Summary: Sequencing microbial cell-free DNA from plasma offers a comprehensive, non-invasive approach to identifying disease-causing pathogens. However, the validation of an open-ended sequencing assay entails unique challenges. Here we describe the analytical and clinical validation of a quantitative next-generation sequencing (NGS) test that detects microbial cell-free DNA (cfDNA) in blood plasma from patients suspected of infectious disease.
Direct Detection and Quantification of Bacterial cell-free DNA in Patients with Bloodstream Infection (BSI) Using the Karius Plasma Next-Generation Sequencing (NGS) Test
Tags: IDWeek 2017, ID, sepsis
Summary: This prospective study of 75 patients demonstrated the utility of the Karius plasma NGS test for direct detection of pathogens in patients with BSI. Pathogen cfDNA signal in plasma remains positive longer than blood culture and combined with quantification, could be a useful means for diagnosing and monitoring infections, particularly in those with sterile blood cultures.
The SEP-SEQ Trial - A Pilot Study Characterizing the Performance of a Novel Plasma Next-Generation Sequencing Assay to Detect Cell-Free Microbial DNA in Patients with Sepsis
Tags: ASM Microbe 2017, sepsis
Summary: This prospective, observational pilot study evaluated the performance of a novel NGS plasma pathogen detection assay in patients presenting to the emergency department with sepsis.
Performance of a Novel Plasma-Based Next-Generation Sequencing Assay in Patients with Bacteremia
Tags: IDWeek 2016, ID, sepsis
Summary: We demonstrate high concordance between a novel plasma NGS assay and blood culture in patients with and without bacteremia. In addition, the assay was able to identify pathogens in plasma corresponding to pathogens identified from culture of other body sites. These results highlight the increased sensitivity and versatility of this assay as an alternative diagnostic test in bacteremia, culture-negative, or diagnostically challenging infections.
Evaluation of the Karius Plasma Next-Generation Sequencing Test for Pathogen Detection in Pediatric Patients At Risk for Invasive Fungal Infection
Presented at ASM Microbe 2018
Summary: We demonstrate the first successful use of cell-free plasma NGS to non-invasively detect invasive fungal infections in immunocompromised pediatric patients.
The DISCOVER Trial: Application of the Karius Plasma Next-Generation Sequencing Test for Pathogen Detection in Stem-Cell Transplant Patients
Tags: IDWeek 2017, immunocompromised
Summary: This prospective study of 20 stem-cell transplant (SCT) patients showed that the Karius NGS plasma test had 100% concordance with CMV qPCR above the lower level of quantitation. Using NGS to monitor SCT patients for infection could permit earlier detection of pathogens including CMV, enabling earlier targeted therapy for this high-risk population.
Performance of the Karius Plasma Next-Generation Sequencing Test in Determining the Etiologic Diagnosis of Febrile Neutropenia: Results from a Pilot Study
Tags: IDWeek 2017, immunocompromised
Summary: This study enrolled 32 patients with neutropenic fever (NF) to compare the performance of the Karius plasma test to blood cultures, which often are unable to identify a pathogen in patients with NF. The Karius® Test detected all organisms found by blood culture, identified polymicrobial infections not detected by standard microbiologic testing, and identified a probable cause of NF more often than blood culture alone.
Liquid Biopsy for Infectious Diseases: Application of a Next-Generation Sequencing Cell-Free Plasma Assay to Detect Invasive Fungal Infections
Tags: ASM Microbe 2017, immunocompromised
Summary: The Karius NGS plasma-based assay is capable of non-invasive detection of cell-free pathogen DNA originating from deep infections. Fungi detected by our open-ended assay included Aspergillus and zygomycetes. This study demonstrates the utility of a non-invasive plasma assay in identifying a causal pathogen in cases of deep fungal infections, which is of particular interest in immunocompromised patients.
