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Pertussis or Whooping cough Secondary care

Chukwuma Iwundu, Clare MacRae, Eleftheria Vasileiou

Type
Disease or syndrome
ID
PH809
Version ID
2233
Valid event data range
01/01/2001 to 31/01/2021
Sex
Female/Male
Agreement Date
2021-12-10
Coding system
ICD10 codes ICD9 codes ICD11 codes
Tags /Collections
BREATHE Phenotype Library

Definition

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

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


Publications

  • 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

  • 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.

  • 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

  • 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

  • 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

  • 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

Clinical Code List

Rows: 3
Code Description BREATHE recommended
1C12.0 Whooping cough due to Bordetella pertussis Y
1C12.1 Whooping cough due to Bordetella parapertussis Y
1C12.Z Whooping cough, unspecified Y
Rows: 4
Code Description BREATHE recommended Sturkenboom et al, 2020 Gini et al, 2020 Becker et al, 2017
033 Whooping cough Y Y Y
033.0 Whooping cough due to bordetella pertussis Y Y
033.8 Whooping cough due to other specified organism Y Y
484.3 Pneumonia in whooping cough Y Y
Rows: 7
Code Description BREATHE recommended Sturkenboom et al, 2020 Gini et al, 2020 Becker et al, 2017 HDR UK National Phenomics Resource Project 2 HDR UK National Phenomics Resource Project 3
A37 Whooping cough Y Y Y Y
A37.0 Whooping cough due to Bordetella pertussis Y Y Y Y
A37.00 Whooping cough due to Bordetella pertussis without pneumonia Y Y
A37.01 Whooping cough due to Bordetella pertussis with pneumonia Y Y
A37.1 Whooping cough due to Bordetella parapertussis Y
A37.8 Whooping cough due to other Bordetella species Y Y
A37.9 Whooping cough, unspecified Y Y
Rows: 3
Code Description
1C12.0 Whooping cough due to Bordetella pertussis
1C12.1 Whooping cough due to Bordetella parapertussis
1C12.Z Whooping cough, unspecified
Rows: 4
Code Description
033 Whooping cough
033.0 Whooping cough due to bordetella pertussis
033.8 Whooping cough due to other specified organism
484.3 Pneumonia in whooping cough
Rows: 7
Code Description
A37 Whooping cough
A37.0 Whooping cough due to Bordetella pertussis
A37.00 Whooping cough due to Bordetella pertussis without pneumonia
A37.01 Whooping cough due to Bordetella pertussis with pneumonia
A37.1 Whooping cough due to Bordetella parapertussis
A37.8 Whooping cough due to other Bordetella species
A37.9 Whooping cough, unspecified

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH809/version/2233/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH809/version/2233/detail/?format=json
R Package

# Download here

library(ConceptLibraryClient)


# Connect to API

client = connect_to_API(public=TRUE)


# Get details of phenotype

details = get_phenotype_detail_by_version('PH809', '2233', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH809/version/2233/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH809/version/2233/export/codes/?format=json
CSV site_root/phenotypes/PH809/version/2233/export/codes/
R Package

# Download here

library(ConceptLibraryClient)


# Connect to API

client = connect_to_API(public=TRUE)


# Get codelists of phenotype

codelists = get_phenotype_code_list('PH809', '2233', api_client=client)

Version History

Version
ID
Name Owner Publish date
2233 Pertussis or Whooping cough Secondary care zinnurar 2022-08-08 currently shown
1697 Pertussis or Whooping cough Secondary care zinnurar 2022-01-17

Export - export all codes into a csv file/JSON/XML for the current phenotype version.

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