Rapid diagnosis of sepsis using genomics

Developing faster and more accurate diagnosis of sepsis

Sepsis is a potentially life-threatening condition that occurs when the body's response to an infection damages its own tissues. Early treatment can improve the chance of survival.

This project looks at developing a novel laboratory approach for faster and better diagnosis and treatment of sepsis, based on whole genome sequencing combined with the use of dosing software.

Development of this novel rapid clinical service will reduce time to administer appropriate antibiotics and determine optimal dosing. The diagnostic accuracy of a real-time genomic sequencing approach compared to standard laboratory tests will also be evaluated.

The project aims to define a consistent and effective approach for fast diagnosis and treatment of sepsis and improve the health outcomes of critically ill patients with this condition.

Outcomes

  • Phase 1 involved recruitment of 136 eligible patients (145 patients tested, of which 44 had culture confirmed sepsis) across all sites – Royal Brisbane and Women’s Hospital, The Prince Charles Hospital, Princess Alexandra Hospital and Queensland Children’s Hospital. Patients had been admitted to paediatric or adult intensive care unit (ICU) at one of the participating recruitment centres with suspected sepsis with or without confirmed organ dysfunction.

  • The project will measure the time to administer effective antibiotics using whole genome sequencing combined with personalised dosing. It will also establish the accuracy of sepsis diagnosis using the rapid pathogen sequencing approach.

  • Phase 1 established a single database for data collection and clinical practice across participating institutions which will harmonise data collection and clinical practice across the participating institutions during the study.

  • The next steps include completion of health economic analysis and Phase 2 of the project, which will look at interventional rapid pathogen sequencing followed by Bayesian software guided dosing recommendations in 50 consecutive patients with suspected sepsis. Phase 2 will be conducted at four Brisbane sites and include a consumer engagement component.

  • This project has developed and tested a pathway for transfer of participant samples from four ICUs to the laboratory for genomic sequencing, and faster identification of pathogens. Bringing together a multi-disciplinary team, it is on the cusp of demonstrating how using novel diagnostics can inform the optimal therapeutic approach, in the hope of reducing antimicrobial resistance and superbugs, and achieving improved health outcomes for kids and adults with sepsis regardless of source of onset.

Project investigators

Project investigators engage with and draw on the expertise of partners within universities, research institutes, and hospital and health services around Queensland.

  • Professor Jason Roberts, The University of Queensland Centre for Clinical Research, Royal Brisbane and Women’s Hospital, Metro North Health (Lead, advice on dosing strategy)

  • Associate Professor Luregn Schlapbach, Children’s Health Queensland, The University of Queensland Centre for Child Health Research (Senior Staff Specialist Paediatric Intensive Care Unit, Medical Lead Paediatric Critical Care Research Group, Project Lead and Paediatric Intensive Care Unit Lead, Queensland Children’s Hospital)

  • Dr Adam Irwin, Children’s Health Queensland, The University of Queensland Centre for Clinical Research (Project Manager, Paediatric Infectious Diseases Specialist)

  • Professor Lachlan Coin, The University of Queensland Institute for Molecular Bioscience (Group Leader, bioinformatic expert)

  • Dr Patrick Harris, The University of Queensland Centre for Clinical Research, Pathology Queensland (Microbiology Specialist, Pathology Queensland Microbiology Lead)

  • Dr Menino Osbert Cotta, The University of Queensland Centre for Clinical Research (Clinical Pharmacist and Postdoctoral Research Fellow)

  • Professor Jeff Lipman, Royal Brisbane and Women’s Hospital (ICU Research Director, Royal Brisbane Women’s Hospital ICU Lead)

  • Associate Professor Peter Kruger, Princess Alexandra Hospital (Prince Alexandra Hospital ICU Lead)

  • Associate Professor Kiran Shekar, The Prince Charles Hospital (ICU Lead)

  • Kara Brady, The Prince Charles Hospital (Research Coordinator)

  • Associate Professor David Whiley, The University of Queensland, The Queensland Paediatric Infectious Diseases group (laboratory diagnostics)

  • Dr Seweryn Bialasiewicz, The Queensland Paediatric Infectious Diseases group (laboratory diagnostics)

  • Associate Professor Scott Beatson, The University Queensland, School of Chemistry and Molecular Bioscience (bioinformatics)

  • Professor David Paterson, The University of Queensland Centre for Clinical Research (infectious disease)

  • Associate Professor Julia Clark, Queensland Children’s Hospital (paediatric infectious disease)

  • Krispin Hajkowicz, Royal Brisbane and Women’s Hospital (Director Infectious Diseases Unit)

  • Dr Sainath Raman, Queensland Children’s Hospital (Paediatric ICU)

Project manager: Luminita Vlad, Centre of Research Excellence Manager, UQCCR, The University of Queensland

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