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Blood transcriptomic discrimination of bacterial and viral infections in the emergency department: a multi-cohort observational validation study.

ABSTRACT: BACKGROUND:There is an urgent need to develop biomarkers that stratify risk of bacterial infection in order to support antimicrobial stewardship in emergency hospital admissions. METHODS:We used computational machine learning to derive a rule-out blood transcriptomic signature of bacterial infection (SeptiCyte™ TRIAGE) from eight published case-control studies. We then validated this signature by itself in independent case-control data from more than 1500 samples in total, and in combination with our previously published signature for viral infections (SeptiCyte™ VIRUS) using pooled data from a further 1088 samples. Finally, we tested the performance of these signatures in a prospective observational cohort of emergency department (ED) patients with fever, and we used the combined SeptiCyte™ signature in a mixture modelling approach to estimate the prevalence of bacterial and viral infections in febrile ED patients without microbiological diagnoses. RESULTS:The combination of SeptiCyte™ TRIAGE with our published signature for viral infections (SeptiCyte™ VIRUS) discriminated bacterial and viral infections in febrile ED patients, with a receiver operating characteristic area under the curve of 0.95 (95% confidence interval 0.90-1), compared to 0.79 (0.68-0.91) for WCC and 0.73 (0.61-0.86) for CRP. At pre-test probabilities 0.35 and 0.72, the combined SeptiCyte™ score achieved a negative predictive value for bacterial infection of 0.97 (0.90-0.99) and 0.86 (0.64-0.96), compared to 0.90 (0.80-0.94) and 0.66 (0.48-0.79) for WCC and 0.88 (0.69-0.95) and 0.60 (0.31-0.72) for CRP. In a mixture modelling approach, the combined SeptiCyte™ score estimated that 24% of febrile ED cases receiving antibacterials without a microbiological diagnosis were due to viral infections. Our analysis also suggested that a proportion of patients with bacterial infection recovered without antibacterials. CONCLUSIONS:Blood transcriptional biomarkers offer exciting opportunities to support precision antibacterial prescribing in ED and improve diagnostic classification of patients without microbiologically confirmed infections.

SUBMITTER: Sampson D

PROVIDER: S-EPMC7372897 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Blood transcriptomic discrimination of bacterial and viral infections in the emergency department: a multi-cohort observational validation study.

Sampson Dayle D Yager Thomas D TD Fox Brian B Shallcross Laura L McHugh Leo L Seldon Therese T Rapisarda Antony A Hendriks Roslyn A RA Brandon Richard B RB Navalkar Krupa K Simpson Nandi N Stafford Sian S Gil Eliza E Venturini Cristina C Tsaliki Evi E Roe Jennifer J Chain Benjamin B Noursadeghi Mahdad M

BMC medicine 20200721 1

<h4>Background</h4>There is an urgent need to develop biomarkers that stratify risk of bacterial infection in order to support antimicrobial stewardship in emergency hospital admissions.<h4>Methods</h4>We used computational machine learning to derive a rule-out blood transcriptomic signature of bacterial infection (SeptiCyte™ TRIAGE) from eight published case-control studies. We then validated this signature by itself in independent case-control data from more than 1500 samples in total, and in ...[more]

