Discriminating Bacterial and Viral Infection Using a Rapid Host Gene Expression Test.

OBJECTIVES: Host gene expression signatures discriminate bacterial and viral infection but have not been translated to a clinical test platform. This study enrolled an independent cohort of patients to describe and validate a first-in-class host response bacterial/viral test. DESIGN: Subjects were recruited from 2006 to 2016. Enrollment blood samples were collected in an RNA preservative and banked for later testing. The reference standard was an expert panel clinical adjudication, which was blinded to gene expression and procalcitonin results. SETTING: Four U.S. emergency departments. PATIENTS: Six-hundred twenty-three subjects with acute respiratory illness or suspected sepsis. INTERVENTIONS: Forty-five-transcript signature measured on the BioFire FilmArray System (BioFire Diagnostics, Salt Lake City, UT) in ~45 minutes. MEASUREMENTS AND MAIN RESULTS: Host response bacterial/viral test performance characteristics were evaluated in 623 participants (mean age 46 yr; 45% male) with bacterial infection, viral infection, coinfection, or noninfectious illness. Performance of the host response bacterial/viral test was compared with procalcitonin. The test provided independent probabilities of bacterial and viral infection in ~45 minutes. In the 213-subject training cohort, the host response bacterial/viral test had an area under the curve for bacterial infection of 0.90 (95% CI, 0.84-0.94) and 0.92 (95% CI, 0.87-0.95) for viral infection. Independent validation in 209 subjects revealed similar performance with an area under the curve of 0.85 (95% CI, 0.78-0.90) for bacterial infection and 0.91 (95% CI, 0.85-0.94) for viral infection. The test had 80.1% (95% CI, 73.7-85.4%) average weighted accuracy for bacterial infection and 86.8% (95% CI, 81.8-90.8%) for viral infection in this validation cohort. This was significantly better than 68.7% (95% CI, 62.4-75.4%) observed for procalcitonin (p < 0.001). An additional cohort of 201 subjects with indeterminate phenotypes (coinfection or microbiology-negative infections) revealed similar performance. CONCLUSIONS: The host response bacterial/viral measured using the BioFire System rapidly and accurately discriminated bacterial and viral infection better than procalcitonin, which can help support more appropriate antibiotic use.

A Patient Reported Approach to Identify Medical Errors and Improve Patient Safety in the Emergency Department.

OBJECTIVE: Medical errors in the emergency department (ED) occur frequently. Yet, common adverse event detection methods, such as voluntary reporting, miss 90% of adverse events. Our objective was to demonstrate the use of patient-reported data in the ED to assess patient safety, including medical errors. METHODS: Analysis of patient-reported survey data collected over a 1-year period in a large, academic emergency department. All patients who provided a valid e-mail or cell phone number received a brief electronic survey within 24 hours of their ED encounter by e-mail or text message with Web link. Patients were asked about ED safety-related processes. RESULTS: From Aug 2012 to July 2013, we sent 52,693 surveys and received 7103 responses (e-mail response rate 25.8%), including 2836 free-text comments (44% of respondents). Approximately 242 (8.5%) of 2836 comments were classified as potential safety issues, including 12 adverse events, 40 near-misses, 23 errors with minimal risk of harm, and 167 general safety issues (eg, gaps in care transitions). Of the 40 near misses, 35 (75.0%) of 40 were preventable. Of the 52 adverse events or near misses, 5 (9.6%) were also identified via an existing patient occurrence reporting system. CONCLUSIONS: A patient-reported approach to assess ED-patient safety yields important, complementary, and potentially actionable safety information.

Post-discharge Health Services Use for Patients with Serious Mental Illness Treated at an Emergency Department Versus a Dedicated Community Mental Health Center.

Emergency Medical Service (EMS) alternative destination programs may lead to improved care quality among those experiencing mental health crises but the association with cost and emergency department (ED) recidivism remains unexamined. We compare rates of post-discharge health services use and Medicaid spending among patients transported to an ED or community mental health center (CMHC) finding higher ED recidivism for patient treated in the ED, compared to those treated in a CMHC (68% vs 34%, p < 0.001). There were no differences in Medicaid spending or health services use post-discharge suggesting EMS-operated alternative destination programs may be cost-neutral for Medicaid programs.

