title: Next-generation sequencing diagnostics of bacteremia in septic patients.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: Fraunhofer IGB, Nobelstr. 12, 70569, Stuttgart, Germany.
authors.forename: Silke
authors.initials: S
authors.lastname: Grumaz
authors.affiliation: IGVP, University of Stuttgart, Nobelstr. 12, 70569, Stuttgart, Germany.|Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria.
authors.forename: Philip
authors.initials: P
authors.lastname: Stevens
authors.affiliation: Fraunhofer IGB, Nobelstr. 12, 70569, Stuttgart, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Grumaz
authors.affiliation: Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany.
authors.forename: Sebastian O
authors.initials: SO
authors.lastname: Decker
authors.affiliation: Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany.
authors.forename: Markus A
authors.initials: MA
authors.lastname: Weigand
authors.affiliation: Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Hofer
authors.affiliation: Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany.
authors.forename: Thorsten
authors.initials: T
authors.lastname: Brenner
authors.affiliation: Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria.|Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria.
authors.forename: Arndt
authors.initials: A
authors.lastname: von Haeseler
authors.affiliation: Fraunhofer IGB, Nobelstr. 12, 70569, Stuttgart, Germany. kai.sohn@igb.fraunhofer.de.|IGVP, University of Stuttgart, Nobelstr. 12, 70569, Stuttgart, Germany. kai.sohn@igb.fraunhofer.de.
authors.forename: Kai
authors.initials: K
authors.lastname: Sohn
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D016470:Bacteremia / Q000097:blood / Q000175:diagnosis* / Q000382:microbiology / Q000473:pathology; D015415:Biomarkers / Q000097:blood; D000071997:Blood Culture; D016022:Case-Control Studies; D016638:Critical Illness; D004269:DNA, Bacterial / Q000097:blood / Q000235:genetics*; D024881:Drug Resistance, Bacterial / Q000235:genetics; D042241:Early Diagnosis; D005260:Female; D006090:Gram-Negative Bacteria / Q000235:genetics* / Q000302:isolation & purification; D006094:Gram-Positive Bacteria / Q000235:genetics* / Q000302:isolation & purification; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007362:Intensive Care Units; D008297:Male; D008875:Middle Aged; D018805:Sepsis / Q000097:blood / Q000175:diagnosis* / Q000382:microbiology / Q000473:pathology; D057188:Workflow
chemical_list: D015415:Biomarkers; D004269:DNA, Bacterial
keywords: Circulating nucleic acids; Diagnostics; Next-generation sequencing; Sepsis