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

Cheng, H. K.; Tan, S. K.; Sweeney, T. E.; Jeganathan, P.; Briese, T.; Khadka, V.; Strouts, F.; Thair, S.; Dalai, S.; Hitchcock, M.; Multani, A.; Aronson, J.; Andermann, T.; Yu, A.; Yang, S.; Holmes, S.; Lipkin, W. I.; Khatri, P.; Relman, D. A.

doi:10.1101/854182

bioRxiv · 10.1101/854182

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

Cheng, H. K.·Tan, S. K.·Sweeney, T. E.·Jeganathan, P.·Briese, T.·Khadka, V.·Strouts, F.·Thair, S.·Dalai, S.·Hitchcock, M.·Multani, A.·Aronson, J.·Andermann, T.·Yu, A.·Yang, S.·Holmes, S.·Lipkin, W. I.·Khatri, P.·Relman, D. A.

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Abstract

BackgroundCurrent diagnostic techniques are inadequate for rapid microbial diagnosis and optimal management of patients with suspected sepsis. We assessed the clinical impact of three powerful molecular diagnostic methods. MethodsWith blood samples from 200 consecutive patients with suspected sepsis, we evaluated 1) metagenomic shotgun sequencing together with a Bayesian inference approach for contaminant sequence removal, for detecting bacterial DNA; 2) viral capture sequencing; and 3) transcript-based host response profiling for classifying patients as infected or not, and if infected, with bacteria or viruses. We then evaluated changes in diagnostic decision-making among three expert physicians by unblinding the results of these methods in a staged fashion. ResultsMetagenomic 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. The data suggested possible bacterial DNA translocation in 8 patients who were originally classified by physicians as noninfected and illustrate how host response profiling can guide interpretation of metagenomic shotgun sequencing results. ConclusionsThe integration of host response profiling, metagenomic shotgun sequencing, and viral capture sequencing enhances the utility of each, and may improve the diagnosis and management of patients with suspected sepsis.

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Cheng, H. K., Tan, S. K., Sweeney, T. E., Jeganathan, P., Briese, T., Khadka, V., Strouts, F., Thair, S., Dalai, S., Hitchcock, M., Multani, A., Aronson, J., Andermann, T., Yu, A., Yang, S., Holmes, S., Lipkin, W. I., Khatri, P., Relman, D. A.. 2019-11-25. Combined use of metagenomic sequencing and host response profiling for the diagnosis of suspected sepsis.. https://doi.org/10.1101/854182

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