Validation of a host response test to distinguish bacterial and viral respiratory infection.

BACKGROUND: Distinguishing bacterial and viral respiratory infections is challenging. Novel diagnostics based on differential host gene expression patterns are promising but have not been translated to a clinical platform nor extensively tested. Here, we validate a microarray-derived host response signature and explore performance in microbiology-negative and coinfection cases. METHODS: Subjects with acute respiratory illness were enrolled in participating emergency departments. Reference standard was an adjudicated diagnosis of bacterial infection, viral infection, both, or neither. An 87-transcript signature for distinguishing bacterial, viral, and noninfectious illness was measured from peripheral blood using RT-PCR. Performance characteristics were evaluated in subjects with confirmed bacterial, viral, or noninfectious illness. Subjects with bacterial-viral coinfection and microbiologically-negative suspected bacterial infection were also evaluated. Performance was compared to procalcitonin. FINDINGS: 151 subjects with microbiologically confirmed, single-etiology illness were tested, yielding AUROCs 0•85-0•89 for bacterial, viral, and noninfectious illness. Accuracy was similar to procalcitonin (88% vs 83%, p = 0•23) for bacterial vs. non-bacterial infection. Whereas procalcitonin cannot distinguish viral from non-infectious illness, the RT-PCR test had 81% accuracy in making this determination. Bacterial-viral coinfection was subdivided. Among 19 subjects with bacterial superinfection, the RT-PCR test identified 95% as bacterial, compared to 68% with procalcitonin (p = 0•13). Among 12 subjects with bacterial infection superimposed on chronic viral infection, the RT-PCR test identified 83% as bacterial, identical to procalcitonin. 39 subjects had suspected bacterial infection; the RT-PCR test identified bacterial infection more frequently than procalcitonin (82% vs 64%, p = 0•02). INTERPRETATION: The RT-PCR test offered similar diagnostic performance to procalcitonin in some subgroups but offered better discrimination in others such as viral vs. non-infectious illness and bacterial/viral coinfection. Gene expression-based tests could impact decision-making for acute respiratory illness as well as a growing number of other infectious and non-infectious diseases.

Patient-Centered Values and Experiences with Emergency Department and Mental Health Crisis Care.

Little is known about what patients value in psychiatric crisis services or how they compare community-based services with those received in the emergency department. Three focus groups (n = 27) were held of participants who had received psychiatric crisis services in emergency departments or a community mental health center. Participants described care experiences and preferences. Focus groups were audio recorded, transcribed, and coded using a value-based lens. Themes included appreciation for feeling respected, basic comforts, and shared decision-making as foundations of quality care. Participants preferred the community mental health center. Research should address long-term outcomes to motivate change in psychiatric crisis care.

Acute Crisis Care for Patients with Mental Health Crises: Initial Assessment of an Innovative Prehospital Alternative Destination Program in North Carolina.

OBJECTIVE: Emergency Departments (ED) are overburdened with patients experiencing acute mental health crises. Pre-hospital transport by Emergency Medical Services (EMS) to community mental health and substance abuse treatment facilities could reduce ED utilization and costs. Our objective was to describe characteristics, treatment, and outcomes of acute mental health crises patients who were transported by EMS to an acute crisis unit at WakeBrook, a North Carolina community mental health center. METHODS: We performed a retrospective cohort study of patients diverted to WakeBrook by EMS from August 2013-July 2014. We abstracted data from WakeBrook medical records and used descriptive statistics to quantify patient characteristics, diagnoses, length of stay (LOS), and 30-day recidivism. RESULTS: A total of 226 EMS patients were triaged at WakeBrook. The median age was 38 years, 55% were male, 58% were white, and 38% were uninsured. The most common chief complaints were suicidal ideation or self-harm (46%) and substance abuse (19%). The most common diagnoses were substance-related and addictive disorders (42%), depressive disorders (32%), and schizophrenia spectrum and other psychotic disorders (22%). Following initial evaluation, 28% of patients were admitted to facilities within WakeBrook, 40% were admitted to external psychiatric facilities, 18% were stabilized and discharged home, 5% were transferred to an ED within 4 hours for further medical evaluation, and 5% refused services. The median LOS at WakeBrook prior to disposition was 12.0 hours (IQR 5.4-21.6). Over a 30-day follow-up period, 60 patients (27%) had a return visit to the ED or WakeBrook for a mental health issue. CONCLUSIONS: A dedicated community mental health center is able to treat patients experiencing acute mental health crises. LOS times were significantly shorter compared to regional EDs. Successful broader programmatic implementation could improve care quality and significantly reduce the volume of patients treated in the ED for acute mental health disorders.

