Table 1

Objectives, outcome measures and methods of analysis for Fast I(n)dentification of Pathogens in Neonates pilot study

ObjectiveOutcome measureMethod of analysis
Co-primary objectives
 1. Recruitment.Successful recruitment is defined as ≥80% of eligible patients.Proportion
 2. Sample collection.Successful sample collection is defined as ≥80% of the blood samples for recruited patients at the first time point.Proportion
 3. Ability to perform NGS on blood samples of premature and term neonates at MCH with suspected sepsis.Description of mechanical or process issuesDescriptive only
Secondary objectives
 1. To describe the blood NGS pathogen output in order to gain a preliminary understanding of the potential clinical role of NGS testing in neonates with suspected sepsis.NGS pathogen output (taxonomy, reads, plausibility from panel review)Descriptive statistics ± case discussions
 2. To describe the serum levels and diagnostic accuracy of biomarkers cfDNA and protein C at time points of 0 and 24 hours between neonates with clinical sepsis, culture-proven sepsis and without sepsis.Levels of blood cfDNA and protein C, sensitivity and specificity (%), likelihood ratiosDescriptive statistics, diagnostic accuracy measures with CIs
 3. To compare the sensitivity and specificity of NGS for bacterial identification compared with gold-standard aerobic blood culture.Sensitivity and specificity (%)Proportion and CIs
 4. To determine blood sample NGS laboratory process time.Process time from thawing sample to sequence acquisition (hours)Descriptive only
 5. To determine consent rate using an exception to consent (deferred consent).The target consent rate is ≥80% of families approachedProportion
  • cfDNA, cell-free DNA; CI, confidence interval; MCH, McMaster Children’s Hospital; NGS, next-generation sequencing.