Detection of Pathogen Cell-Free DNA in Maternal Plasma in Patients with Chorioamnionitis Using a Non-Invasive Next-Generation Sequencing Assay
Tags: SRI 2018, ID
Summary: Subclinical intra-amniotic infection (IAI) has been linked to spontaneous preterm labor and complications such as neonatal sepsis. The Karius Test was used to show the detection of relevant pathogen cfDNA in maternal plasma during IAI for the first time. Next-generation sequencing may lead to the development of a specific assay to detect perinatal infections for targeted therapy: a non-invasive method to detect fetal exposure to pathogens.
Detection of Pathogen DNA using a Novel Plasma-Based Next-Generation Sequencing Assay in Patients with Acute Respiratory Infection
Tags: IDWeek 2016, ID
Summary: Determining the etiology of lower respiratory tract infection is challenging. Blood cultures are positive in only 5-14% of patients with pneumonia and it can be difficult to distinguish colonization from infection among organisms identified in sputum or endotracheal cultures. The Karius Test was able to detect both bacterial and viral causes of respiratory infection and may be useful in identifying the etiology of acute respiratory tract infections directly from blood.
Diagnosis of Mycobacterium tuberculosis and Non-tuberculous Mycobacterium Infections Using a Novel Plasma-Based Next-Generation Sequencing Assay
Tags: ASM Microbe 2016, ID
Summary: Mycobacterial infections can be difficult to diagnose by conventional culturing methods. This is the first demonstration of the use of a new NGS-based plasma assay to diagnose invasive mycobacterial disease. The high sensitivity and open-ended nature of this NGS assay are advantages that can aid in the diagnosis of deep infections with other fastidious organisms.
Diagnosis of Culture-Negative Infections Using a Novel Plasma-Based Next-Generation Sequencing Assay
Tags: ASM Microbe 2016, ID
Summary: We report two patients in whom the etiologic diagnosis for febrile illness was confirmed with the Karius Test. The first patient had an implantable cardiac defibrillator infection. Initial blood cultures were negative but culture of the explanted device yielded S. aureus, which was identified by NGS from a plasma specimen obtained prior to device removal. The second patient had extensive cutaneous disease, which on biopsy was thought to be consistent with leprosy. NGS of plasma, however, revealed high levels of Epstein-Barr virus, which was confirmed by quantitative PCR.
Rapid Detection of Invasive Mycobacterium chimaera Infection by Using a Novel Plasma-Based Next-Generation Sequencing Assay
Tags: IDWeek 2017, M. chimaera
Summary: This is the first reported detection of Mycobacterium chimaera (Mc), a member of the M. avium complex (MAC), using a plasma-based NGS assay. The Karius M. chimaera assay identified Mc approximately 15 days sooner than AFB culture positivity and 36 days sooner than speciation from AFB culture. Given widespread exposure to contaminated heater-cooler devices and the high case-fatality rate after infection, an urgent need exists for rapid, sensitive, noninvasive assays to detect Mc.
Detection of Nocardia cyriacigeorgica from a Deep Pulmonary Infection Using a Novel Plasma-Based Next-Generation Sequencing Assay
Tags: ASM Microbe 2017, ID
Summary: The diagnosis of deep life-threatening infections often requires invasive sampling of infected tissue for microbiologic diagnosis. However, such procedures are often avoided because of the risk of complications. We describe identification of Nocardia cyriacigeorgica causing a deep lung infection using a novel plasma-based next-generation sequencing (NGS) assay in a patient with chronic granulomatous disease (CGD).
Diagnosis of Capnocytophaga canimorsus Sepsis by a Novel Cell-free DNA Sequencing Assay
Tags: ASM Microbe 2016, sepsis
Summary: We report the first use of an open-ended cell-free DNA NGS assay to identify the causal pathogen in a patient with sepsis within a clinically actionable timeframe. This technology has the potential to improve targeted therapy for patients with sepsis of unclear etiology.