Host gene expression classifiers diagnose acute respiratory illness etiology.

Acute respiratory infections caused by bacterial or viral pathogens are among the most common reasons for seeking medical care. Despite improvements in pathogen-based diagnostics, most patients receive inappropriate antibiotics. Host response biomarkers offer an alternative diagnostic approach to direct antimicrobial use. This observational cohort study determined whether host gene expression patterns discriminate noninfectious from infectious illness and bacterial from viral causes of acute respiratory infection in the acute care setting. Peripheral whole blood gene expression from 273 subjects with community-onset acute respiratory infection (ARI) or noninfectious illness, as well as 44 healthy controls, was measured using microarrays. Sparse logistic regression was used to develop classifiers for bacterial ARI (71 probes), viral ARI (33 probes), or a noninfectious cause of illness (26 probes). Overall accuracy was 87% (238 of 273 concordant with clinical adjudication), which was more accurate than procalcitonin (78%, P < 0.03) and three published classifiers of bacterial versus viral infection (78 to 83%). The classifiers developed here externally validated in five publicly available data sets (AUC, 0.90 to 0.99). A sixth publicly available data set included 25 patients with co-identification of bacterial and viral pathogens. Applying the ARI classifiers defined four distinct groups: a host response to bacterial ARI, viral ARI, coinfection, and neither a bacterial nor a viral response. These findings create an opportunity to develop and use host gene expression classifiers as diagnostic platforms to combat inappropriate antibiotic use and emerging antibiotic resistance.

Potential Cost-effectiveness of Early Identification of Hospital-acquired Infection in Critically Ill Patients.

RATIONALE: Limitations in methods for the rapid diagnosis of hospital-acquired infections often delay initiation of effective antimicrobial therapy. New diagnostic approaches offer potential clinical and cost-related improvements in the management of these infections. OBJECTIVES: We developed a decision modeling framework to assess the potential cost-effectiveness of a rapid biomarker assay to identify hospital-acquired infection in high-risk patients earlier than standard diagnostic testing. METHODS: The framework includes parameters representing rates of infection, rates of delayed appropriate therapy, and impact of delayed therapy on mortality, along with assumptions about diagnostic test characteristics and their impact on delayed therapy and length of stay. Parameter estimates were based on contemporary, published studies and supplemented with data from a four-site, observational, clinical study. Extensive sensitivity analyses were performed. The base-case analysis assumed 17.6% of ventilated patients and 11.2% of nonventilated patients develop hospital-acquired infection and that 28.7% of patients with hospital-acquired infection experience delays in appropriate antibiotic therapy with standard care. We assumed this percentage decreased by 50% (to 14.4%) among patients with true-positive results and increased by 50% (to 43.1%) among patients with false-negative results using a hypothetical biomarker assay. Cost of testing was set at $110/d. MEASUREMENTS AND MAIN RESULTS: In the base-case analysis, among ventilated patients, daily diagnostic testing starting on admission reduced inpatient mortality from 12.3 to 11.9% and increased mean costs by $1,640 per patient, resulting in an incremental cost-effectiveness ratio of $21,389 per life-year saved. Among nonventilated patients, inpatient mortality decreased from 7.3 to 7.1% and costs increased by $1,381 with diagnostic testing. The resulting incremental cost-effectiveness ratio was $42,325 per life-year saved. Threshold analyses revealed the probabilities of developing hospital-acquired infection in ventilated and nonventilated patients could be as low as 8.4 and 9.8%, respectively, to maintain incremental cost-effectiveness ratios less than $50,000 per life-year saved. CONCLUSIONS: Development and use of serial diagnostic testing that reduces the proportion of patients with delays in appropriate antibiotic therapy for hospital-acquired infections could reduce inpatient mortality. The model presented here offers a cost-effectiveness framework for future test development.

