169. Performance of a Novel Plasma-Based Next-Generation Sequencing Assay in Patients with Bacteremia
Session: Poster Abstract Session: Diagnostics: Bacteremia
Thursday, October 27, 2016
Room: Poster Hall
  • Karius_IDWeek2016_169.pdf (136.4 kB)
  • Background: Blood cultures are routinely obtained during the diagnostic evaluation for a number of infectious conditions such as sepsis, febrile neutropenia, and pneumonia. Despite its ubiquitous use, blood cultures have poor sensitivity due to a number of factors including previous antibiotic therapy or the presence of poorly-growing fastidious organisms. There is a need for higher sensitivity, comprehensive diagnostic tests that can overcome these limitations to aid in guiding therapy.


    Methods: We developed a plasma next-generation sequencing (NGS) assay capable of detecting over 5,000 bacteria, viruses and eukaryotic pathogens. To evaluate this assay in bacteremia, patients with multi-set positive and negative blood cultures were identified. We used our assay to analyze residual plasma samples that were obtained on the same day as the blood cultures. DNA was extracted from plasma and NGS performed. After filtering human reads, remaining reads were aligned to a pathogen sequence database. Relative abundance of each individual microorganism was calculated and pathogens estimated to be present with high statistical significance were identified.


    Results: In comparing this novel NGS assay to blood culture and all other microbiologic data obtained from the patient, Sensitivity was 80.9% (38/47) and Specificity was 90.7% (39/43). When comparing directly to blood culture, there was agreement in culture-positive specimens in 32 of 43 specimens (74.4%). For blood culture-negative specimens, NGS did not detect a pathogen in 39 out of 47 specimens (83.0%). Of the eight false positives detected by the NGS assay as compared with blood culture, four were found to be true positives when compared with microbiologic data from the patient. These included detection of pathogens by plasma NGS that were found in endotracheal cultures, nasopharyngeal PCR, peritoneal cultures, or recently positive blood cultures.


    Conclusion: We present data that show high concordance between a novel 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 in culture-negative infections and the broad nature of this assay.

    David Hong, MD1, Mickey Kertesz, PhD1, Tim Blauwkamp, PhD1, Cynthia Truong, BS2 and Niaz Banaei, MD2, (1)Karius, Inc., Menlo Park, CA, (2)Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA


    D. Hong, Karius, Inc.: Employee , Salary

    M. Kertesz, Karius, Inc.: Employee , Salary

    T. Blauwkamp, Karius, Inc.: Employee , Salary

    C. Truong, Karius Inc.: Investigator , Research support

    N. Banaei, Karius Inc: Investigator , Research support

    Findings in the abstracts are embargoed until 12:01 a.m. CDT, Wednesday Oct. 26th with the exception of research findings presented at the IDWeek press conferences.