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Next-generation sequencing diagnostics of bacteremia in septic patients

Grumaz, Silke ; Stevens, Philip ; Grumaz, Christian ; Decker, Sebastian O. ; Weigand, Markus A. ; Hofer, Stefan ; Brenner, Thorsten ; Haeseler, Arndt ; Sohn, Kai

In: Genome Medicine, 8 (2016), Nr. 73. pp. 1-13. ISSN 1756-994X

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Download (1MB) | Lizenz: Creative Commons LizenzvertragNext-generation sequencing diagnostics of bacteremia in septic patients by Grumaz, Silke ; Stevens, Philip ; Grumaz, Christian ; Decker, Sebastian O. ; Weigand, Markus A. ; Hofer, Stefan ; Brenner, Thorsten ; Haeseler, Arndt ; Sohn, Kai underlies the terms of Creative Commons Attribution 3.0 Germany

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Background: Bloodstream infections remain one of the major challenges in intensive care units, leading to sepsis or even septic shock in many cases. Due to the lack of timely diagnostic approaches with sufficient sensitivity, mortality rates of sepsis are still unacceptably high. However a prompt diagnosis of the causative microorganism is critical to significantly improve outcome of bloodstream infections. Although various targeted molecular tests for blood samples are available, time-consuming blood culture-based approaches still represent the standard of care for the identification of bacteria. Methods: Here we describe the establishment of a complete diagnostic workflow for the identification of infectious microorganisms from seven septic patients based on unbiased sequence analyses of free circulating DNA from plasma by next-generation sequencing. Results: We found significant levels of DNA fragments derived from pathogenic bacteria in samples from septic patients. Quantitative evaluation of normalized read counts and introduction of a sepsis indicating quantifier (SIQ) score allowed for an unambiguous identification of Gram-positive as well as Gram-negative bacteria that exactly matched with blood cultures from corresponding patient samples. In addition, we also identified species from samples where blood cultures were negative. Reads of non-human origin also comprised fragments derived from antimicrobial resistance genes, showing that, in principle, prediction of specific types of resistance might be possible. Conclusions: The complete workflow from sample preparation to species identification report could be accomplished in roughly 30 h, thus making this approach a promising diagnostic platform for critically ill patients suffering from bloodstream infections.

Document type: Article
Journal or Publication Title: Genome Medicine
Volume: 8
Number: 73
Publisher: BioMed Central
Place of Publication: London
Date Deposited: 06 Jul 2016 08:18
Date: 2016
ISSN: 1756-994X
Page Range: pp. 1-13
Faculties / Institutes: Medizinische Fakultät Heidelberg > Universitätsklinik für Anaesthesiologie
DDC-classification: 610 Medical sciences Medicine
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