Next-generation sequencing diagnostics of bacteremia in sepsis (Next GeneSiS-Trial): Study protocol of a prospective, observational, noninterventional, multicenter, clinical trial

Thorsten Brenner, Sebastian O Decker, Silke Grumaz, Philip Stevens, Thomas Bruckner, Thomas Schmoch, Mathias W Pletz, Hendrik Bracht, Stefan Hofer, Gernot Marx, Markus A Weigand, Kai Sohn, TIFOnet Critical Care Trials Group, Thorsten Brenner, Sebastian O Decker, Silke Grumaz, Philip Stevens, Thomas Bruckner, Thomas Schmoch, Mathias W Pletz, Hendrik Bracht, Stefan Hofer, Gernot Marx, Markus A Weigand, Kai Sohn, TIFOnet Critical Care Trials Group

Abstract

Background: Sepsis remains a major challenge, even in modern intensive care medicine. The identification of the causative pathogen is crucial for an early optimization of the antimicrobial treatment regime. In this context, culture-based diagnostic procedures (e.g., blood cultures) represent the standard of care, although they are associated with relevant limitations. Accordingly, culture-independent molecular diagnostic procedures might be of help for the identification of the causative pathogen in infected patients. The concept of an unbiased sequence analysis of circulating cell-free DNA (cfDNA) from plasma samples of septic patients by next-generation sequencing (NGS) has recently been identified to be a promising diagnostic platform for critically ill patients suffering from bloodstream infections. Although this new approach might be more sensitive and specific than culture-based state-of-the-art technologies, additional clinical trials are needed to exactly define the performance as well as clinical value of a NGS-based approach.

Methods: Next GeneSiS is a prospective, observational, noninterventional, multicenter study to assess the diagnostic performance of a NGS-based approach for the detection of relevant infecting organisms in patients with suspected or proven sepsis [according to recent sepsis definitions (sepsis-3)] by the use of the quantitative sepsis indicating quantifier (SIQ) score in comparison to standard (culture-based) microbiological diagnostics. The clinical value of this NGS-based approach will be estimated by a panel of independent clinical specialists, retrospectively identifying potential changes in patients' management based on NGS results. Further subgroup analyses will focus on the clinical value especially for patients suffering from a failure of empiric treatment within the first 3 days after onset [as assessed by death of the patient or lack of improvement of the patient's clinical condition (in terms of an inadequate decrease of SOFA-score) or persistent high procalcitonin levels].

Discussion: This prospective, observational, noninterventional, multicenter study for the first time investigates the performance as well as the clinical value of a NGS-based approach for the detection of bacteremia in patients with sepsis and may therefore be a pivotal step toward the clinical use of NGS in this indication.

Trial registration: DRKS-ID: DRKS00011911 (registered October 9, 2017) https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL_ID=DRKS00011911; ClinicalTrials.gov Identifier: NCT03356249 (registered November 29, 2017) https://ichgcp.net/clinical-trials-registry/NCT03356249.

Conflict of interest statement

The authors have no conflicts of interest.

Figures

Figure 1
Figure 1
Detailed flow chart of specific procedures, assessments and visits (Spirit figure). PCT = procalcitonin.

