Combined use of metagenomic sequencing and host response profiling for the diagnosis of suspected sepsis.

Background: Current diagnostic techniques are inadequate for rapid microbial diagnosis and optimal management of patients with suspected sepsis. We assessed the impact of metagenomic sequencing and host response profiling individually and in combination on microbiological diagnosis in these patients. Methods: In this cohort study of 200 consecutive patients with suspected sepsis we evaluated three molecular diagnostic methods with blood specimens: 1) direct bacterial DNA detection and characterization with metagenomic shotgun next generation sequencing and contaminant sequence removal using Bayesian inference; 2) direct viral DNA and RNA enrichment and detection with viral capture sequencing; and 3) transcript-based host response profiling with a previously-defined 18-gene qRT-PCR assay. We then evaluated changes in diagnostic decision-making among three expert physicians in a chart review by unblinding our three molecular test results in a staged fashion. Findings: Metagenomic shotgun sequencing confirmed positive blood culture results in 14 of 26 patients. In 17 of 200 patients, metagenomic sequencing and viral capture sequencing revealed organisms that were 1) not detected by conventional hospital tests within 5 days after presentation, and 2) classified as of probable clinical relevance by physician consensus. Host response profiling led at least two of three physicians to change their diagnostic decisions in 46 of 100 patients. Finally, we report on potential bacterial DNA translocation in 8 patients who were originally classified by physicians as noninfected and show how host response profiling can guide interpretation of metagenomic shotgun sequencing results. Interpretation: The integration of host response profiling, metagenomic shotgun sequencing, and viral capture sequencing synergistically enhances the utility of each of these approaches, and may improve the diagnosis of infections in patients with suspected sepsis.