Empyema or pyothorax or purulent pleuritis Primary care

Chukwuma Iwundu, Clare MacRae, Eleftheria Vasileiou

PH802 / 2226 Clinical-Coded Phenotype

  1. Overview

    Phenotype Type
    Disease or syndrome
    Sex
    Both
    Valid Event Date Range
    01/01/2001 to 31/01/2021
    Coding System
    Read codes v2SNOMED CT codes
    Data Sources
    Welsh Longitudinal General Practice Dataset (WLGP), Clinical Practice Research Datalink AURUM, Clinical Practice Research Datalink GOLD
    Collections
    BREATHEPhenotype Library
    Tags
    No data

  2. Definition

    • Not found code search
    • Hamilton et al, 2020Clinical coding of pleural empyema was validated using coding data from three hospitals in England, UK. The coded diagnoses of pleural empyema is defined as J86-, also known as pyothorax. Empyema was considered as a pleural effusion that had a documented pH of less than 7.2, microscopic evidence of infection, or frank pus. If microscopic evidence was not available, then clear clinical management as empyema (supporting radiology, clinical progress, and biochemistry) was used.The clinical diagnosis of empyema was made on retrospective review of the notes, discharge summary, radiology, and microbiology available.Empyema was considered as a pleural effusion that had a documented pH of less than 7.2, microscopic evidence of infection, or frank pus. If microscopic evidence was not available, then clear clinical management as empyema (supporting radiology, clinical progress, and biochemistry) was used.Empyema coding was generally good (>85% accuracy), although some cases were miscoded. Using codes for elective admissions helped to differentiate post-operative from community acquired empyema. It is likely empyema is under rather than over-recorded in HES data.Using codes for elective admissions helped to differentiate post-operative from community acquired empyema. It is likely empyema is under rather than over-recorded in HES data.

  3. Implementation

    Implementation

    These codes are not intended to be mandatory, but are to be used as a starting point for the identification of empyema in routine Electronic Health Record (EHR). Each study may differ in the sensitivity and specificity of the coding required.

    According to the National Health Service (NHS), Empyema is defined as pocketcs of pus that have collected insided a body cavity. They can form if a bacterial infection is left untreated, or if it fails to fully respond to treatment. The term is most commonly used to refer to pus-filled pockets that develop in the pleural space.

    https://www.nhs.uk/conditions/empyema/

    Not found code search

  4. Clinical Code List

  5. Publication

    • Publications in 2020-2021 identified in PubMed

    • Arnold DT, Hamilton FW, Morris TT, Suri T, Morley A, Frost V, Vipond IB, Medford AR, Payne RA, Muir P, Maskell NA. Epidemiology of pleural empyema in English hospitals and the impact of influenza. Eur Respir J. 2021 Jun 17;57(6):2003546. doi: 10.1183/13993003.03546-2020. PMID: 33334937.

      (DOI:10.1183/13993003.03546-2020)

    • Strachan R, Homaira N, Beggs S, Bhuiyan MU, Gilbert GL, Lambert SB, Macartney K, Marshall H, Martin AC, McCallum GB, McCullagh A, McDonald T, McIntyre P, Oftadeh S, Ranganathan S, Suresh S, Wainwright CE, Wilson A, Wong M, Snelling T, Jaffé A. Assessing the impact of the 13 valent pneumococcal vaccine on childhood empyema in Australia. Thorax. 2021 May;76(5):487-493. doi: 10.1136/thoraxjnl-2020-216032. Epub 2021 Jan 27. PMID: 33504566.

      (DOI:10.1136/thoraxjnl-2020-216032)

    • Code repositories

    • ID- 1 - Repository- Manchester ClinicalCodes - Description- The association between smoking and hospitalisations for cardiovascular events and respiratory infection in patients with rheumatoid arthritis: a retrospective cohort study using the Clinical Practice Research Datalink - Conditions- Respiratory tract infection - Publication- Unpublished - Clinical codes- ICD-10

    • ID- 2 - Repository- Manchester ClinicalCodes - Description- Smoking-related mortality in patients with early rheumatoid arthritis – a retrospective cohort study using the Clinical Practice Research Datalink - Conditions- Respiratory tract infection - Publication- https://doi.org/10.1002/acr.22882 - Clinical codes- ICD-10

      (DOI:10.1002/acr.22882)

    • ID- 3 - Repository- Manchester ClinicalCodes - Description- Antibiotic prescribing for common infections in UK general practice: variability and drivers - Conditions- LRTI - Publication- https://doi.org/10.1093/jac/dkz163 - Clinical codes- Read Version 2

      (DOI:10.1093/jac/dkz163)

    • ID- 4 - Repository- HDR UK National Phenomics Resource Project - Description- - Conditions- Bacterial diseases (excl TB) - Publication- - Clinical codes- ICD-10

    • ID- 5 - Repository- HDR UK National Phenomics Resource Project - Description- - Conditions- Lower respiratory tract infections - Publication- - Clinical codes- ICD-10

    Citation Example

    Chukwuma Iwundu, Clare MacRae, Eleftheria Vasileiou. PH802 / 2226 - Empyema or pyothorax or purulent pleuritis Primary care. Phenotype Library [Online]. 04 August 2022. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH802/version/2226/detail/. [Accessed 02 December 2024]

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH802/version/2226/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(
     'PH802',
     version_id=2226
    )

    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(
     'PH802',
     version_id=2226
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH802/version/2226/export/codes/?format=json
    CSV site_root/phenotypes/PH802/version/2226/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(
     'PH802',
     version_id=2226
    )

    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(
     'PH802',
     version_id=2226
    )

  7. Version History

    Version IDNameOwnerPublish date
    2226 Empyema or pyothorax or purulent pleuritis Primary care zinnurar2022-08-08currently shown
    1683 Empyema or pyothorax or purulent pleuritis Primary care zinnurar2022-01-17