Pertussis or Whooping cough Primary care
Chukwuma Iwundu, Clare MacRae, Eleftheria Vasileiou
PH808 / 2232 Clinical-Coded Phenotype
Overview
Phenotype TypeDisease or syndromeSexBothValid Event Date Range01/01/2001 to 31/01/2021Coding SystemRead codes v2SNOMED CT codesCTV3 codesCollectionsBREATHEPhenotype LibraryTagsNo dataDefinition
- Not found code search
- No validations were found via PubMed in the last 12 months
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
Clinical Code List
PUBLISHED - 8 Codes
PUBLISHED - 29 Codes
PUBLISHED - 22 Codes
PUBLISHED - 8 Codes
PUBLISHED - 10 Codes
PUBLISHED - 10 Codes
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)
No dataCitation Requirements
API
To Export Phenotype Details:
Format API JSON site_root/api/v1/phenotypes/PH808/version/2232/detail/?format=json R Package library(ConceptLibraryClient)
# Connect to API
client = ConceptLibraryClient::Connection$new(public=TRUE)
# Get details of phenotype
phenotype_details = client$phenotypes$get_detail(
'PH808',
version_id=2232
)Py Package from pyconceptlibraryclient import Client
# Connect to API
client = Client(public=True)
# Get codelist of phenotype
phenotype_codelist = client.phenotypes.get_detail(
'PH808',
version_id=2232
)To Export Phenotype Code List:
Format API JSON site_root/api/v1/phenotypes/PH808/version/2232/export/codes/?format=json CSV site_root/phenotypes/PH808/version/2232/export/codes/ R Package library(ConceptLibraryClient)
# Connect to API
client = ConceptLibraryClient::Connection$new(public=TRUE)
# Get codelist of phenotype
phenotype_codelist = client$phenotypes$get_codelist(
'PH808',
version_id=2232
)Py Package from pyconceptlibraryclient import Client
# Connect to API
client = Client(public=True)
# Get codelist of phenotype
phenotype_codelist = client.phenotypes.get_codelist(
'PH808',
version_id=2232
)Version History