Validity of the coding for herpes simplex encephalitis in the Danish National Patient Registry

Risk factors for status epilepticus after brain disorders in adults: A multi-cohort national register study

PURPOSE

We aimed to describe risks of status epilepticus (SE) after different brain disorders in adults using population-wide register data. Our hypothesis was that SE would be more common in disorders with widespread pathology and that the risk would increase with disorder severity.

METHODS

We analyzed five large datasets created from the Swedish National Patient Register, the Cause of Death Register, and national quality registers with adults in Sweden with brain infections, dementia, multiple sclerosis (MS), stroke, and traumatic brain injury (TBI). Risk factors were assessed using Cox regression.

RESULTS

In adults with TBI, stroke, dementia, MS, or brain infections, the incidence rate of SE was highest in survivors of brain infections (64/100,000 person years) and stroke (64/100,000), followed by TBI (37/100,000), dementia (36/100,000), and MS (26/100,000). SE was considerably more common in patients with epilepsy after their brain disorder. Across all datasets severe disorder increased SE-risk. Herpes simplex encephalitis (HR 5.5 95 % CI: 2.6-12), progressive MS (HR 2.3, 95 % CI: 1.1-4.7), structural TBI (2.0, 95 % CI: 1.6-2.6), and intracerebral hemorrhage (HR 1.5, 95 % CI: 1.2-2.0) were the subtypes of brain disorders with the highest relative risk of SE. Having another CNS disorder increased SE-risk in TBI (HR 2.9, 95 % CI: 2.3-3.7), brain infections (HR 2.8, 95 % CI: 1.7-4.5), and dementia (HR 2.5, 95 % CI: 1.5-4.2).

CONCLUSION

SE-risk increases with disorder severity and number of CNS comorbidities. These findings can guide treatment strategy by allowing identification of high-risk patients. Pathophysiological studies are needed to better understand remote symptomatic SE.

Machine Learning for Risk Group Identification and User Data Collection in a Herpes Simplex Virus Patient Registry: Algorithm Development and Validation Study

BACKGROUND

Researching people with herpes simplex virus (HSV) is challenging because of poor data quality, low user engagement, and concerns around stigma and anonymity.

OBJECTIVE

This project aimed to improve data collection for a real-world HSV registry by identifying predictors of HSV infection and selecting a limited number of relevant questions to ask new registry users to determine their level of HSV infection risk.

METHODS

The US National Health and Nutrition Examination Survey (NHANES, 2015-2016) database includes the confirmed HSV type 1 and type 2 (HSV-1 and HSV-2, respectively) status of American participants (14-49 years) and a wealth of demographic and health-related data. The questionnaires and data sets from this survey were used to form two data sets: one for HSV-1 and one for HSV-2. These data sets were used to train and test a model that used a random forest algorithm (devised using Python) to minimize the number of anonymous lifestyle-based questions needed to identify risk groups for HSV.

RESULTS

The model selected a reduced number of questions from the NHANES questionnaire that predicted HSV infection risk with high accuracy scores of 0.91 and 0.96 and high recall scores of 0.88 and 0.98 for the HSV-1 and HSV-2 data sets, respectively. The number of questions was reduced from 150 to an average of 40, depending on age and gender. The model, therefore, provided high predictability of risk of infection with minimal required input.

CONCLUSIONS

This machine learning algorithm can be used in a real-world evidence registry to collect relevant lifestyle data and identify individuals' levels of risk of HSV infection. A limitation is the absence of real user data and integration with electronic medical records, which would enable model learning and improvement. Future work will explore model adjustments, anonymization options, explicit permissions, and a standardized data schema that meet the General Data Protection Regulation, Health Insurance Portability and Accountability Act, and third-party interface connectivity requirements.

Development of a diagnostic algorithm identifying cases of dislocation after primary total hip arthroplasty-based on 31,762 patients from the Danish Hip Arthroplasty Register

Background and purpose - Dislocation of total hip arthroplasties (THA) is often treated with closed reduction and traditionally not registered in orthopedic registers. This study aimed to create an algorithm designed to identify cases of dislocations of THAs with high sensitivity, specificity, and positive predictive value (PPV) based on codes from the Danish National Patient Register (DNPR).Patients and methods - All patients (n = 31,762) with primary osteoarthritis undergoing THA from January 1, 2010 to December 31, 2014 were included from the Danish Hip Arthroplasty Register (DHR). We extracted available data for every hospital contact in the DNPR during a 2-year follow-up period, then conducted a comprehensive nationwide review of 5,096 patient files to register all dislocations and applied codes.Results - We identified 1,890 hip dislocations among 1,094 of the included 31,762 THAs. More than 70 different diagnoses and 55 procedural codes were coupled to the hospital contacts with dislocation. A combination of the correct codes produced a sensitivity of 63% and a PPV of 98%. Adding alternative and often applied codes increased the sensitivity to 91%, while the PPV was maintained at 93%. Additional steps increased sensitivity to 95% but at the expense of an unacceptable decrease in the PPV to 82%. Specificity was, in all steps, greater than 99%.Interpretation - The developed algorithm achieved high and acceptable values for sensitivity, specificity, and predictive values. We found that surgeons in most cases coded correctly. However, the codes were not always transferred to the discharge summary. In perspective, this kind of algorithm may be used in Danish quality registers.

