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.
T. Blauwkamp, Karius, Inc.: Employee , Salary
C. Truong, Karius Inc.: Investigator , Research support
N. Banaei, Karius Inc: Investigator , Research support