Pertussis or Whooping cough Primary care

Chukwuma Iwundu, Clare MacRae, Eleftheria Vasileiou

PH808 / 1695 Clinical-Coded Phenotype

  1. Overview

    Phenotype Type
    Disease or syndrome
    Phenotype UUID
    excel-breathe-idXJCIA
    Sex
    Both
    Valid Event Date Range
    01/01/2001 to 31/01/2021
    Coding System
    Read codes v2SNOMED CT codesCTV3 codes
    Data Sources
    Collections
    BREATHEPhenotype Library
    Tags
    No data
  2. Definition

    • Not found code search
    • No validations were found via PubMed in the last 12 months
  3. Implementation

    Implementation

    These codes are not intended to be mandatory, but are to be used as a starting point for the identification of pertussis or whooping cough 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), whooping cough (also called pertussis) is a bacterial infection of the lungs and breathing tubes. It causes repeated coughing bouts that can last for two to three months or more, and can make babies and young children in particular very ill. The first symptoms of whooping cough are similar to those of a cold, such as a runny nose, red and watery eyes, a sore throat, and a slightly raised temperature. Intense coughing bouts start about a week later.

    https://www.nhs.uk/conditions/whooping-cough/

    https://www.nhsinform.scot/illnesses-and-conditions/infections-and-poisoning/whooping-cough

    According to the National Institute for Health and Care Excellence (NICE) guidelines, Whooping cough, also known as pertussis, is a highly infectious disease caused by the bacterium Bordetella pertussis. It is spread by aerosol droplets released during coughing, and disproportionately affects infants and young children. The incubation period of whooping cough is usually about 7 days, and the person is infectious for 3 weeks after the onset of symptoms.

    https://cks.nice.org.uk/topics/whooping-cough/

    Not found code search

  4. Clinical Code List

  5. Publication

    • Publications in 2020-2021 identified in PubMed

    • Sturkenboom M, Braeye T, van der Aa L, Danieli G, Dodd C, Duarte-Salles T, Emborg HD, Gheorghe M, Kahlert J, Gini R, Huerta-Alvarez C, Martín-Merino E, McGee C, de Lusignan S, Picelli G, Roberto G, Tramontan L, Villa M, Weibel D, Titievsky L. ADVANCE database characterisation and fit for purpose assessment for multi-country studies on the coverage, benefits and risks of pertussis vaccinations. Vaccine. 2020 Dec 22;38 Suppl 2:B8-B21. doi: 10.1016/j.vaccine.2020.01.100. Epub 2020 Feb 12. PMID: 320

      (DOI:10.1016/j.vaccine.2020.01.100)
    • Gini R, Dodd CN, Bollaerts K, Bartolini C, Roberto G, Huerta-Alvarez C, Martín-Merino E, Duarte-Salles T, Picelli G, Tramontan L, Danieli G, Correa A, McGee C, Becker BFH, Switzer C, Gandhi-Banga S, Bauwens J, van der Maas NAT, Spiteri G, Sdona E, Weibel D, Sturkenboom M. Quantifying outcome misclassification in multi-database studies: The case study of pertussis in the ADVANCE project. Vaccine. 2020 Dec 22;38 Suppl 2:B56-B64. doi: 10.1016/j.vaccine.2019.07.045. Epub 2019 Oct 31. PMID: 31677950.

      (DOI:10.1016/j.vaccine.2019.07.045)
    • Code repositories

    • ID- 1 - Repository- Manchester ClinicalCodes - Description- Antibiotic prescribing for common infections in UK general practice: variability and drivers - Conditions- Cough/cold - Publication- https://doi.org/10.1093/jac/dkz163 - Clinical codes- Read Version 2

      (DOI:10.1093/jac/dkz163)
    • ID- 2 - 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)
    • ID- 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-11

      (DOI:10.1016/S2589-7500(19)30012-3)
    • ID- 4 - Repository- HDR UK National Phenomics Resource Project - Description- Incidence of Community-Acquired Lower Respiratory Tract Infections and Pneumonia among Older Adults in the United Kingdom: A Population-Based Study - Conditions- Pneumonia - Publication- https://doi.org/10.1371/journal.pone.0075131 - Clinical codes- Read Version 2, SNOMED CT, ICD-10 & ICD-11

      (DOI:10.1371/journal.pone.0075131)

    Citation Example

    Chukwuma Iwundu, Clare MacRae, Eleftheria Vasileiou. PH808 / 1695 - Pertussis or Whooping cough Primary care. Phenotype Library [Online]. 17 January 2022. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH808/version/1695/detail/. [Accessed 23 July 2024]

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH808/version/1695/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(
     'PH808',
     version_id=1695
    )

    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(
     'PH808',
     version_id=1695
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH808/version/1695/export/codes/?format=json
    CSV site_root/phenotypes/PH808/version/1695/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(
     'PH808',
     version_id=1695
    )

    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(
     'PH808',
     version_id=1695
    )

  7. Version History

    Version IDNameOwnerPublish date
    2232 Pertussis or Whooping cough Primary care zinnurar2022-08-08
    1695 Pertussis or Whooping cough Primary care zinnurar2022-01-17currently shown