Phenotypes > Tuberculosis Primary care

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Tuberculosis Primary care

Chukwuma Iwundu, Clare MacRae, Eleftheria Vasileiou

ID
PH818
Version ID
2252
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
2022-01-21
Coding system
Read codes v2 SNOMED CT codes
Collections
BREATHE Phenotype Library
Tags
No tags

Definition

The aim of this research work was to identify relevant diagnosis codes available in routine electronic health records from primary and secondary care settings in the UK. We looked for relevant codes in code repositories such as the University of Cambrigdge Primary Care Unit, Manchester Clinical Codes, HDR UK National Phenomics Resource Project, Oxford-RCGP RSC, OpenSAFELY and LSHTM Data Compass. We also searched for peer-reviewed studies published via PubMed in the last 12 months for any relevant codes. Please note that these codes are not intended to be mandatory, but are to be used as a starting point for the identification of Tuberculosis in routine electronic health record. Therefore, each study may differ in the sensitivity and specificity of the coding required. - No validation available

Implementation

According to NHS, tuberculosis is a bacterial infection spread through inhaling tiny droplets from the coughs or sneezes of an infected person. It mainly affects the lungs, but it can affect any part of the body, including the tummy (abdomen), glands, bones and nervous system.

https://www.nhs.uk/conditions/tuberculosis-tb/

Not found code search


Publications

  • No publications idenified via Pubmed in the last 12 months

Clinical Code List

Expand All  /  Collapse All
Rows: 68
Code Description SNOMED CT Concept ID Read v2 BREATHE recommended
128905016 Isolated tracheal tuberculosis 77668003 Y
130160016 Tuberculosis of intrathoracic lymph nodes 78436002 Y
132741012 Isolated bronchial tuberculosis 80010008 Y
1760211000006110 Mycobacterium tuberculosis 113861009 Y
1788181018 Nodular lung tuberculosis 80602006 Y
1834101000006110 Sputum culture mycobacterium tuberculosis positive 1834101000006100 Y
239551014 Pulmonary tuberculosis 154283005 Y
2437721000000110 Extensively drug resistant tuberculosis 710106005 Y
2533735010 Streptomycin resistant tuberculosis 415622003 Y
2533736011 Rifampicin resistant tuberculosis 415345001 Y
2533737019 Pyrazinamide resistant tuberculosis 415222009 Y
2533738012 Isoniazid resistant tuberculosis 414546009 Y
2533739016 Ethionamide resistant tuberculosis 414149006 Y
2533740019 Ethambutol resistant tuberculosis 414146004 Y
2533741015 Ciprofloxacin resistant tuberculosis 413852006 Y
2646197017 Multidrug resistant tuberculosis 423092005 Y
281631019 Disseminated tuberculosis 182159002 Y
286214019 Tuberculous pleurisy in primary progressive tuberculosis 186172004 Y
286215018 Other primary progressive tuberculosis 111832004 Y
286217014 Infiltrative lung tuberculosis 186175002 Y
286219012 Tuberculosis of lung with cavitation 186177005 Y
286220018 Tuberculosis of bronchus 186178000 Y
286221019 Other specified pulmonary tuberculosis 154283005 Y
286222014 Pulmonary tuberculosis NOS 154283005 Y
286223016 Other respiratory tuberculosis 154283005 Y
286224010 Tuberculosis of pleura 186182003 Y
286231014 Tuberculosis of intrathoracic lymph nodes NOS 78436002 Y
286232019 Isolated tracheal or bronchial tuberculosis 700273003 Y
286235017 Isolated tracheal or bronchial tuberculosis NOS 700273003 Y
286238015 Tuberculosis of lung, confirmed by culture only 186194007 Y
286239011 Tuberculosis of lung, confirmed histologically 186195008 Y
