Phenotypes > Pertussis or Whooping cough Primary care

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Pertussis or Whooping cough Primary care

Chukwuma Iwundu, Clare MacRae, Eleftheria Vasileiou

ID
PH808
Version ID
2232
Type
Disease or syndrome
Data Sources
Welsh Longitudinal General Practice Dataset (WLGP) , Clinical Practice Research Datalink AURUM , Clinical Practice Research Datalink GOLD
Valid event data range
01/01/2001 to 31/01/2021
Sex
♀  Female ♂  Male
Agreement Date
2021-12-10
Coding system
Read codes v2 CTV3 codes SNOMED CT codes
Collections
BREATHE Phenotype Library
Tags
No tags

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

Expand All  /  Collapse All
Rows: 8
Code Description BREATHE recommended Gini et al, 2020
65VA. Notification of whooping cough Y Y
A33z. Whooping cough due to unspecified organism Y Y
Ayu3A Whooping cough due to unspecified organism Y Y
H243. Pneumonia in pertussis Y Y
X70I8 Bordetella infections Y Y
X76Hf Whooping cough due to unspecified organism Y Y
XE0Qw Bordetella infections Y Y
XM00D Whooping cough-like syndrome Y Y
Rows: 29
Code Description SNOMED CT Concept ID SNOMED CT Description ID Read v2 BREATHE recommended Sturkenboom et al, 2020 Gini et al, 2020 Becker et al, 2017 HDR UK National Phenomics Resource Project 4
1227543018 [V]Whooping cough vaccination 39343008 65969010 ZV03611
1229516015 Whooping cough vaccination 39343008 1229516015 655..11
286448015 Whooping cough - other specified organism 27836007 46586010 A33y.00 Y Y
286451010 Other whooping cough NOS 27836007 46586010 A33yz00 Y Y
286452015 Whooping cough NOS 27836007 46589015 A33z.00 Y Y
288039014 [X]Whooping cough due to other Bordetella species 27836007 46586010 Ayu3900 Y Y
2946741000006110 Infection due to Bordetella pertussis 27836007 46588011
301128017 Acute bronchiolitis due to respiratory syncytial virus 195739001 301128017 H061500
301362011 Pneumonia due to respiratory syncytial virus 195881003 301362011 H201.00
3133011000006112 Whooping cough immunization 39343008 65970011
3133041000006111 RSV nucleic acid detection 39343008 492037018
317301000006111 [M]Syncytial meningioma 68944005 114505018 BBd3.12
3208291000006112 Hodgkin's disease, nodular sclerosis, syncytial variant 43985008 73345016
3621181000006115 Syncytial meningioma 68944005 114505018
4780491000006118 Acute respiratory syncytial virus bronchitis 195727009 301115012
4780571000006115 Acute bronchiolitis caused by respiratory syncytial virus 195739001 3290582012
4781131000006116 Pneumonia caused by respiratory syncytial virus 195881003 3291454010
689481000000119 Respiratory syncytial virus A detected 440929004 2791867012 4JU9.00
689541000000114 Respiratory syncytial virus B detected 441048007 2794534015 4JUA.00
689601000000110 Respiratory syncytial virus untyped strain detected 441278007 2790181019 4JUB.00
743621000033110 Pertussis Toxoid 743621000033106 743621000033110
885221000006117 Whooping cough pneumonia 59475000 885221000006117 H243.99
92677014 Respiratory syncytial virus infection 55735004 92677014 A79A.00
Not added - 1 Whooping cough Not added Not added A33.. Y Y
Not added - 2 Bordetella pertussis Not added Not added A330. Y Y Y
Not added - 3 [X] Whooping cough, unspecified Not added Not added Ayu3A Y Y Y Y
Not added - 4 Pneumonia with whooping cough 59475000 1230000000 H243. Y Y Y Y Y
Not added - 5 Whooping cough-like syndrome Not added Not added XM00D Y Y
Not added -6 Notification of whooping cough Not added Not added 65VA. Y Y
Rows: 22
Code Description CPRD GOLD Med BREATHE recommended Sturkenboom et al, 2020 Gini et al, 2020 Becker et al, 2017 Manchester Clinical Codes 1 HDR UK National Phenomics Resource Project 4
43jk.00 RSV nucleic acid detection 70173
43wE.00 Bordetella pertussis deoxyribonucleic acid detection 110596
4JU9.00 Respiratory syncytial virus A detected 96556
4JUA.00 Respiratory syncytial virus B detected 96323
65VA. Notification of whooping cough Y Y
A33.. Whooping cough Y Y Y
A330. Bordetella pertussis Y Y Y
A33y.00 Whooping cough - other specified organism 53897 Y Y
A33yz00 Other whooping cough NOS 64286 Y Y
A33z.00 Whooping cough NOS 42548 Y Y
A79A.00 Respiratory syncytial virus infection 12573
A7y0200 Resp syncytial virus as cause of dis class to other chapters 24462
Ayu3900 [X]Whooping cough due to other Bordetella species 114952 Y Y
Ayu3A [X] Whooping cough, unspecified Y Y Y Y
H060D00 Acute bronchitis due to respiratory syncytial virus 48593
H061500 Acute bronchiolitis due to respiratory syncytial virus 18451
H201.00 Pneumonia due to respiratory syncytial virus 31269
H243. Pneumonia with whooping cough Y Y Y Y Y
SLK8.00 Diptheria,tetanus,pertussis and polio vaccine poisoning 51676
XM00D Whooping cough-like syndrome Y Y
ZV03611 [V]Whooping cough vaccination 30197
ZV06200 [V]Diphtheria-tetanus-pertussis + typhoid-paratyphoid vacc 51652
Rows: 8
Code Description
65VA. Notification of whooping cough
A33z. Whooping cough due to unspecified organism
Ayu3A Whooping cough due to unspecified organism
H243. Pneumonia in pertussis
X70I8 Bordetella infections
X76Hf Whooping cough due to unspecified organism
XE0Qw Bordetella infections
XM00D Whooping cough-like syndrome
Rows: 10
Code Description
286448015 Whooping cough - other specified organism
286451010 Other whooping cough NOS
286452015 Whooping cough NOS
288039014 [X]Whooping cough due to other Bordetella species
Not added - 1 Whooping cough
Not added - 2 Bordetella pertussis
Not added - 3 [X] Whooping cough, unspecified
Not added - 4 Pneumonia with whooping cough
Not added - 5 Whooping cough-like syndrome
Not added -6 Notification of whooping cough
Rows: 10
Code Description
65VA. Notification of whooping cough
A33.. Whooping cough
A330. Bordetella pertussis
A33y.00 Whooping cough - other specified organism
A33yz00 Other whooping cough NOS
A33z.00 Whooping cough NOS
Ayu3900 [X]Whooping cough due to other Bordetella species
Ayu3A [X] Whooping cough, unspecified
H243. Pneumonia with whooping cough
XM00D Whooping cough-like syndrome

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH808/version/2232/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH808/version/2232/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('PH808', '2232', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH808/version/2232/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH808/version/2232/export/codes/?format=json
CSV site_root/phenotypes/PH808/version/2232/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('PH808', '2232', api_client=client)

Version History

Version
ID		 Name Owner Publish date
2232 Pertussis or Whooping cough Primary care zinnurar 2022-08-08 currently shown
1695 Pertussis or Whooping cough Primary care zinnurar 2022-01-17

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

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