Epilepsy after brain infection in adults: A register-based population-wide study

OBJECTIVE

To describe risk and risk factors of epilepsy after hospitalization for brain infection in adults in Sweden.

METHODS

This was a matched retrospective cohort study based on the comprehensive National Patient and Cause of Death Registers. All individuals age >18 without prior epilepsy who received inpatient care in 2000-2010 for a brain infection were included, with 3 age- and sex-matched unexposed controls per exposed individual (n = 12,101 exposed and 36,228 controls). Kaplan-Meier risks of epilepsy after different brain infections were calculated and risk factors identified by Cox regression. Patients were followed until the end of 2017.

RESULTS

The 10-year risk of epilepsy was 5.9% (95% confidence interval [CI] 5.5-6.3) in cases and 1.2% (95% CI 1.0-1.4) in controls: 1.7% (95% CI 0.7-2.7) after tick-borne encephalitis, 4.1% (95% CI 3.3-4.9) after bacterial meningitis, 26.0% (95% CI 21.5-30.5) after herpes simplex virus encephalitis, and 30.2% (95% CI 27.1-33.3) after brain abscess. In Cox regression, seizure during the index admission and mechanical ventilation were epilepsy risk factors.

CONCLUSIONS

Epilepsy is common after several types of brain infections in adults. The type of infection, its severity, and propensity to cause seizures in the acute phase influence the risk of subsequent epilepsy.

CLASSIFICATION OF EVIDENCE

This study provides Class II evidence that in adults, brain infection is associated with an increased risk of subsequent epilepsy.

Long-Term Survival, Morbidity, Social Functioning and Risk of Disability in Patients with a Herpes Simplex Virus Type 1 or Type 2 Central Nervous System Infection, Denmark, 2000-2016

Background

The long-term prognosis following herpes simplex virus (HSV) central nervous system (CNS) infection is still debated.

Patients and Methods

We examined outcomes in all Danish residents who, during 2000–2016, tested PCR positive for HSV-1 (n=208) or HSV-2 (n=283) in the cerebrospinal fluid, compared to comparison cohorts from the general population (n=2080 and n=2830).

Results

One-year mortality was increased among HSV-1 patients (difference 19.3%; 95% CI: 13.6% to 25.0%) and HSV-2 patients (difference 5.3%; 95% CI: 2.5% to 8.1%), but thereafter mortality was not increased. After exclusion of persons diagnosed with cancer prior to study inclusion, one-year mortality difference for HSV-2 patients was 1.7% (−0.1% to 3.5%). After five years, HSV-1 patients had lower employment (difference −19.8%; 95% CI: −34.7% to −4.8%) and higher disability pension rates (difference 22.2%; 95% CI: 8.4% to 36.0%) than the comparison cohort, but similar number of inpatient days, outpatient visits, and sick leave. HSV-2 patients had employment and disability pension rates comparable to the comparison cohort, but more inpatient days (difference 1.5/year; 95% CI: −0.2 to 3.2), outpatient visits (difference 1.3/year; 95% CI: 0.3 to 3.2), and sick leave days (difference 9.1/year; 95% CI: 7.9 to 10.4).

Conclusion

HSV-1 and HSV-2 CNS infections differ substantially with respect to prognosis. HSV-1 CNS infection is followed by increased short-term mortality and long-term risk of disability. HSV-2 CNS infection has no substantial impact on mortality or working capability but is associated with increased morbidity.