286242017 Tuberculosis of lung, confirmed by unspecified means 154283005 Y
286252018 Other specified respiratory tuberculosis 154283005 Y
286257012 Other specified respiratory tuberculosis NOS 154283005 Y
286332017 Acute miliary tuberculosis 186276006 Y
286333010 Acute miliary tuberculosis of a single specified site 186276006 Y
286334016 Acute miliary tuberculosis of multiple sites 186278007 Y
286335015 Other specified miliary tuberculosis 47604008 Y
286336019 Miliary tuberculosis NOS 47604008 Y
287959013 Late effects of respiratory tuberculosis 187252008 Y
288006011 [X]Acute miliary tuberculosis, unspecified 186276006 Y
288007019 [X]Other miliary tuberculosis 47604008 Y
288008012 [X]Miliary tuberculosis, unspecified 47604008 Y
288298014 [X]Sequelae of respiratory and unspecified tuberculosis 187251001 Y
301563019 Pneumoconiosis associated with tuberculosis 196017002 Y
3269821000006110 MTB - Miliary tuberculosis 47604008 Y
3421371000006110 TB - Tuberculosis 56717001 Y
3529611000006110 Primary tuberculosis 63309002 Y
3529631000006110 Primary (TB) tuberculosis 63309002 Y
3643901000006110 Laryngeal tuberculosis 70341005 Y
3643911000006110 Tuberculosis (TB) with laryngitis 70341005 Y
3763601000006110 Tuberculosis of trachea 77668003 Y
3811041000006110 Nodular tuberculosis of lung 80602006 Y
429601000006111 [X]Tuberculosis 56717001 Y
4514601000006110 PTB - Pulmonary tuberculosis 154283005 Y
4514611000006110 TB - Pulmonary tuberculosis 154283005 Y
4711621000006110 Generalized tuberculosis 182159002 Y
4711631000006110 Generalised tuberculosis 182159002 Y
4740991000006110 Primary progressive tuberculosis with tuberculous pleurisy 186172004 Y
4741011000006110 Infiltrative tuberculosis of lung 186175002 Y
732921000006113 Lung tuberculosis 154283005 Y
878951000006115 Primary tuberculosis infection 63309002 Y
89091000006114 Tuberculosis lung bact and histological examin not done 186204008 Y
89391000006112 Tuberculosis of larynx, trachea & bronchus conf bact/hist'y 186199002 Y
89451000006113 Tuberculosis of lung, bacteriologically & histolog'y neg 186203002 Y
907551000006110 [RFC] Tuberculosis 907551000006106 Y
93954019 Tuberculosis of nasopharynx 56498009 Y
94320019 Tuberculosis 56717001 Y
Rows: 44
Code Description CPRD GOLD Med BREATHE recommended
65Y2.00 Streptomycin resistant tuberculosis 91666 Y
65Y3.00 Rifampicin resistant tuberculosis 115044 Y
65Y5.00 Isoniazid resistant tuberculosis 102673 Y
A1...00 Tuberculosis 1840 Y
A101.00 Tuberculous pleurisy in primary progressive tuberculosis 46272 Y
A10y.00 Other primary progressive tuberculosis 42630 Y
A11..00 Pulmonary tuberculosis 635 Y
A11..11 Lung tuberculosis 47336 Y
A110.00 Infiltrative lung tuberculosis 53701 Y
A111.00 Nodular lung tuberculosis 48580 Y
A112.00 Tuberculosis of lung with cavitation 16331 Y
A113.00 Tuberculosis of bronchus 62468 Y
A11z.00 Pulmonary tuberculosis NOS 38110 Y
A12..00 Other respiratory tuberculosis 63959 Y
A120000 Tuberculosis of pleura 37834 Y
A121.00 Tuberculosis of intrathoracic lymph nodes 58827 Y
A121000 Tuberculosis of hilar lymph nodes 5145 Y
A121200 Tuberculosis of tracheobronchial lymph nodes 49503 Y
A122.00 Isolated tracheal or bronchial tuberculosis 69260 Y
A122000 Isolated tracheal tuberculosis 93015 Y
A122100 Isolated bronchial tuberculosis 93948 Y
A122z00 Isolated tracheal or bronchial tuberculosis NOS 53473 Y
A124100 Tuberculosis of lung, confirmed by culture only 93071 Y
A124200 Tuberculosis of lung, confirmed histologically 62530 Y
