Enhanced Performance of Next-Generation Sequencing Diagnostics Compared With Standard of Care Microbiological Diagnostics in Patients Suffering From Septic Shock

Objectives: Culture-based diagnostics represent the standard of care in septic patients, but are highly insensitive and in many cases unspecific. We recently demonstrated the general feasibility of next-generation sequencing-based diagnostics using free circulating nucleic acids (cell-free DNA) in plasma samples of septic patients. Within the presented investigation, higher performance of next-generation sequencing-based diagnostics was validated by comparison to matched blood cultures. Design: A secondary analysis of a prospective, observational, single-center study. Setting: Surgical ICU of a university hospital and research laboratory. Patients: Fifty patients with septic shock, 20 uninfected patients with elective surgery as control cohort. Interventions: None. Measurements and Main Results: From 256 plasma samples of 48 septic patients at up to seven consecutive time points within the 28-day observation period, cell-free DNA was isolated and analyzed by next-generation sequencing and relevance scoring. In parallel, results from culture-based diagnostics (e.g., blood culture) were obtained. Plausibility of blood culture and next-generation sequencing results as well as adequacy of antibiotic therapy was evaluated by an independent expert panel. In contrast to blood culture with a positivity rate of 33% at sepsis onset, the positivity rate for next-generation sequencing-based pathogen identification was 72%. Over the whole study period, blood culture positivity was 11%, and next-generation sequencing positivity was 71%. Ninety-six percent of positive next-generation sequencing results for acute sepsis time points were plausible and would have led to a change to a more adequate therapy in 53% of cases as assessed by the expert evaluation. Conclusions: Our results show that next-generation sequencing-based analyses of bloodstream infections provide a valuable diagnostic platform for the identification of clinically relevant pathogens with higher sensitivity and specificity than blood culture, indicating that patients might benefit from a more appropriate therapy based on next-generation sequencing-based diagnosis. This is an open access article distributed under the Creative Commons Attribution License 4.0 (CCBY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Drs. Brenner and Sohn share senior authorship. Drs. S. Grumaz, Decker, Hofer, Brenner, and Sohn conceived of, designed, and supervised the study. Drs. Decker, Hofer, and Brenner collected clinical samples and clinical data. Drs. S. Grumaz, C. Grumaz, and Glanz performed all sample processing and next-generation sequencing experiments. Drs. Vainshtein and Stevens performed bioinformatic data processing and statistical analyses. Drs. S. Grumaz, C. Grumaz, Stevens, and Sohn analyzed the data. Drs. Hofer, Weigand, Brenner, and Sohn provided materials. Drs. S. Grumaz and C. Grumaz prepared the tables and figures. Drs. S. Grumaz and Sohn wrote the article with contributions from all other authors. All authors read, critically revised, and approved the final article. A data visualization tool associated with this article can be viewed here: http://bit.ly/2GsAPTP. Supplemental digital content is available for this article. Direct URL citations appear in the printed text and are provided in the HTML and PDF versions of this article on the journal’s website (http://bit.ly/29S62lw). Supported, in part, by the Fraunhofer IGB (Stuttgart, Germany), Fraunhofer Future Foundation, Department of Anesthesiology (University of Heidelberg, Germany), Heidelberg Foundation of Surgery (University of Heidelberg, Germany). Our study sponsors were not involved in study design, collection, analysis, or interpretation of data. Drs. Decker and Brenner received project funding from Heidelberg Foundation of Surgery. Drs. S. Grumaz, Stevens, and Sohn disclosed that they are co-founders of the company Noscendo active in molecular diagnostics for infectious diseases. The remaining authors have disclosed that they do not have any potential conflicts of interest. For information regarding this article, E-mail: kai.sohn@igb.fraunhofer.de Copyright © by 2019 by the Society of Critical Care Medicine and Wolters Kluwer Health, Inc. All Rights Reserved.

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