Pneumonia

PH15 / 30

Eleanor L Axson, Jennifer K Quint

Oct 6, 2021

Clinical-Coded Phenotype

  1. Overview

    Phenotype Type
    Disease or syndrome
    Sex
    Both
    Valid Event Date Range
    01/01/2001 - 31/12/2019
    Coding System
    ICD10 codesRead codes v2SNOMED CT codesICD11 codes
    Data Sources
    CPRD GOLD
    CPRD Aurum
    HES Admitted Patient Care data for CPRD GOLD
    HES Admitted Patient Care data for CPRD Aurum
    Death Registration data for CPRD GOLD
    Death Registration data for CPRD Aurum
    UK Biobank
    Collections
    Phenotype Library
    Tags
    No data
    Ontology
    No data

  2. Definition

    These codes will capture both community- and hospital-acquired pneumonia. These codes are not intended to be mandatory, but are to be used as a starting point for the identification of pneumonia in routine EHR. Each study may differ in the sensitivity and specificity of the coding required.

    Defining a community-acquired pneumonia occurrence in CPRD and HES, Millett et al. 2013 used the following algorithm:

    1) Pneumonia records wtihin 28 days of each other were considered to be separate consultations for the same illness 2) First record of pneumonia was the index date 3) End of a pneumonia occurrence was defined as 28 days after the last pneumonia code within the illness episode 4) In HES, pneumonia coded as the primary diagnosis on the first day of a hospital admission

    Defining a hospital-acquired pneumonia occurrence in HES and CPRD, Millett et al. 2013 used the following algorithm:

    1) Pneumonia coded at any time beyond the first day of a hospital admission 2) Using CPRD in conjunction with HES, pneumonia coded in CPRD within 14 days of a hospital admission (for any cause) was deemed hospital-acquired 3) In CPRD, use of a hospital-acquired pneumonia code at any time during the pneumonia occurrence

    Millett, E. R., Quint, J. K., Smeeth, L., Daniel, R. M., & Thomas, S. L. (2013). Incidence of community-acquired lower respiratory tract infections and pneumonia among older adults in the United Kingdom: a population-based study. PLoS One, 8(9), e75131. doi:10.1371/journal.pone.0075131

    Defining a community-acquired pneumonia resulting in hospitalisation occurrence in HES, Hicks et al. 2016 used the following algorithm:

    1) In HES, hospital admission following A&E visit, where pneumonia was coded as the primary diagnosis within two days of admission

    Defining a hospital-acquired pneumonia occurrence in CPRD and HES, Hicks et al. 2016 used the following algorithm:

    1) Pneumonia diagnosis in HES >2 days after hospital admission 2) Pneumonia diagnosed in CPRD within 7 days after hospital discharge

    Hicks, B. M., Yin, H., Bladou, F., Ernst, P., & Azoulay, L. (2017). Androgen deprivation therapy for prostate cancer and the risk of hospitalisation for community-acquired pneumonia. Thorax, 72(7), 596-597. doi:10.1136/thoraxjnl-2016-209512

  3. Implementation

    Phenoflow ID

    Please see the PhenoFLOW website here for more information on workflow-based Phenotypes.

    PhenoFLOW Reference: https://kclhi.org/phenoflow/workflows/github.com/phenoflow/Pneumonia---239c81c0-16f6-11ef-9de4-4d4ea830ad16/blob/read-potential-cases-fhir/Pneumonia.cwl

    Implementation

    No data

  4. Clinical Codelist

  5. Publication

    Related publications

    • Publications identifying pneumonia in CPRD and/or HES:

    • Millett, E. R., Quint, J. K., Smeeth, L., Daniel, R. M., & Thomas, S. L. (2013). Incidence of community-acquired lower respiratory tract infections and pneumonia among older adults in the United Kingdom: a population-based study. PLoS One, 8(9), e75131. doi:10.1371/journal.pone.0075131"

      (DOI: 10.1371/journal.pone.0075131)

    • Braeken, D. C., Rohde, G. G., Franssen, F. M., Driessen, J. H., van Staa, T. P., Souverein, P. C., . . . de Vries, F. (2017). Risk of community-acquired pneumonia in chronic obstructive pulmonary disease stratified by smoking status: a population-based cohort study in the United Kingdom. Int J Chron Obstruct Pulmon Dis, 12, 2425-2432. doi:10.2147/COPD.S138435"

      (DOI: 10.2147/COPD.S138435)

    • Hicks, B. M., Yin, H., Bladou, F., Ernst, P., & Azoulay, L. (2017). Androgen deprivation therapy for prostate cancer and the risk of hospitalisation for community-acquired pneumonia. Thorax, 72(7), 596-597. doi:10.1136/thoraxjnl-2016-209512"

      (DOI: 10.1136/thoraxjnl-2016-209512)

    • Sun, X., Douiri, A., & Gulliford, M. (2019). Pneumonia incidence trends in UK primary care from 2002 to 2017: population-based cohort study. Epidemiol Infect, 147, e263. doi:10.1017/S0950268819001559"

      (DOI: 10.1017/S0950268819001559)

    Citation Example

    Eleanor L Axson, Jennifer K Quint. PH15 / 30 - Pneumonia. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH15/version/30/detail/. [Accessed 27 January 2026]

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH15/version/30/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(
     'PH15',
     version_id=30
    )

    Py Package

    # Download here

    from pyconceptlibraryclient import Client


    # Connect to API

    client = Client(public=True)


    # Get details of Phenotype

    phenotype_detail = client.phenotypes.get_detail(
     'PH15',
     version_id=30
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH15/version/30/export/codes/?format=json
    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(
     'PH15',
     version_id=30
    )

    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(
     'PH15',
     version_id=30
    )

  7. Version History

    Version IDNameOwnerPublish date
    Pneumonia ieuan.scanlon2021-10-06 15:59