecA and mecC), vancomycin (vanA and vanB), extended-spectrum cephalosporins, aztreonam (blaCTX-M), and carbapenems (blaKPC). These new features can inform antimicrobial management, even in culture-negative cases.  

How could Karius Test results with AMR markers improve antimicrobial therapy options?

Karius Test pathogen identification and the addition of genotypic AMR detection may help clinicians to optimize antimicrobial treatment. The Karius Test typically provides pathogen detection results within one day after sample receipt with AMR marker detection results available 48 hours after sample receipt. Positive detections of AMR markers may be interpreted as consistent with the presence of antibiotic resistance associated with the specific AMR marker. The absence of specific AMR markers should be interpreted with caution since other resistance mechanisms exist. 

Antimicrobial therapy decisions should be made based on all available diagnostic tests and comprehensive clinical context. Confirmation by phenotypic antimicrobial susceptibility testing is recommended, if possible.