Renal systems biology of patients with systemic inflammatory response syndrome.

A systems biology approach was used to comprehensively examine the impact of renal disease and hemodialysis (HD) on patient response during critical illness. To achieve this, we examined the metabolome, proteome, and transcriptome of 150 patients with critical illness, stratified by renal function. Quantification of plasma metabolites indicated greater change as renal function declined, with the greatest derangements in patients receiving chronic HD. Specifically, 6 uremic retention molecules, 17 other protein catabolites, 7 modified nucleosides, and 7 pentose phosphate sugars increased as renal function declined, consistent with decreased excretion or increased catabolism of amino acids and ribonucleotides. Similarly, the proteome showed increased levels of low-molecular-weight proteins and acute-phase reactants. The transcriptome revealed a broad-based decrease in mRNA levels among patients on HD. Systems integration revealed an unrecognized association between plasma RNASE1 and several RNA catabolites and modified nucleosides. Further, allantoin, N1-methyl-4-pyridone-3-carboxamide, and N-acetylaspartate were inversely correlated with the majority of significantly downregulated genes. Thus, renal function broadly affected the plasma metabolome, proteome, and peripheral blood transcriptome during critical illness; changes were not effectively mitigated by hemodialysis. These studies allude to several novel mechanisms whereby renal dysfunction contributes to critical illness.

Organizational characteristics and patient experiences with hospital care: a survey study of hospital chief patient experience officers.

Beginning in fiscal year 2013, scores based on the Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) constitute 30% of incentive-based payments from Medicare's Value-Based Purchasing (VBP) initiative. Yet there is little empirical work to understand hospital approaches to improving the patient experience. In this study, chief patient experience officers at 416 VHA hospitals were surveyed to assess the relationship between organizational characteristics and publicly reported HCAHPS scores. Of 416 institutions, 143 (34.4%) participated. Respondents reported that boards (68%) and chief executive officers (81%) viewed the patient experience as extremely important. In contrast, they reported that in only 15% and 34% of hospitals, respectively, physicians and nurses were supportive of efforts to improve the patient experience. Hospitals with collaborative cultures and higher physician engagement had higher VBP total HCAHPS scores (6.9 points and 8.2 points higher, respectively; both P < .05). These areas should be addressed to improve the patient experience in provider organizations.

An integrated transcriptome and expressed variant analysis of sepsis survival and death.

BACKGROUND: Sepsis, a leading cause of morbidity and mortality, is not a homogeneous disease but rather a syndrome encompassing many heterogeneous pathophysiologies. Patient factors including genetics predispose to poor outcomes, though current clinical characterizations fail to identify those at greatest risk of progression and mortality. METHODS: The Community Acquired Pneumonia and Sepsis Outcome Diagnostic study enrolled 1,152 subjects with suspected sepsis. We sequenced peripheral blood RNA of 129 representative subjects with systemic inflammatory response syndrome (SIRS) or sepsis (SIRS due to infection), including 78 sepsis survivors and 28 sepsis non-survivors who had previously undergone plasma proteomic and metabolomic profiling. Gene expression differences were identified between sepsis survivors, sepsis non-survivors, and SIRS followed by gene enrichment pathway analysis. Expressed sequence variants were identified followed by testing for association with sepsis outcomes. RESULTS: The expression of 338 genes differed between subjects with SIRS and those with sepsis, primarily reflecting immune activation in sepsis. Expression of 1,238 genes differed with sepsis outcome: non-survivors had lower expression of many immune function-related genes. Functional genetic variants associated with sepsis mortality were sought based on a common disease-rare variant hypothesis. VPS9D1, whose expression was increased in sepsis survivors, had a higher burden of missense variants in sepsis survivors. The presence of variants was associated with altered expression of 3,799 genes, primarily reflecting Golgi and endosome biology. CONCLUSIONS: The activation of immune response-related genes seen in sepsis survivors was muted in sepsis non-survivors. The association of sepsis survival with a robust immune response and the presence of missense variants in VPS9D1 warrants replication and further functional studies. TRIAL REGISTRATION: ClinicalTrials.gov NCT00258869. Registered on 23 November 2005.

