Optimising Treatment Outcomes for Children and Adults Through Rapid Genome Sequencing of Sepsis Pathogens. A Study Protocol for a Prospective, Multi-Centre Trial (DIRECT)

Abstract

Background: Sepsis contributes significantly to morbidity and mortality globally. In Australia, 20,000 develop sepsis every year, resulting in 5,000 deaths, and more than AUD$846 million in expenditure. Prompt, appropriate antibiotic therapy is effective in improving outcomes in sepsis. Conventional culture-based methods to identify appropriate therapy have limited yield and take days to complete. Recently, nanopore technology has enabled rapid sequencing with real-time analysis of pathogen DNA. We set out to demonstrate the feasibility and diagnostic accuracy of pathogen sequencing direct from clinical samples, and estimate the impact of this approach on time to effective therapy when integrated with personalised software-guided antimicrobial dosing in children and adults on ICU with sepsis.

Methods: The DIRECT study is a pilot prospective, non-randomized multicentre trial of an integrated diagnostic and therapeutic algorithm combining rapid direct pathogen sequencing and software-guided, personalised antibiotic dosing in children and adults with sepsis on ICU.

Participants and interventions: DIRECT will collect microbiological and pharmacokinetic samples from approximately 200 children and adults with sepsis admitted to one of four ICUs in Brisbane. In Phase 1, we will evaluate Oxford Nanopore Technologies MinION sequencing direct from blood in 50 blood culture-proven sepsis patients recruited from consecutive patients with suspected sepsis. In Phase 2, a further 50 consecutive patients with suspected sepsis will be recruited in whom MinION sequencing will be combined with Bayesian software-guided (ID-ODS) personalised antimicrobial dosing.

Outcome measures: The primary outcome is time to effective antimicrobial therapy, defined as trough drug concentrations above the MIC of the pathogen. Secondary outcomes are diagnostic accuracy of MinION sequencing from whole blood, time to pathogen identification and susceptibility testing using sequencing direct from whole blood and from positive blood culture broth.

Discussion: Rapid pathogen sequencing coupled with antimicrobial dosing software has great potential to overcome the limitations of conventional diagnostics which often result in prolonged inappropriate antimicrobial therapy. Reduced time to optimal antimicrobial therapy may reduce sepsis mortality and ICU length of stay. This pilot study will yield key feasibility data to inform further, urgently needed sepsis studies. Phase 2 of the trial protocol is registered with the ANZCTR (ACTRN12620001122943).

Trial registration: Registered with the Australia New Zealand Clinical Trials Registry Number ACTRN12620001122943.

Keywords: antimicrobial resistance; antimicrobials; nanopore sequencing; personalised dosing; sepsis diagnostics; trial protocol.

Figure 1

Study flow diagram. Phase 1: In an initial observational phase of the study, participants will be recruited to a diagnostic accuracy study of MinION nanopore pathogen sequencing. The sample size for this phase of the study is 50 patients with blood culture-confirmed sepsis admitted to ICU. Phase 2: In Phase 2, consecutive patients with suspected sepsis admitted to ICU will undergo MinION nanopore pathogen sequencing integrated with personalised antibiotic therapy using a combination of Bayesian dosing software (ID-ODS™) and measured antibiotic plasma concentrations. A senior ICU pharmacist/clinician at each site will lead this software-guided intervention of antimicrobial dose optimisation. All dosing regimens will be checked by both the senior ICU pharmacist and attending ICU consultant prior to prescription. The final decision regarding the use of the optimised dosing of antibiotics will remain at the discretion of the attending ICU consultant. Software-guided dosing will continue until either: 1) the study antibiotic(s) have been ceased by the treating clinician, 2) the patient is discharged from ICU, 3) after 5 days of study antibiotic therapy. If antibiotic therapy is still required thereafter, dosing will be guided by the treating clinician. Adherence to dosing strategies informed by the dosing software will be supported by the use of senior ICU pharmacists trained in the use of this software-guided approach to antimicrobial dose optimisation. All dosing regimens will be checked by both the senior ICU pharmacist and attending ICU consultant prior to prescription, to ensure appropriateness and safety.