Respiratory Tract Infection

Rebecca M Joseph, Mohammad Movahedi, William G Dixon, Deborah P M Symmons

PH487 / 974 Clinical-Coded Phenotype

  1. Overview

    Phenotype Type
    Disease or syndrome
    Phenotype UUID
    WZ3Sgn38yyKqmPTDEUxdpt
    Sex
    Both
    Valid Event Date Range
    01/01/1998 - 10/01/2012
    Coding System
    ICD10 codesICD9 codes
    Data Sources
    Collections
    ClinicalCodes RepositoryPhenotype Library
    Tags
    No data
  2. Definition

    Objective:

    To investigate the association between smoking status and smoking cessation with mortality in patients with rheumatoid arthritis (RA).

    Methods:

    An incident cohort of patients with RA was identified using the Clinical Practice Research Datalink, a database of UK primary care electronic medical records. Time-varying smoking status, years of cessation, and amount smoked were determined frompatients’medical records. The date and underlying cause of deathwere identified by linkagewith Office for National Statistics records. The associations between smoking status and smoking cessation with all-cause and causespecific mortality (circulatory disease, all cancers, lung cancer, respiratory disease, and respiratory infection) were investigated using adjusted Cox (all-causemortality) and Fine-Gray (cause-specificmortality) regression.

    Results:

    The cohort comprised 5,677 patients (median age 61.4 years, 68% women), with 40% as never smokers, 34% former smokers, and 26% current smokers at baseline. Compared to never smoking, current smokingwas associated with an increased risk of all-causemortality (hazard ratio 1.98 [95% confidence interval (95% CI) 1.56, 2.53]), andmortality due to circulatory disease (subdistribution hazard ratio [SHR] 1.96 [95% CI 1.33, 2.90]) and lung cancer (SHR 23.2 [95% CI 5.15, 105]). Each year of smoking cessation was associated with a decreased risk of all-cause mortality (former heavy smokers SHR 0.85 [95% CI 0.77, 0.94], former light smokers SHR 0.90 [95%CI 0.84, 0.97]).

    Conclusion:

    Current smoking is associated with an increased risk of all-cause, cardiovascular, and lung cancermortality in patientswith RA. Each year of cessation is associated with a reduced risk of all-causemortality. This information may prove helpful in smoking cessation programs for patients with RA.

  3. Implementation

    Implementation

    No data
  4. Clinical Code List

  5. Publication

    • Rebecca M Joseph, Mohammad Movahedi, William G Dixon, Deborah P M Symmons, Smoking-Related Mortality in Patients With Early Rheumatoid Arthritis: A Retrospective Cohort Study Using the Clinical Practice Research Datalink. Authritis Care and Research, 68(11), 1598-1606, 2016.

    Citation Example

    Rebecca M Joseph, Mohammad Movahedi, William G Dixon, Deborah P M Symmons. PH487 / 974 - Respiratory Tract Infection. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH487/version/974/detail/. [Accessed 25 July 2024]

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH487/version/974/detail/?format=json
    R Package

    # Download here

    library(ConceptLibraryClient)


    # Connect to API

    client = ConceptLibraryClient::Connection$new(public=TRUE)


    # Get details of phenotype

    phenotype_details = client$phenotypes$get_detail(
     'PH487',
     version_id=974
    )

    Py Package

    # Download here

    from pyconceptlibraryclient import Client


    # Connect to API

    client = Client(public=True)


    # Get codelist of phenotype

    phenotype_codelist = client.phenotypes.get_detail(
     'PH487',
     version_id=974
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH487/version/974/export/codes/?format=json
    CSV site_root/phenotypes/PH487/version/974/export/codes/
    R Package

    # Download here

    library(ConceptLibraryClient)


    # Connect to API

    client = ConceptLibraryClient::Connection$new(public=TRUE)


    # Get codelist of phenotype

    phenotype_codelist = client$phenotypes$get_codelist(
     'PH487',
     version_id=974
    )

    Py Package

    # Download here

    from pyconceptlibraryclient import Client


    # Connect to API

    client = Client(public=True)


    # Get codelist of phenotype

    phenotype_codelist = client.phenotypes.get_codelist(
     'PH487',
     version_id=974
    )

  7. Version History

    Version IDNameOwnerPublish date
    974 Respiratory Tract Infection ieuan.scanlon2021-10-06currently shown