Fighting infectious disease with cfDNA
Karius has developed a cell-free-DNA-based diagnostic test capable of identifying bacteria, mycobacteria, DNA viruses, fungi and protozoa in the blood down to the species level, thereby rapidly improving the diagnosis of infectious diseases.
The discovery that cell-free DNA (cfDNA), short fragments of DNA released from tissues into the blood, can be isolated and sequenced is driving a wave of innovation in diagnostics. cfDNA-based testing has transformed prenatal genetic screening to allow earlier, noninvasive fetal trisomy detection, and ‘liquid biopsy’ of circulating tumor DNA (ctDNA) offers oncologists new insights into individual cancers. Karius was founded to bring the power of cfDNA to infectious disease. Pathogen-derived cfDNA is present in only minute amounts relative to normal human cfDNA, or even ctDNA. By leveraging early work in Steven Quake’s laboratory at Stanford University, the Karius team has overcome this challenge to develop a Clinical Laboratory Improvement Amendments (CLIA)-certified blood test that can detect >1,000 different pathogens simultaneously within 1–2 days from a single blood draw.
According to CEO Mickey Kertesz, “The Karius test arms physicians with a single test that can deliver a potentially life-saving diagnosis, often more quickly than traditional testing methods, when time is criti-cal.” The Karius test proved faster and more sensitive in many instances when compared head-to-head with several traditional methods, and the test detected pathogens that were missed by standard culture- based methods, as presented at IDWeek 20171. Because the Karius test measures microbial cfDNA released into the patient’s blood, it can detect fastidi-ous organisms, including those that cannot be cul-tured. Owing to the reliance on sequencing, the test can identify a wide array of bacteria, mycobacteria, DNA viruses, fungi and protozoa down to the spe-cies level. As detailed below, studies indicate that the Karius test can detect pathogen cfDNA in the blood even when patients are pretreated with antibiotics or have a deep-seated infection that would typically require a diagnostic biopsy to identify the causal pathogen (Box 1).
Clinical validation and utility
The Karius cfDNA test has undergone broad clinical testing, including studies in sepsis, febrile neutro-penia, bloodstream infection (BSI) and in patients who have received stem cell transplants. Initial findings support the clinical validity and utility of the test in all of these areas. In a study of 350 patients with sepsis (SEP-SEQ), samples were tested with both the Karius cfDNA test and standard microbiological methods. An interim analysis presented at IDWeek 2017 showed that the Karius test identified a pathogen in almost 3 times more patients than detected by initial blood cultures. A clinical adjudication committee judged the Karius findings consistent with the potential cause of the septic event in a large majority of the cases.
David K. Hong, VP Medical Affairs and Clinical Development at Karius and a co-author on the SEP-SEQ study, noted, “Our results in septic patients show the Karius test can identify pathogens missed by other microbiology tests and has the potential to become the new standard of care.”
The Karius test has also shown promise in immunocompromised patients whose infections, like those of patients with sepsis, can be difficult to diagnose. In a study of 32 patients with chemotherapy- induced neutropenic fever at Stanford University, the Karius test identified pathogens in 18 of 27 samples that had negative blood culture results. In the five blood cultures that were positive, the Karius test and blood culture results agreed in all cases. Over half of the patients (18 of 32) were receiving antibiotics (13) or antifungal treatment (5) at the time of testing, which demonstrates that the Karius test can be informative even in a treatment setting where antibiotic or antifungal therapy can obscure traditional culture results. To further support this idea, a prospective study of 108 patients with BSI found that the Karius test detected the continued presence of pathogen significantly longer than did blood culture (6.5 days versus 3.4 days). These findings suggest that the Karius test would be well suited to the identification of infection in patients with sterile blood cultures due to pretreatment with antibiotics.
The determination of whether a transplant patient is experiencing infection or rejection is another impor-tant clinical challenge. In the DISCOVER trial at the University of California, San Francisco, Karius testing was conducted weekly in 20 patients following stem cell transplantation and compared with conventional microbiology test results. Staphylococcus aureus was detected 1 day and 7 days prior to blood culture and Chlamydia trachomatis infection was identified an impressive 30 days earlier with the Karius test than with traditional testing. Similarly, in a case series from a Los Angeles hospital system, invasive Mycobacterium chimaera infections were detected with the Karius test in five of six (83%) patients who had undergone cardiac surgery within a median of 5 days, whereas invasive biopsy cultures typically were not positive until over 2 weeks later, at a median of 20 days.
Additional clinical trials are underway to gather data on the impact of Karius testing in invasive fungal infections in pediatric oncology patients, and in people with fever and neutropenia, endocarditis and other culture-negative sepsis syndromes. Given that the test has already shown itself to be sensitive and at times faster than traditional methods, it appears well positioned to become an important tool for clinicians working in infectious disease, oncology, transplantation and critical care.
Box 1. Karius infectious disease testing in the clinic* |
The Karius test has broad clinical utility, including fast, accurate pathogen identification in sepsis, febrile neutropenia, and infections at difficult-to- access sites, such as the brain and heart.
Case 1: Sepsis with negative blood cultures Presentation: elderly male admitted to ICU with sepsis and respiratory failure, continued worsening despite broad-spectrum antibiotics Findings: bilateral pulmonary infiltrates on chest X-ray; cultures, including bronchoalveolar lavage, all initially negative Karius result: Mycobacterium tuberculosis Outcome: patient steadily improved with antituberculosis treatment. Three weeks later culture confirmed M. tuberculosis and bone marrow biopsy showed granulomas consistent with disseminated tuberculosis
Case 2: Febrile neutropenia in immunocompromised patient Presentation: child with high-risk pre-B-cell ALL admitted with febrile neutropenia and Klebsiella pneumoniae bacteremia. After initial improvement on antibiotics, fever recurred Findings: large pulmonary nodule found on chest CT Karius result: Rhizopus oryzae Outcome: targeted antifungal therapy initiated
Case 3: Brain abscess with inconclusive biopsy Presentation: adult male, newly diagnosed HIV+, with brain abscess close to basal ganglia Findings: positive serology for toxoplasma, inconclusive brain biopsy Karius result: Toxoplasma gondii Outcome: patient placed on targeted therapy, avoiding a risky second biopsy
*Disclaimer: Every case has been changed so as not to reveal patient identifying information and, while every attempt has been made to provide accurate information, errors may occur. This information is provided for educational purposes only, and not intended to provide medical advice.
ICU, intensive care unit; CT, computed tomography.
1. Thair, S. et al. The SEP-SEQ trial—clinical validation of the Karius plasma next-generation sequencing test for pathogen detection in sepsis. Abstract presented at IDWeek 2017, San Diego, CA, 4–8 October 2017.
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