Derivation, validation, and transcriptomic assessment of pediatric septic shock phenotypes identified through latent profile analyses: Results from a prospective multi-center observational cohort.

Background: Sepsis poses a grave threat, especially among children, but treatments are limited due to clinical and biological heterogeneity among patients. Thus, there is an urgent need for precise subclassification of patients to guide therapeutic interventions. Methods: We used clinical, laboratory, and biomarker data from a prospective multi-center pediatric septic shock cohort to derive phenotypes using latent profile analyses. Thereafter, we trained a support vector machine model to assign phenotypes in a hold-out validation set. We tested interactions between phenotypes and common sepsis therapies on clinical outcomes and conducted transcriptomic analyses to better understand the phenotype-specific biology. Finally, we compared whether newly identified phenotypes overlapped with established gene-expression endotypes and tested the utility of an integrated subclassification scheme. Findings: Among 1,071 patients included, we identified two phenotypes which we named 'inflamed' (19.5%) and an 'uninflamed' phenotype (80.5%). The 'inflamed' phenotype had an over 4-fold risk of 28-day mortality relative to those 'uninflamed'. Transcriptomic analysis revealed overexpression of genes implicated in the innate immune response and suggested an overabundance of developing neutrophils, pro-T/NK cells, and NK cells among those 'inflamed'. There was no significant overlap between endotypes and phenotypes. However, an integrated subclassification scheme demonstrated varying survival probabilities when comparing endophenotypes. Interpretation: Our research underscores the reproducibility of latent profile analyses to identify clinical and biologically informative pediatric septic shock phenotypes with high prognostic relevance. Pending validation, an integrated subclassification scheme, reflective of the different facets of the host response, holds promise to inform targeted intervention among those critically ill.

Cost Impact Model of a Novel Multi-mRNA Host Response Assay for Diagnosis and Risk Assessment of Acute Respiratory Tract Infections and Sepsis in the Emergency Department.

BACKGROUND: Early identification of acute infections and sepsis remains an unmet medical need. While early detection and initiation of treatment reduces mortality, inappropriate treatment leads to adverse events and the development of antimicrobial resistance. Current diagnostic and prognostic solutions, including procalcitonin, lack required accuracy. A novel blood-based host response test, HostDx™ Sepsis by Inflammatix, Inc., assesses the likelihood of a bacterial infection, the likelihood of a viral infection, and the severity of the condition. OBJECTIVES: We estimated the economic impact of adopting HostDx Sepsis testing among patients with suspected acute respiratory tract infection (ARTI) in the emergency department (ED). METHODS: Our cost impact model estimated costs for adult ED patients with suspected ARTI under the standard of care versus with the adoption of HostDx Sepsis from the perspective of US payers. Included costs were those assumed to be associated with an episode of sepsis diagnosis, management, and treatment. Projected accuracies for test predictions, disease prevalence, and clinical parameters was derived from patient-level meta-analysis data of randomized trials, supplemented with published performance data for HostDx Sepsis. One-way sensitivity analysis was performed on key input parameters. RESULTS: Compared to standard of care including procalcitonin, the superior test characteristics of HostDx Sepsis resulted in an average cost savings of approximately US$1974 per patient (-31.3%) exclusive of the cost of HostDx Sepsis. Reductions in hospital days (-0.80 days, -36.7%), antibiotic days (-1.49 days, -29.5%), and percent 30-day mortality (-1.67%, -13.64%) were driven by HostDx Sepsis providing fewer "noninformative" moderate risk predictions and more "certain" low- or high-risk predictions compared to standard of care, especially for patients who were not severely ill. These results were robust to changes in key parameters, including disease prevalence. CONCLUSIONS: Our model shows substantial savings associated with introduction of HostDx Sepsis among patients with ARTIs in EDs. These results need confirmation in interventional trials.

Assessment of Validity of a Blood-Based 3-Gene Signature Score for Progression and Diagnosis of Tuberculosis, Disease Severity, and Treatment Response.

Importance: The World Health Organization identified the need for a non-sputum-based triage test to identify those in need of further tuberculosis (TB) testing. Objective: To determine whether the 3-gene TB score can be a diagnostic tool throughout the course of TB disease, from latency to diagnosis to treatment response, and posttreatment residual inflammation. Design, Setting, and Participants: This nested case-control study analyzed the 3-gene TB score in 3 cohorts, each focusing on a different stage of TB disease: (1) the Adolescent Cohort Study profiled whole-blood samples from adolescents with latent Mycobacterium tuberculosis infection, some of which progressed to active TB (ATB), using RNA sequencing; (2) the Brazil Active Screen Study collected whole blood from an actively screened case-control cohort of adult inmates from 2 prisons in Mato Grosso do Sul, Brazil, for ATB from January 2016 to February 2016; and (3) the Catalysis Treatment Response Cohort (CTRC) identified culture-positive adults in primary health care clinics in Cape Town, South Africa, from 2005 to 2007 and collected whole blood for RNA sequencing from patients with ATB at diagnosis and weeks 1, 4, and 24. The CTRC patients also had positron emission tomography-computed tomography scans at diagnosis, week 4, and week 24. Analyses were performed from September 2017 to June 2018. Main Outcomes and Measures: A 3-gene messenger RNA expression score, measured by quantitative polymerase chain reaction or RNA sequencing, was evaluated for distinguishing the following: individuals who progressed to ATB from those who did not, individuals with ATB from those without, and individuals with slower treatment response during TB therapy. Results: Patients evaluated in this study included 144 adolescents from the Adolescent Cohort Study (aged 12-18 years; 96 female and 48 male), 81 adult prison inmates from the Brazil Active Screen Study (aged 20-72 years; 81 male), and 138 adult community members from the CTRC (aged 17-64 years; 81 female and 57 male). The 3-gene TB score identified progression from latent M tuberculosis infection to ATB 6 months prior to sputum conversion with 86% sensitivity and 84% specificity (area under the curve [AUC], 0.86; 95% CI, 0.77-0.96) and patients with ATB in the Brazil Active Screen Study cohort (AUC, 0.87; 95% CI, 0.78-0.95) and CTRC (AUC, 0.94; 95% CI, 0.88-0.99). It also identified CTRC patients with failed treatment at the end of treatment (AUC, 0.93; 95% CI, 0.83-1.00). Collectively, across all cohorts, the 3-gene TB score identified patients with ATB with 90% sensitivity, 70% specificity, and 99.3% negative predictive value at 4% prevalence. Conclusions and Relevance: Across 3 independent prospective cohorts, the 3-gene TB score approaches the World Health Organization target product profile benchmarks for non-sputum-based triage test with high negative predictive value. This gene expression diagnostic approach should be considered for further validation and future implementation.