References

    1. Mayr FB, Yende S, Angus DC. Epidemiology of severe sepsis. Virulence 2014;5:4–11.
    1. Walkey AJ, Wiener RS, Lindenauer PK. Utilization patterns and outcomes associated with central venous catheter in septic shock: a population-based study. Crit Care Med 2013;41:1450–7.
    1. SepNet Critical Care Trials Group. Incidence of severe sepsis and septic shock in German intensive care units: the prospective, multicentre INSEP study. Intensive Care Med 2016;42:1980–9.
    1. Dellinger RP, Levy MM, Rhodes A, et al. Surviving sepsis campaign: international guidelines for management of severe sepsis and septic shock: 2012. Crit Care Med 2013;41:580–637.
    1. Vincent JL, Brealey D, Libert N, et al. Rapid diagnosis of infection in the critically ill, a multicenter study of molecular detection in bloodstream infections, pneumonia, and sterile site infections. Crit Care Med 2015;43:2283–91.
    1. Bacconi A, Richmond GS, Baroldi MA, et al. Improved sensitivity for molecular detection of bacterial and Candida infections in blood. J Clin Microbiol 2014;52:3164–74.
    1. Ecker DJ, Sampath R, Li H, et al. New technology for rapid molecular diagnosis of bloodstream infections. Expert Rev Mol Diagn 2010;10:399–415.
    1. Eshoo MW, Crowder CD, Li H, et al. Detection and identification of Ehrlichia species in blood by use of PCR and electrospray ionization mass spectrometry. J Clin Microbiol 2010;48:472–8.
    1. Kaleta EJ, Clark AE, Cherkaoui A, et al. Comparative analysis of PCR-electrospray ionization/mass spectrometry (MS) and MALDI-TOF/MS for the identification of bacteria and yeast from positive blood culture bottles. Clin Chem 2011;57:1057–67.
    1. Kaleta EJ, Clark AE, Johnson DR, et al. Use of PCR coupled with electrospray ionization mass spectrometry for rapid identification of bacterial and yeast bloodstream pathogens from blood culture bottles. J Clin Microbiol 2011;49:345–53.
    1. Grumaz S, Stevens P, Grumaz C, et al. Next-generation sequencing diagnostics of bacteremia in septic patients. Genome Med 2016;8:73.
    1. Decker SO, Sigl A, Grumaz C, et al. Immune-response patterns and next generation sequencing diagnostics for the detection of mycoses in patients with septic shock-results of a combined clinical and experimental investigation. Int J Mol Sci 2017;18:pii: E1796.
    1. Singer M, Deutschman CS, Seymour CW, et al. The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3). JAMA 2016;315:801–10.
    1. Gumbinger C, Hug A, Murle B, et al. Early blood-based microbiological testing is ineffective in severe stroke patients. J Neurol Sci 2013;325:46–50.
    1. Brenner T, Rosenhagen C, Hornig I, et al. Viral infections in septic shock (VISS-trial)-crosslinks between inflammation and immunosuppression. J Surg Res 2012;176:571–82.
    1. Mischnik A, Mieth M, Busch CJ, et al. First evaluation of automated specimen inoculation for wound swab samples by use of the Previ Isola system compared to manual inoculation in a routine laboratory: finding a cost-effective and accurate approach. J Clin Microbiol 2012;50:2732–6.
    1. Mischnik A, Trampe M, Zimmermann S. Evaluation of the impact of automated specimen inoculation, using Previ Isola, on the quality of and technical time for stool cultures. Ann Lab Med 2015;35:82–8.
    1. Horie M, Honda T, Suzuki Y, et al. Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature 2010;463:84–7.
    1. Salter SJ, Cox MJ, Turek EM, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 2014;12:87.
    1. De Pauw B, Walsh TJ, Donnelly JP, et al. Revised definitions of invasive fungal disease from the European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) Consensus Group. Clin Infect Dis 2008;46:1813–21.
    1. GCP Ordinance (GCP-Verordnung, GCP-V) 2004.
    1. ICH. E6(R1): International Conference on Harmonisation Tripartite Guideline: Good Clinical Practice (1996). 1996. Available at: . Accessed May 6, 2016.
    1. World Medical A. World Medical Association Declaration of Helsinki: ethical principles for medical research involving human subjects. JAMA 2013;310:2191–4.
    1. Federal Data Protection Act (Bundesdatenschutzgesetz, BDSG). 1990. .
    1. Brunkhorst FM, Oppert M, Marx G, et al. Effect of empirical treatment with moxifloxacin and meropenem vs meropenem on sepsis-related organ dysfunction in patients with severe sepsis: a randomized trial. JAMA 2012;307:2390–9.
    1. Engel C, Brunkhorst FM, Bone HG, et al. Epidemiology of sepsis in Germany: results from a national prospective multicenter study. Intensive Care Med 2007;33:606–18.
    1. Schmitz RP, Keller PM, Baier M, et al. Quality of blood culture testing: a survey in intensive care units and microbiological laboratories across four European countries. Crit Care 2013;17:R248.
    1. Kirn TJ, Weinstein MP. Update on blood cultures: how to obtain, process, report, and interpret. Clin Microbiol Infect 2013;19:513–20.
    1. Be NA, Allen JE, Brown TS, et al. Microbial profiling of combat wound infection through detection microarray and next-generation sequencing. J Clin Microbiol 2014;52:2583–94.
    1. Brown JR, Morfopoulou S, Hubb J, et al. Astrovirus VA1/HMO-C: an increasingly recognized neurotropic pathogen in immunocompromised patients. Clin Infect Dis 2015;60:881–8.
    1. Kommedal O, Wilhelmsen MT, Skrede S, et al. Massive parallel sequencing provides new perspectives on bacterial brain abscesses. J Clin Microbiol 2014;52:1990–7.
    1. Naccache SN, Peggs KS, Mattes FM, et al. Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing. Clin Infect Dis 2015;60:919–23.
    1. Wilson MR, Naccache SN, Samayoa E, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med 2014;370:2408–17.
    1. Naccache SN, Federman S, Veeraraghavan N, et al. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res 2014;24:1180–92.
    1. Strong MJ, Xu G, Morici L, et al. Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples. PLoS Pathog 2014;10:e1004437.

Source: PubMed

Patrocinadores e Colaboradores

Condições médicas

Intervenções de drogas

3
Se inscrever