Congenital Heart Disease and Risk of Central Nervous System Infections: A Nationwide Cohort Study

Congenital heart disease (CHD) is associated with risk factors of central nervous system (CNS) infections including infective endocarditis, cardiac shunt physiology, and immune deficiencies. We aimed to investigate the risk of CNS infections in the CHD population compared to the general population. In this cohort study, we used Danish nationwide medical registries to identify individuals diagnosed with CHD at any age, born between 1977 and 2012. For each CHD individual, we matched 10 individuals on sex and birth year from the general population. Subjects were followed until first-time hospital diagnosis of CNS infection, death, emigration, or end of study. We computed cumulative incidences of CNS infections with death as a competing risk, as well as hazard ratios (HRs) with corresponding 95% confidence intervals (CIs) adjusted for birth year and sex. We identified 17,550 individuals with CHD (50% male). Among subjects with CHD, the cumulative incidence of CNS infection at age 30 years was 1.0% compared to 0.6% in the general population. The overall HR of CNS infections in CHD subjects relative to the general population was 2.1 (95% CI 1.6-2.7). The HR was 1.9 (95% CI 1.4-2.7) for mild to moderate CHD, 2.1 (95% CI 1.3-3.3) for severe CHD and 3.0 (95% CI 1.1-8.2) for univentricular physiology. The HR for CHD subjects without record of infective endocarditis was 2.0 (95% CI 1.5-2.5). The risk of CNS infections was increased among individuals with CHD compared to the general population, and the risk was not limited to individuals with infective endocarditis.

Engineering Requirements of a Herpes Simplex Virus Patient Registry: Discovery Phase of a Real-World Evidence Platform to Advance Pharmacogenomics and Personalized Medicine

Comprehensive pharmacogenomic understanding requires both robust genomic and demographic data. Patient registries present an opportunity to collect large amounts of robust, patient-level data. Pharmacogenomic advancement in the treatment of infectious diseases is yet to be fully realised. Herpes simplex virus (HSV) is one disease for which pharmacogenomic understanding is wanting. This paper aims to understand the key factors that impact data collection quality for medical registries and suggest potential design features of an HSV medical registry to overcome current constraints and allow for this data to be used as a complement to genomic and clinical data to further the treatment of HSV. This paper outlines the discovery phase for the development of an HSV registry with the aim of learning about the users and their contexts, the technological constraints and the potential improvements that can be made. The design requirements and user stories for the HSV registry have been identified for further alpha phase development. The current landscape of HSV research and patient registry development were discussed. Through the analysis of the current state of the art and thematic user analysis, potential design features were elucidated to facilitate the collection of high-quality, robust patient-level data which could contribute to advances in pharmacogenomic understanding and personalised medicine in HSV. The user requirements specification for the development of an HSV registry has been summarised and implementation strategies for the alpha phase discussed.

Validity of administrative database detection of previously resolved hepatitis B virus in Japan

The risk of hepatitis B virus (HBV) reactivation has increased owing to advances in the immunosuppressive therapy field. However, the HBV reactivation incidence among patients with previously resolved HBV (prHBV) infection during immunosuppressive therapy for rheumatoid arthritis (RA) remains unclear. The objective of this work is to describe the validity of detecting prHBV infection from administrative data through comparisons with chart abstraction and determine the incidence of HBV reactivation during immunosuppressive therapy for RA in Japan. In this retrospective cohort study, data on selected patients were extracted from administrative claims data. To identify patients with prHBV infection and de novo hepatitis, and HBsAg carriers, we conducted chart abstraction. The incidence rate of de novo hepatitis was 1.23 of 100 person‐years. The positive predictive value (PPV) and its 95% confidence interval (CI) of administrative data for the identification of suspected prHBV infections was 85.8% (95% CI: 81.7%‐89.3%). This study evaluated the PPV of the algorithm of HBV‐DNA testing with immunosuppressive therapy performed four times or more per year for the detection of prHBV infection from administrative data. Additionally, we determined the incidence rate of HBV reactivation among preHBV infections during immunosuppressive therapy for RA to be 1.23 of 100 person‐years.

Mutations in RNA Polymerase III genes and defective DNA sensing in adults with varicella-zoster virus CNS infection

Recently, deficiency in the cytosolic DNA sensor RNA Polymerase III was described in children with severe primary varicella-zoster virus (VZV) infection in the CNS and lungs. In the present study we examined adult patients with VZV CNS infection caused by viral reactivation. By whole exome sequencing we identified mutations in POL III genes in two of eight patients. These mutations were located in the coding regions of the subunits POLR3A and POLR3E. In functional assays, we found impaired expression of antiviral and inflammatory cytokines in response to the POL III agonist Poly(dA:dT) as well as increased viral replication in patient cells compared to controls. Altogether, this study provides significant extension on the current knowledge on susceptibility to VZV infection by demonstrating mutations in POL III genes associated with impaired immunological sensing of AT-rich DNA in adult patients with VZV CNS infection.