PMID: 32690014

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Project description:BackgroundWhether or not to administer antibiotics is a common and challenging clinical decision in patients with suspected infections presenting to the emergency department (ED). We prospectively validate InSep, a 29-mRNA blood-based host response test for the prediction of bacterial and viral infections.MethodsThe PROMPT trial is a prospective, non-interventional, multi-center clinical study that enrolled 397 adult patients presenting to the ED with signs of acute infection and at least one vital sign change. The infection status was adjudicated using chart review (including a syndromic molecular respiratory panel, procalcitonin and C-reactive protein) by three infectious disease physicians blinded to InSep results. InSep (version BVN-2) was performed using PAXgene Blood RNA processed and quantified on NanoString nCounter SPRINT. InSep results (likelihood of bacterial and viral infection) were compared to the adjudicated infection status.ResultsSubject mean age was 64 years, comorbidities were significant for diabetes (17.1%), chronic obstructive pulmonary disease (13.6%), and severe neurological disease (6.8%); 16.9% of subjects were immunocompromised. Infections were adjudicated as bacterial (14.1%), viral (11.3%) and noninfected (0.25%): 74.1% of subjects were adjudicated as indeterminate. InSep distinguished bacterial vs. viral/noninfected patients and viral vs. bacterial/noninfected patients using consensus adjudication with AUROCs of 0.94 (95% CI 0.90-0.99) and 0.90 (95% CI 0.83-0.96), respectively. AUROCs for bacterial vs. viral/noninfected patients were 0.88 (95% CI 0.79-0.96) for PCT, 0.80 (95% CI 0.72-89) for CRP and 0.78 (95% CI 0.69-0.87) for white blood cell counts (of note, the latter biomarkers were provided as part of clinical adjudication). To enable clinical actionability, InSep incorporates score cutoffs to allocate patients into interpretation bands. The Very Likely (rule in) InSep bacterial band showed a specificity of 98% compared to 94% for the corresponding PCT band (> 0.5 µg/L); the Very Unlikely (rule-out) band showed a sensitivity of 95% for InSep compared to 86% for PCT. For the detection of viral infections, InSep demonstrated a specificity of 93% for the Very Likely band (rule in) and a sensitivity of 96% for the Very Unlikely band (rule out).ConclusionsInSep demonstrated high accuracy for predicting the presence of both bacterial and viral infections in ED patients with suspected acute infections or suspected sepsis. When translated into a rapid, point-of-care test, InSep will provide ED physicians with actionable results supporting early informed treatment decisions to improve patient outcomes while upholding antimicrobial stewardship. Registration number at Clinicaltrials.gov NCT03295825.

Project description:IntroductionAcute bacterial skin and skin structure infections (ABSSSIs) are frequently treated in emergency departments (EDs) or observation units (OUs) initially with intravenous (IV) antibiotics before discharge on oral therapy. This study aims to describe ABSSSI patients discharged directly from EDs/OUs.MethodsThis is a retrospective cohort study of patients with ABSSSIs treated in EDs/OUs of the Detroit Medical Center from 2012 to 2014. Adults with less than 24 h of IV antibiotics without hospital admission were included. Demographics, clinical characteristics, and severity were compared between ED and OU patients. Resource utilization, including tissue and blood cultures, and use of radiographic analysis was also collected. The primary outcome was 96-h ED revisit/hospitalization.ResultsAnalysis included 308 patients; 219 ED and 89 OU. OU patients were significantly more likely to be obese, have COPD/asthma, be diagnosed with cellulitis, and meet at least one systemic inflammatory response syndrome (SIRS) criterion. Tissue cultures were obtained in 21.7% of abscesses in the ED; 67.9% were in uncomplicated abscesses. In the OU tissue cultures were obtained in 48.8% of abscesses and 37.5% were uncomplicated cases. Blood cultures were drawn in 18.3% of ED patients and 56.2% of OU patients, not significantly associated with the presence of SIRS criteria. Radiology was used in the diagnosis of ABSSSIs in 33.5% of ED versus 69.5% OU patients (p < 0.001), Plain film radiograph being the most common. Thirty patients revisited the ED or required hospitalization within 96 h, 23 from the ED (p = 0.479). Prior history of ABSSSI (adjusted odds ratio [aOR] = 2.382, 95% confidence interval [CI] 1.264-6.346) and location on torso/buttocks (aOR = 2.355, 95% CI 1.067-5.197) were independent predictors.ConclusionsThe low rate of ED revisit/hospitalization supports the use of OUs for low acuity ABSSSIs requiring initial IV therapy. Resource utilization within EDs/OUs for the management of ABSSSIs needs to be evaluated for unnecessary testing/procures.

Dataset Information

Blood transcriptomic discrimination of bacterial and viral infections in the emergency department: a multi-cohort observational validation study.

Publications

Blood transcriptomic discrimination of bacterial and viral infections in the emergency department: a multi-cohort observational validation study.

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