Use of prehospital 12-lead electrocardiography and treatment times among ST-elevation myocardial infarction patients with atypical symptoms.

OBJECTIVES: Guidelines advise that a prehospital electrocardiogram (ECG) should be obtained in any patients with chest pain, yet up to 20% of patients with ST-elevation myocardial infarction (STEMI) do not present with chest pain. The objective was to determine the association of atypical presentations in the prehospital setting on the likelihood of receiving a prehospital ECG and subsequent time to reperfusion therapy. METHODS: This study used a data set that linked prehospital medical information from a statewide EMS data system with a clinical registry of treatment and outcomes data for patients with STEMI. Among 2,639 STEMI patients from 2008 to 2010, the association between non-chest pain presentations, prehospital ECG use, and reperfusion times among patients undergoing primary percutaneous coronary intervention (PCI) were examined. Inverse probability weights were used to account for observed baseline confounders. RESULTS: Overall, 318 of 2,639 patients (12.1%) presented without chest pain. A prehospital ECG was obtained in 2,021 of 2,321 (87.1%) patients with chest pain compared with only 230 of 318 (72.3%) without chest pain (odds ratio [OR] = 2.24, 95% confidence interval [CI] = 1.69 to 2.98). Among patients without chest pain, those who received a prehospital ECG had significantly shorter first medical contact (FMC) to device times (30.9% < 90 minutes vs. 11.4% > 90 minutes, adjusted OR = 2.81, 95% CI = 1.29 to 6.11, p < 0.01). CONCLUSIONS: Over one-quarter of STEMI patients presenting without chest pain did not receive prehospital ECGs and had significantly longer FMC to device times. Future efforts are needed to promote the use of prehospital ECGs to achieve more rapid identification of STEMI patients with atypical presentations in the prehospital setting.

The mis-measure of physician performance.

The Affordable Care Act directs the Secretary of Health and Human Services to compare individual physicians using patient experience measures. This policy initiative will utilize the Clinician and Group Consumer Assessment of Healthcare Providers and Systems (CG-CAHPS) survey program. It will impact over 700,000 eligible physicians and will be tied to reimbursement and the Centers for Medicare and Medicaid Services' Physician Compare reporting feature starting in 2015. We believe that the relevance of this framework to today's clinical environment is a critical issue to address before implementing this regulatory mandate. In this article we discuss our concerns about tying individual physician performance to CG-CAHPS scores, including: 1) intrinsic versus extrinsic approaches to assessing the patient experience, 2) measurement issues, and 3) unintended consequences. We also suggest an alternative pathway and opt-out mechanism to facilitate more rapid translation of service excellence into clinical practice.

Variation in the use of 12-lead electrocardiography for patients with chest pain by emergency medical services in North Carolina.

BACKGROUND: Prehospital 12-lead electrocardiography (ECG) is critical to timely STEMI care although its use remains inconsistent. Previous studies to identify reasons for failure to obtain a prehospital ECG have generally only focused on individual emergency medical service (EMS) systems in urban areas. Our study objective was to identify patient, geographic, and EMS agency-related factors associated with failure to perform a prehospital ECG across a statewide geography. METHODS AND RESULTS: We analyzed data from the Prehospital Medical Information System (PreMIS) in North Carolina from January 2008 to November 2010 for patients >30 years of age who used EMS and had a prehospital chief complaint of chest pain. Among 3.1 million EMS encounters, 134 350 patients met study criteria. From 2008-2010, 82 311 (61%) persons with chest pain received a prehospital ECG; utilization increased from 55% in 2008 to 65% in 2010 (trend P<0.001). Utilization by health referral region ranged from 22.9% to 74.2% and was lowest in rural areas. Men were more likely than women to have an ECG performed (63.0% vs 61.3%, adjusted RR 1.02, 95% CI 1.01 to 1.04). The certification-level of the EMS provider (paramedic vsbasic/intermediate) and system-level ECG equipment availability were the strongest predictors of ECG utilization. Persons in an ambulance with a certified paramedic were significantly more likely to receive a prehospital ECG than nonparamedics (RR 2.15, 95% CI 1.55, 2.99). CONCLUSIONS: Across a large geographic area prehospital ECG use increased significantly, although important quality improvement opportunities remain. Increasing ECG availability and improving EMS certification and training levels are needed to improve overall care and reduce rural-urban treatment differences.