A124300 Tuberculosis of lung, confirmed by unspecified means 58588 Y
A124500 Tuberculosis of larynx, trachea & bronchus conf bact/hist'y 44039 Y
A125000 Tuberculosis of lung, bacteriologically & histolog'y neg 47832 Y
A125100 Tuberculosis lung bact and histological examin not done 41051 Y
A12y100 Tuberculosis of nasopharynx 72402 Y
A12yz00 Other specified respiratory tuberculosis NOS 50147 Y
A18..00 Miliary tuberculosis 16414 Y
A180.00 Acute miliary tuberculosis 72008 Y
A180000 Acute miliary tuberculosis of a single specified site 31844 Y
A18y.00 Other specified miliary tuberculosis 32459 Y
A18z.00 Miliary tuberculosis NOS 53331 Y
A19..00 Disseminated tuberculosis 110373 Y
A1A..00 Multidrug resistant tuberculosis 111299 Y
A1z..00 Tuberculosis NOS 15158 Y
AE00.00 Late effects of respiratory tuberculosis 65464 Y
Ayu1.00 [X]Tuberculosis 73149 Y
Ayu1700 [X]Acute miliary tuberculosis, unspecified 113107 Y
Ayu1800 [X]Other miliary tuberculosis 106521 Y
Ayu1900 [X]Miliary tuberculosis, unspecified 97922 Y
AyuJ400 [X]Sequelae of respiratory and unspecified tuberculosis 93768 Y
Rows: 68
Code Description
128905016 Isolated tracheal tuberculosis
130160016 Tuberculosis of intrathoracic lymph nodes
132741012 Isolated bronchial tuberculosis
1760211000006110 Mycobacterium tuberculosis
1788181018 Nodular lung tuberculosis
1834101000006110 Sputum culture mycobacterium tuberculosis positive
239551014 Pulmonary tuberculosis
2437721000000110 Extensively drug resistant tuberculosis
2533735010 Streptomycin resistant tuberculosis
2533736011 Rifampicin resistant tuberculosis
2533737019 Pyrazinamide resistant tuberculosis
2533738012 Isoniazid resistant tuberculosis
2533739016 Ethionamide resistant tuberculosis
2533740019 Ethambutol resistant tuberculosis
2533741015 Ciprofloxacin resistant tuberculosis
2646197017 Multidrug resistant tuberculosis
281631019 Disseminated tuberculosis
286214019 Tuberculous pleurisy in primary progressive tuberculosis
286215018 Other primary progressive tuberculosis
286217014 Infiltrative lung tuberculosis
286219012 Tuberculosis of lung with cavitation
286220018 Tuberculosis of bronchus
286221019 Other specified pulmonary tuberculosis
286222014 Pulmonary tuberculosis NOS
286223016 Other respiratory tuberculosis
286224010 Tuberculosis of pleura
286231014 Tuberculosis of intrathoracic lymph nodes NOS
286232019 Isolated tracheal or bronchial tuberculosis
286235017 Isolated tracheal or bronchial tuberculosis NOS
286238015 Tuberculosis of lung, confirmed by culture only
286239011 Tuberculosis of lung, confirmed histologically
286242017 Tuberculosis of lung, confirmed by unspecified means
286252018 Other specified respiratory tuberculosis
286257012 Other specified respiratory tuberculosis NOS
286332017 Acute miliary tuberculosis
286333010 Acute miliary tuberculosis of a single specified site
286334016 Acute miliary tuberculosis of multiple sites
286335015 Other specified miliary tuberculosis
286336019 Miliary tuberculosis NOS
287959013 Late effects of respiratory tuberculosis
288006011 [X]Acute miliary tuberculosis, unspecified
288007019 [X]Other miliary tuberculosis
288008012 [X]Miliary tuberculosis, unspecified
288298014 [X]Sequelae of respiratory and unspecified tuberculosis
301563019 Pneumoconiosis associated with tuberculosis
3269821000006110 MTB - Miliary tuberculosis
3421371000006110 TB - Tuberculosis
3529611000006110 Primary tuberculosis
3529631000006110 Primary (TB) tuberculosis
3643901000006110 Laryngeal tuberculosis
3643911000006110 Tuberculosis (TB) with laryngitis
3763601000006110 Tuberculosis of trachea
