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Comparison of Automated Sepsis Identification Methods and Electronic Health Record-based Sepsis Phenotyping: Improving Case Identification Accuracy by Accounting for Confounding Comorbid Conditions.

ABSTRACT: To develop and evaluate a novel strategy that automates the retrospective identification of sepsis using electronic health record data. Design:Retrospective cohort study of emergency department and in-hospital patient encounters from 2014 to 2018. Setting:One community and two academic hospitals in Maryland. Patients:All patients 18 years old or older presenting to the emergency department or admitted to any acute inpatient medical or surgical unit including patients discharged from the emergency department. Interventions:None. Measurements and Main Results:From the electronic health record, 233,252 emergency department and inpatient encounters were identified. Patient data were used to develop and validate electronic health record-based sepsis phenotyping, an adaptation of "the Centers for Disease Control Adult Sepsis Event toolkit" that accounts for comorbid conditions when identifying sepsis patients. The performance of this novel system was then compared with 1) physician case review and 2) three other commonly used strategies using metrics of sensitivity and precision relative to sepsis billing codes, termed "billing code sensitivity" and "billing code predictive value." Physician review of electronic health record-based sepsis phenotyping identified cases confirmed 79% as having sepsis; 88% were confirmed or had a billing code for sepsis; and 99% were confirmed, had a billing code, or received at least 4 days of antibiotics. At comparable billing code sensitivity (0.91; 95% CI, 0.88-0.93), electronic health record-based sepsis phenotyping had a higher billing code predictive value (0.32; 95% CI, 0.30-0.34) than either the Centers for Medicare and Medicaid Services Sepsis Core Measure (SEP-1) definition or the Sepsis-3 consensus definition (0.12; 95% CI, 0.11-0.13; and 0.07; 95% CI, 0.07-0.08, respectively). When compared with electronic health record-based sepsis phenotyping, Adult Sepsis Event had a lower billing code sensitivity (0.75; 95% CI, 0.72-0.78) and similar billing code predictive value (0.29; 95% CI, 0.26-0.31). Electronic health record-based sepsis phenotyping identified patients with higher in-hospital mortality and nearly one-half as many false-positive cases when compared with SEP-1 and Sepsis-3. Conclusions:By accounting for comorbid conditions, electronic health record-based sepsis phenotyping exhibited better performance when compared with other automated definitions of sepsis.

SUBMITTER: Henry KE

PROVIDER: S-EPMC7063888 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Comparison of Automated Sepsis Identification Methods and Electronic Health Record-based Sepsis Phenotyping: Improving Case Identification Accuracy by Accounting for Confounding Comorbid Conditions.

Henry Katharine E KE Hager David N DN Osborn Tiffany M TM Wu Albert W AW Saria Suchi S

Critical care explorations 20191030 10

To develop and evaluate a novel strategy that automates the retrospective identification of sepsis using electronic health record data.<h4>Design</h4>Retrospective cohort study of emergency department and in-hospital patient encounters from 2014 to 2018.<h4>Setting</h4>One community and two academic hospitals in Maryland.<h4>Patients</h4>All patients 18 years old or older presenting to the emergency department or admitted to any acute inpatient medical or surgical unit including patients dischar ...[more]

PMID: 32166234

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Project description:Background. While often first treated in the emergency department (ED), identification of sepsis is difficult. Electronic medical record (EMR) clinical decision tools offer a novel strategy for identifying patients with sepsis. The objective of this study was to test the accuracy of an EMR-based, automated sepsis identification system. Methods. We tested an EMR-based sepsis identification tool at a major academic, urban ED with 64,000 annual visits. The EMR system collected vital sign and laboratory test information on all ED patients, triggering a "sepsis alert" for those with ?2 SIRS (systemic inflammatory response syndrome) criteria (fever, tachycardia, tachypnea, leukocytosis) plus ?1 major organ dysfunction (SBP ? 90 mm Hg, lactic acid ?2.0 mg/dL). We confirmed the presence of sepsis through manual review of physician, nursing, and laboratory records. We also reviewed a random selection of ED cases that did not trigger a sepsis alert. We evaluated the diagnostic accuracy of the sepsis identification tool. Results. From January 1 through March 31, 2012, there were 795 automated sepsis alerts. We randomly selected 300 cases without a sepsis alert from the same period. The true prevalence of sepsis was 355/795 (44.7%) among alerts and 0/300 (0%) among non-alerts. The positive predictive value of the sepsis alert was 44.7% (95% CI [41.2-48.2%]). Pneumonia and respiratory infections (38%) and urinary tract infection (32.7%) were the most common infections among the 355 patients with true sepsis (true positives). Among false-positive sepsis alerts, the most common medical conditions were gastrointestinal (26.1%), traumatic (25.7%), and cardiovascular (20.0%) conditions. Rates of hospital admission were: true-positive sepsis alert 91.0%, false-positive alert 83.0%, no sepsis alert 5.7%. Conclusions. This ED EMR-based automated sepsis identification system was able to detect cases with sepsis. Automated EMR-based detection may provide a viable strategy for identifying sepsis in the ED.