An integrated clinico-metabolomic model improves prediction of death in sepsis.

Sepsis is a common cause of death, but outcomes in individual patients are difficult to predict. Elucidating the molecular processes that differ between sepsis patients who survive and those who die may permit more appropriate treatments to be deployed. We examined the clinical features and the plasma metabolome and proteome of patients with and without community-acquired sepsis, upon their arrival at hospital emergency departments and 24 hours later. The metabolomes and proteomes of patients at hospital admittance who would ultimately die differed markedly from those of patients who would survive. The different profiles of proteins and metabolites clustered into the following groups: fatty acid transport and ß-oxidation, gluconeogenesis, and the citric acid cycle. They differed consistently among several sets of patients, and diverged more as death approached. In contrast, the metabolomes and proteomes of surviving patients with mild sepsis did not differ from survivors with severe sepsis or septic shock. An algorithm derived from clinical features together with measurements of five metabolites predicted patient survival. This algorithm may help to guide the treatment of individual patients with sepsis.

Prehospital system delay in ST-segment elevation myocardial infarction care: a novel linkage of emergency medicine services and in hospital registry data.

BACKGROUND: Emergency medical services (EMS) are critical in the treatment of ST-segment elevation myocardial infarction (STEMI). Prehospital system delays are an important target for improving timely STEMI care, yet few limited data are available. METHODS: Using a deterministic approach, we merged EMS data from the North Carolina Pre-hospital Medical Information System (PreMIS) with data from the Reperfusion of Acute Myocardial Infarction in Carolina Emergency Departments-Emergency Response (RACE-ER) Project. Our sample included all patients with STEMI from June 2008 to October 2010 who arrived by EMS and who had primary percutaneous coronary intervention (PCI). Prehospital system delays were compared using both RACE-ER and PreMIS to examine agreement between the 2 data sources. RESULTS: Overall, 8,680 patients with STEMI in RACE-ER arrived at a PCI hospital by EMS; 21 RACE-ER hospitals and 178 corresponding EMS agencies across the state were represented. Of these, 6,010 (69%) patients were successfully linked with PreMIS. Linked and notlinked patients were similar. Overall, 2,696 patients were treated with PCI only and were taken directly to a PCI-capable hospital by EMS; 1,750 were transferred from a non-PCI facility. For those being transported directly to a PCI center, 53% reached the 90-minute target guideline goal. For those transferred from a non-PCI facility, 24% reached the 120-minute target goal for primary PCI. CONCLUSIONS: We successfully linked prehospital EMS data with in hospital clinical data. With this linked STEMI cohort, less than half of patients reach goals set by guidelines. Such a data source could be used for future research and quality improvement interventions.

Gene expression-based classifiers identify Staphylococcus aureus infection in mice and humans.

Staphylococcus aureus causes a spectrum of human infection. Diagnostic delays and uncertainty lead to treatment delays and inappropriate antibiotic use. A growing literature suggests the host's inflammatory response to the pathogen represents a potential tool to improve upon current diagnostics. The hypothesis of this study is that the host responds differently to S. aureus than to E. coli infection in a quantifiable way, providing a new diagnostic avenue. This study uses Bayesian sparse factor modeling and penalized binary regression to define peripheral blood gene-expression classifiers of murine and human S. aureus infection. The murine-derived classifier distinguished S. aureus infection from healthy controls and Escherichia coli-infected mice across a range of conditions (mouse and bacterial strain, time post infection) and was validated in outbred mice (AUC>0.97). A S. aureus classifier derived from a cohort of 94 human subjects distinguished S. aureus blood stream infection (BSI) from healthy subjects (AUC 0.99) and E. coli BSI (AUC 0.84). Murine and human responses to S. aureus infection share common biological pathways, allowing the murine model to classify S. aureus BSI in humans (AUC 0.84). Both murine and human S. aureus classifiers were validated in an independent human cohort (AUC 0.95 and 0.92, respectively). The approach described here lends insight into the conserved and disparate pathways utilized by mice and humans in response to these infections. Furthermore, this study advances our understanding of S. aureus infection; the host response to it; and identifies new diagnostic and therapeutic avenues.