3811041000006110 Nodular tuberculosis of lung
429601000006111 [X]Tuberculosis
4514601000006110 PTB - Pulmonary tuberculosis
4514611000006110 TB - Pulmonary tuberculosis
4711621000006110 Generalized tuberculosis
4711631000006110 Generalised tuberculosis
4740991000006110 Primary progressive tuberculosis with tuberculous pleurisy
4741011000006110 Infiltrative tuberculosis of lung
732921000006113 Lung tuberculosis
878951000006115 Primary tuberculosis infection
89091000006114 Tuberculosis lung bact and histological examin not done
89391000006112 Tuberculosis of larynx, trachea & bronchus conf bact/hist'y
89451000006113 Tuberculosis of lung, bacteriologically & histolog'y neg
907551000006110 [RFC] Tuberculosis
93954019 Tuberculosis of nasopharynx
94320019 Tuberculosis
Rows: 44
Code Description
65Y2.00 Streptomycin resistant tuberculosis
65Y3.00 Rifampicin resistant tuberculosis
65Y5.00 Isoniazid resistant tuberculosis
A1...00 Tuberculosis
A101.00 Tuberculous pleurisy in primary progressive tuberculosis
A10y.00 Other primary progressive tuberculosis
A11..00 Pulmonary tuberculosis
A11..11 Lung tuberculosis
A110.00 Infiltrative lung tuberculosis
A111.00 Nodular lung tuberculosis
A112.00 Tuberculosis of lung with cavitation
A113.00 Tuberculosis of bronchus
A11z.00 Pulmonary tuberculosis NOS
A12..00 Other respiratory tuberculosis
A120000 Tuberculosis of pleura
A121.00 Tuberculosis of intrathoracic lymph nodes
A121000 Tuberculosis of hilar lymph nodes
A121200 Tuberculosis of tracheobronchial lymph nodes
A122.00 Isolated tracheal or bronchial tuberculosis
A122000 Isolated tracheal tuberculosis
A122100 Isolated bronchial tuberculosis
A122z00 Isolated tracheal or bronchial tuberculosis NOS
A124100 Tuberculosis of lung, confirmed by culture only
A124200 Tuberculosis of lung, confirmed histologically
A124300 Tuberculosis of lung, confirmed by unspecified means
A124500 Tuberculosis of larynx, trachea & bronchus conf bact/hist'y
A125000 Tuberculosis of lung, bacteriologically & histolog'y neg
A125100 Tuberculosis lung bact and histological examin not done
A12y100 Tuberculosis of nasopharynx
A12yz00 Other specified respiratory tuberculosis NOS
A18..00 Miliary tuberculosis
A180.00 Acute miliary tuberculosis
A180000 Acute miliary tuberculosis of a single specified site
A18y.00 Other specified miliary tuberculosis
A18z.00 Miliary tuberculosis NOS
A19..00 Disseminated tuberculosis
A1A..00 Multidrug resistant tuberculosis
A1z..00 Tuberculosis NOS
AE00.00 Late effects of respiratory tuberculosis
Ayu1.00 [X]Tuberculosis
Ayu1700 [X]Acute miliary tuberculosis, unspecified
Ayu1800 [X]Other miliary tuberculosis
Ayu1900 [X]Miliary tuberculosis, unspecified
AyuJ400 [X]Sequelae of respiratory and unspecified tuberculosis

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH818/version/2252/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH818/version/2252/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('PH818', '2252', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH818/version/2252/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH818/version/2252/export/codes/?format=json
CSV site_root/phenotypes/PH818/version/2252/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('PH818', '2252', api_client=client)

Version History

Version
ID		 Name Owner Publish date
2252 Tuberculosis Primary care zinnurar 2022-08-09 currently shown
1715 Tuberculosis Primary care zinnurar 2022-01-21

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

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