Project description:Real-world data have been critical for rapid-knowledge generation throughout the COVID-19 pandemic. To ensure high-quality results are delivered to guide clinical decision making and the public health response, as well as characterize the response to interventions, it is essential to establish the accuracy of COVID-19 case definitions derived from administrative data to identify infections and hospitalizations. Electronic Health Record (EHR) data were obtained from the clinical data warehouse of the Yale New Haven Health System (Yale, primary site) and 3 hospital systems of the Mayo Clinic (validation site). Detailed characteristics on demographics, diagnoses, and laboratory results were obtained for all patients with either a positive SARS-CoV-2 PCR or antigen test or ICD-10 diagnosis of COVID-19 (U07.1) between April 1, 2020 and March 1, 2021. Various computable phenotype definitions were evaluated for their accuracy to identify SARS-CoV-2 infection and COVID-19 hospitalizations. Of the 69,423 individuals with either a diagnosis code or a laboratory diagnosis of a SARS-CoV-2 infection at Yale, 61,023 had a principal or a secondary diagnosis code for COVID-19 and 50,355 had a positive SARS-CoV-2 test. Among those with a positive laboratory test, 38,506 (76.5%) and 3449 (6.8%) had a principal and secondary diagnosis code of COVID-19, respectively, while 8400 (16.7%) had no COVID-19 diagnosis. Moreover, of the 61,023 patients with a COVID-19 diagnosis code, 19,068 (31.2%) did not have a positive laboratory test for SARS-CoV-2 in the EHR. Of the 20 cases randomly sampled from this latter group for manual review, all had a COVID-19 diagnosis code related to asymptomatic testing with negative subsequent test results. The positive predictive value (precision) and sensitivity (recall) of a COVID-19 diagnosis in the medical record for a documented positive SARS-CoV-2 test were 68.8% and 83.3%, respectively. Among 5,109 patients who were hospitalized with a principal diagnosis of COVID-19, 4843 (94.8%) had a positive SARS-CoV-2 test within the 2 weeks preceding hospital admission or during hospitalization. In addition, 789 hospitalizations had a secondary diagnosis of COVID-19, of which 446 (56.5%) had a principal diagnosis consistent with severe clinical manifestation of COVID-19 (e.g., sepsis or respiratory failure). Compared with the cohort that had a principal diagnosis of COVID-19, those with a secondary diagnosis had a more than 2-fold higher in-hospital mortality rate (13.2% vs 28.0%, P<0.001). In the validation sample at Mayo Clinic, diagnosis codes more consistently identified SARS-CoV-2 infection (precision of 95%) but had lower recall (63.5%) with substantial variation across the 3 Mayo Clinic sites. Similar to Yale, diagnosis codes consistently identified COVID-19 hospitalizations at Mayo, with hospitalizations defined by secondary diagnosis code with 2-fold higher in-hospital mortality compared to those with a primary diagnosis of COVID-19. COVID-19 diagnosis codes misclassified the SARS-CoV-2 infection status of many people, with implications for clinical research and epidemiological surveillance. Moreover, the codes had different performance across two academic health systems and identified groups with different risks of mortality. Real-world data from the EHR can be used to in conjunction with diagnosis codes to improve the identification of people infected with SARS-CoV-2.

Project description:Background and purposeOral anticoagulation is generally indicated for cardioembolic strokes, but not for other stroke causes. Consequently, subtype classification of ischemic stroke is important for risk stratification and secondary prevention. Because manual classification of ischemic stroke is time-intensive, we assessed the accuracy of automated algorithms for performing cardioembolic stroke subtyping using an electronic health record (EHR) database.MethodsWe adapted TOAST (Trial of ORG 10172 in Acute Stroke Treatment) features associated with cardioembolic stroke for derivation in the EHR. Using administrative codes and echocardiographic reports within Mass General Brigham Biobank (N=13 079), we iteratively developed EHR-based algorithms to define the TOAST cardioembolic stroke features, revising regular expression algorithms until achieving positive predictive value ≥80%. We compared several machine learning-based statistical algorithms for discriminating cardioembolic stroke using the feature algorithms applied to EHR data from 1598 patients with acute ischemic strokes from the Massachusetts General Hospital Ischemic Stroke Registry (2002-2010) with previously adjudicated TOAST and Causative Classification of Stroke subtypes.ResultsRegular expression-based feature extraction algorithms achieved a mean positive predictive value of 95% (range, 88%-100%) across 11 echocardiographic features. Among 1598 patients from the Massachusetts General Hospital Ischemic Stroke Registry, 1068 had any cardioembolic stroke feature within predefined time windows in proximity to the stroke event. Cardioembolic stroke tended to occur at an older age, with more TOAST-based comorbidities, and with atrial fibrillation (82.3%). The best model was a random forest with 92.2% accuracy and area under the receiver operating characteristic curve of 91.1% (95% CI, 87.5%-93.9%). Atrial fibrillation, age, dilated cardiomyopathy, congestive heart failure, patent foramen ovale, mitral annulus calcification, and recent myocardial infarction were the most discriminatory features.ConclusionsMachine learning-based identification of cardioembolic stroke using EHR data is feasible. Future work is needed to improve the accuracy of automated cardioembolic stroke identification and assess generalizability of electronic phenotyping algorithms across clinical settings.

Dataset Information

Comparison of Automated Sepsis Identification Methods and Electronic Health Record-based Sepsis Phenotyping: Improving Case Identification Accuracy by Accounting for Confounding Comorbid Conditions.

Publications

Comparison of Automated Sepsis Identification Methods and Electronic Health Record-based Sepsis Phenotyping: Improving Case Identification Accuracy by Accounting for Confounding Comorbid Conditions.

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