Text mining applied to electronic cardiovascular procedure reports to identify patients with trileaflet aortic stenosis and coronary artery disease

BACKGROUND

Interrogation of the electronic health record (EHR) using billing codes as a surrogate for diagnoses of interest has been widely used for clinical research. However, the accuracy of this methodology is variable, as it reflects billing codes rather than severity of disease, and depends on the disease and the accuracy of the coding practitioner. Systematic application of text mining to the EHR has had variable success for the detection of cardiovascular phenotypes. We hypothesize that the application of text mining algorithms to cardiovascular procedure reports may be a superior method to identify patients with cardiovascular conditions of interest.

METHODS

We adapted the Oracle product Endeca, which utilizes text mining to identify terms of interest from a NoSQL-like database, for purposes of searching cardiovascular procedure reports and termed the tool "PennSeek". We imported 282,569 echocardiography reports representing 81,164 individuals and 27,205 cardiac catheterization reports representing 14,567 individuals from non-searchable databases into PennSeek. We then applied clinical criteria to these reports in PennSeek to identify patients with trileaflet aortic stenosis (TAS) and coronary artery disease (CAD). Accuracy of patient identification by text mining through PennSeek was compared with ICD-9 billing codes.

RESULTS

Text mining identified 7115 patients with TAS and 9247 patients with CAD. ICD-9 codes identified 8272 patients with TAS and 6913 patients with CAD. 4346 patients with AS and 6024 patients with CAD were identified by both approaches. A randomly selected sample of 200-250 patients uniquely identified by text mining was compared with 200-250 patients uniquely identified by billing codes for both diseases. We demonstrate that text mining was superior, with a positive predictive value (PPV) of 0.95 compared to 0.53 by ICD-9 for TAS, and a PPV of 0.97 compared to 0.86 for CAD.

CONCLUSION

These results highlight the superiority of text mining algorithms applied to electronic cardiovascular procedure reports in the identification of phenotypes of interest for cardiovascular research.

Cerebrospinal fluid pleocytosis in infectious and noninfectious central nervous system disease: A retrospective cohort study

Cerebrospinal fluid (CSF) analysis is the most important tool for assessing central nervous system (CNS) disease. An elevated CSF leukocyte count rarely provides the final diagnosis, but is almost always an indicator of inflammation within the CNS.The present study investigated the variety of diseases associated with CSF pleocytosis.CSF analyses were identified through the biochemical database used in the capital region of Denmark in the period from 2003 to 2010. In patients >15 years, clinical diagnoses associated with the finding of a CSF leukocyte count >10 × 10 cells/L were obtained from discharge records and patient files.A total of 1058 CSF samples from 1054 patients were included in the analysis. The median age was 50 (interquartile range: 36-67) and 53% were male. Eighty-one different diagnoses were identified in 1058 cases with an elevated CSF leukocyte count, besides unknown causes. Infections were the most common cause of CSF pleocytosis (61.4%) followed by miscellaneous causes (12.7%), vascular (9.7%), neurodegenerative (7%), neoplastic (5%), and inflammatory conditions (4.2%). Only infections presented with leukocyte counts >10,000 × 10/L. Infections represented 82.6% of all cases with a leukocyte count >100 × 10/L whereas 56.3% of cases with at leukocyte counts <100 × 10/L were dominated by disease not related to infection.The present study may serve as a reminder to clinicians of what diseases and disease categories to suspect when patients present with CSF biochemistry indicating CNS inflammation.

Incidence and mortality of herpes simplex encephalitis in Denmark: A nationwide registry-based cohort study

OBJECTIVES

We aimed to investigate the incidence and mortality of herpes simplex encephalitis (HSE) in a nationwide cohort.

METHODS

From the Danish National Patient Registry, we identified all adults hospitalised with a first-time diagnosis of HSE in Denmark during 2004-2014. The HSE diagnoses were verified using medical records and microbiological data. Patients were followed for mortality through the Danish Civil Registry System. We estimated age-standardised incidence rates of HSE and 30-day, 60-day, and 1-year cumulative mortality. Furthermore, we assessed whether calendar year, age, gender, level of comorbidity, virus type, and department type was associated with HSE mortality.

RESULTS

We identified a total of 230 cases of HSE. Median age was 60.7 years (interquartile range: 49.3-71.6). The overall incidence rate was 4.64 cases per million population per year (95% confidence interval: 4.06-5.28). The cumulative mortality within 30 days, 60 days, and 1 year of the HSE admission was 8.3%, 11.3%, and 18.6%, respectively. Advanced age and presence of comorbidity were associated with increased 60-day and 1-year mortality.

CONCLUSIONS

This nationwide study of verified HSE found a higher incidence than reported in previous nationwide studies. Presence of comorbidity was identified as a novel adverse prognostic factor. Mortality rates following HSE remain high.