Acute bronchitis Biobank

Eleftheria Vasileiou, Chukwuma Iwundu, Alex Williams, Clare MacRae

PH787 / 2211 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
    UKBioBank codes
    Data Sources
    UK Biobank
    Collections
    BREATHEPhenotype Library
    Tags
    No data

  2. Definition

    • Not found code search
    • The definition of acute bronchitis has not been validated.No publications to validate codes for Acute Bronchitis were found between 2020-2021

  3. Implementation

    Implementation

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

    According to the National Institute for Health and Care Excellence (NICE) guidelines and the British Medical Journal (BMJ), Acute Bronchitis is defined as a lower respiratory tract infection which causes inflammation in the bronchial airways. It is a clinical diagnosis characterized by cough resulting from acute inflammation of the trachea and large airways but with no evidence of pneumonia. It is therefore recommended that these codes are used for individuals with a respiratory tract infection restricted to trachea and large airways.

    https://cks.nice.org.uk/topics/chest-infections-adult/background-information/definition/

    https://bestpractice.bmj.com/topics/en-gb/135

    Not found code search

  4. Clinical Code List

  5. Publication

    • Publications in 2020-2021 identified in PubMed

    • Zhuo C, Wei X, Zhang Z, Hicks JP, Zheng J, Chen Z, Haldane V, Walley J, Guan Y, Xu H, Zhong N. An antibiotic stewardship programme to reduce inappropriate antibiotic prescribing for acute respiratory infections in rural Chinese primary care facilities: study protocol for a clustered randomised controlled trial. Trials. 2020 May 12;21(1):394. doi: 10.1186/s13063-020-04303-4. PMID: 32398065; PMCID: PMC7216131.

      (DOI:10.1186/s13063-020-04303-4)

    • Code repositories

    • Repository- Manchester ClinicalCodes - Description- Risks of smoking and benefits of smoking cessation on 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- https://doi.org/10.1136/rmdopen-2017-000506 - Clinical codes- ICD-10

      (DOI:10.1136/rmdopen-2017-000506)

    • 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)

    • 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)

    • Repository- Oxford-RCGP RSC - Description- Surveillance & acute pathways of care theme - Conditions- Bronchitis-WRpt - Publication- - Clinical codes-

    • Repository- HDR UK National Phenomics Resource Project - Description- A chronological map of 308 physical and mental health conditions from 4 million individuals in the English National Health Service - Conditions- Bacterial diseases (excl TB) - Publication- https://doi.org/10.1016/S2589-7500(19)30012-3 - Clinical codes- ICD-10

      (DOI:10.1016/S2589-7500(19)30012-3)

    • Repository- HDR UK National Phenomics Resource Project - Description- A chronological map of 308 physical and mental health conditions from 4 million individuals in the English National Health Service - Conditions- Lower respiratory tract infections - Publication- https://doi.org/10.1016/S2589-7500(19)30012-3 - Clinical codes- ICD-10

      (DOI:10.1016/S2589-7500(19)30012-3)

    • Repository- HDR UK National Phenomics Resource Project - Description- A chronological map of 308 physical and mental health conditions from 4 million individuals in the English National Health Service - Conditions- Other or unspecified infectious organisms - Publication- https://doi.org/10.1016/S2589-7500(19)30012-3 - Clinical codes- ICD-10

      (DOI:10.1016/S2589-7500(19)30012-3)

    • Repository- HDR UK National Phenomics Resource Project - Description- A chronological map of 308 physical and mental health conditions from 4 million individuals in the English National Health Service - Conditions- Viral diseases (excl chronic hepatitis/HIV) - Publication- https://doi.org/10.1016/S2589-7500(19)30012-3 - Clinical codes- ICD-10

      (DOI:10.1016/S2589-7500(19)30012-3)

    • Repository- OpenSAFELY - Description- Codes indicating a diagnosis of a lower respiratory tract infection excluding pneumonia - Conditions- Lower respiratory tract infection - Publication- - Clinical codes- CTV3 (Read V3) with TPP extensions

    • Repository- LSHTM Data Compass - Description- Read codes and terms for an lower respiratory tract infection (LRTI) (exacerbations algorithm) (CPRD) - Conditions- Lower respiratory tract infection - Publication- https://doi.org/10.17037/DATA.00001652 - Clinical codes- CPRD GOLD Medcodes

      (DOI:10.17037/DATA.00001652)

    • Repository- LSHTM Data Compass - Description- Read codes for lower respiratory tract infections - Conditions- Lower respiratory tract infection - Publication- https://doi.org/10.17037/DATA.00002049 - Clinical codes- CPRD GOLD Medcodes

      (DOI:10.17037/DATA.00002049)

    • Repository- LSHTM Data Compass - Description- ICD-10 codes for lower respiratory tract infections - Conditions- Lower respiratory tract infection - Publication- https://doi.org/10.17037/DATA.00002050 - Clinical codes- ICD-10

      (DOI:10.17037/DATA.00002050)

    Citation Example

    Eleftheria Vasileiou, Chukwuma Iwundu, Alex Williams, Clare MacRae. PH787 / 2211 - Acute bronchitis Biobank. Phenotype Library [Online]. 04 August 2022. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH787/version/2211/detail/. [Accessed 21 November 2024]

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH787/version/2211/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(
     'PH787',
     version_id=2211
    )

    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(
     'PH787',
     version_id=2211
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH787/version/2211/export/codes/?format=json
    CSV site_root/phenotypes/PH787/version/2211/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(
     'PH787',
     version_id=2211
    )

    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(
     'PH787',
     version_id=2211
    )

  7. Version History

    Version IDNameOwnerPublish date
    2211 Acute bronchitis Biobank zinnurar2022-08-09currently shown
    1653 Acute bronchitis Biobank zinnurar2022-01-17