170. Detection of Pathogen DNA using a Novel Plasma-Based Next-Generation Sequencing Assay in Patients with Acute Respiratory Infection
Session: Poster Abstract Session: Diagnostics: Bacteremia
Thursday, October 27, 2016
Room: Poster Hall
  • Karius_IDWeek2016_170.pdf (264.4 kB)
  • Background: 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 low sensitivity and specificity current diagnostic tests results in empirical treatment, which can lead to antibiotic overuse, particularly in the treatment of hospital-acquired pneumonia. There is a need for better diagnostics to aid in the management of respiratory infections.

    Methods: We have developed a plasma next-generation sequencing (NGS) assay capable of detecting a wide breadth of over 5,000 bacteria, viruses and eukaryotic pathogens. For this study, patients with negative blood cultures but positive respiratory microbiology tests were identified. We used our NGS assay to analyze residual plasma samples that were obtained on the same day as the blood culture samples. DNA was extracted from plasma and NGS performed. After filtering human sequences, remaining sequences were aligned to a pathogen reference sequence database. Relative abundance of each individual microorganism was calculated and pathogens estimated to be present with high statistical significance were identified.

    Results: We identified six patients that had negative blood cultures and positive respiratory sample within 7 days before or after the blood culture. Of these six patients, four had positive NGS plasma assays that identified the same species as was found in the respiratory test. These included confirmation of Enterobacter aerogenes in an endotracheal tube culture (2 patients), Serratia marcescens in an endotracheal culture, and adenovirus detected by NP swab PCR. The two remaining patients with negative NGS assays had respiratory cultures positive for a single colony of mold and a single colony of Klebsiella pneumoniae.

    Conclusion: A novel plasma-based NGS assay was able to detect pathogen DNA from patients with microbiologically confirmed respiratory infection despite negative blood cultures. This open-ended assay was able to detect both bacterial and viral causes of respiratory infection and may be useful in the diagnosis of the etiology of acute respiratory tract infection directly from blood.

    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.