Pneumonia Biobank

Eleftheria Vasileiou, Chukwuma Iwundu, Alex Williams, Clare MacRae

PH796 / 1671 Clinical-Coded Phenotype

  1. Overview

    Phenotype Type
    Disease or syndrome
    Sex
    Both
    Valid Event Date Range
    01/01/2001 to 31/01/2021
    Coding System
    UKBioBank codes
    Data Sources
    Hospital Episode Statistics Admitted Patient Care, UK Biobank, CPRD Aurum, Office of National Statistics (ONS), CPRD GOLD
    Collections
    BREATHEPhenotype Library
    Tags
    No data

  2. Definition

    • Not found code search
    • The definition of pneumonia has not been validated.

  3. Implementation

    Implementation

    These codes will capture both community- and hospital-acquired pneumonia. These codes are not intended to be mandatory, but are to be used as a starting point for the identification of pneumonia in routine EHR. Each study may differ in the sensitivity and specificity of the coding required.

    Defining a community-acquired pneumonia occurrence in CPRD and HES, Millett et al. 2013 used the following algorithm:

    1) Pneumonia records wtihin 28 days of each other were considered to be separate consultations for the same illness

    2) First record of pneumonia was the index date

    3) End of a pneumonia occurrence was defined as 28 days after the last pneumonia code within the illness episode

    4) In HES, pneumonia coded as the primary diagnosis on the first day of a hospital admission

    Defining a hospital-acquired pneumonia occurrence in HES and CPRD, Millett et al. 2013 used the following algorithm:

    1) Pneumonia coded at any time beyond the first day of a hospital admission

    2) Using CPRD in conjunction with HES, pneumonia coded in CPRD within 14 days of a hospital admission (for any cause) was deemed hospital-acquired

    3) In CPRD, use of a hospital-acquired pneumonia code at any time during the pneumonia occurrence

    Millett, E. R., Quint, J. K., Smeeth, L., Daniel, R. M., & Thomas, S. L. (2013). Incidence of community-acquired lower respiratory tract infections and pneumonia among older adults in the United Kingdom: a population-based study. PLoS One, 8(9), e75131. doi:10.1371/journal.pone.0075131

    Defining a community-acquired pneumonia resulting in hospitalisation occurrence in HES, Hicks et al. 2016 used the following algorithm:

    1) In HES, hospital admission following A&E visit, where pneumonia was coded as the primary diagnosis within two days of admission

    Defining a hospital-acquired pneumonia occurrence in CPRD and HES, Hicks et al. 2016 used the following algorithm:

    1) Pneumonia diagnosis in HES >2 days after hospital admission

    2) Pneumonia diagnosed in CPRD within 7 days after hospital discharge

    Hicks, B. M., Yin, H., Bladou, F., Ernst, P., & Azoulay, L. (2017). Androgen deprivation therapy for prostate cancer and the risk of hospitalisation for community-acquired pneumonia. Thorax, 72(7), 596-597. doi:10.1136/thoraxjnl-2016-209512

    Defining a hospital-acquired respiratory infection including pneumonia occcurence using ICD-10 codes, Timmers et al. 2020 used the following algorithm:

    1) The main diagnosis of acute hospital admission records, excluding any secondary diagnoses, was used to classify records into disease categories, which corresponded to disease blocks as described in the chapters of ICD-10.

    2) Mortality trends were modelled using morbidity trends: we first determined the major disease categories (ICD-10 blocks) associated with the most lives lost.

    Timmers PRHJ, Kerssens JJ, Minton J, Grant I, Wilson JF, Campbell H, Fischbacher CM, Joshi PK. Trends in disease incidence and survival and their effect on mortality in Scotland: nationwide cohort study of linked hospital admission and death records 2001-2016. BMJ Open. 2020 Mar 25;10(3):e034299. doi: 10.1136/bmjopen-2019-034299. PMID: 32217562; PMCID: PMC7170664.

    Defining a hospital-acquired respiratory infection including pneumonia occcurence using ICD-10 codes, Brunner-La Rocca et al. 2020 used the following algorithm:

    1) Both bespoke chronic diseases (ICD-classification) and Clinical Classification Software (CCS) codes were used to define bacterial pneumonia as index hospitalisation.

    Brunner-La Rocca HP, Peden CJ, Soong J, Holman PA, Bogdanovskaya M, Barclay L. Reasons for readmission after hospital discharge in patients with chronic diseases-Information from an international dataset. PLoS One. 2020 Jun 30;15(6):e0233457. doi: 10.1371/journal.pone.0233457. PMID: 32603361; PMCID: PMC7326238.

    Defining a hospital-acquired respiratory infection including pneumonia occcurence using ICD-10 codes, Reynurn et al. 2020 used the following algorithm:

    1) all-cause pneumonia (which is highly sensitive but not specific), and three clinical definitions based on WHO definitions of severe or very severe pneumonia, hypoxic pneumonia (which indicates severe disease and is the main cause for pneumonia-associated death), and radiological pneumonia

    2) All-cause pneumonia included ICD-10 codes J10·0–18·9, J21, and J22. Bronchiolitis (ICD-10 code J21) was included because clinicians in Fiji code pneumonia according to Integrated Management of Childhood Illnesses definitions (cough and breathing rate, according to age) and this includes bronchiolitis.

    3) Severe or very severe pneumonia was based on the WHO 2005 pneumonia case definitions10 with the addition of oxygen saturation of less than 90% in room air, or death due to pneumonia (confirmed by a pathologist at autopsy).

    4) Hypoxic pneumonia was defined as any child with pneumonia and oxygen saturation of less than 90% in room air, or death due to pneumonia.

    5) Radiological pneumonia was defined as primary endpoint consolidation according to the WHO 2005 standard case definition as re-read by a paediatric radiologist (MdC). Individuals with pneumonia who died from pneumonia before having a chest radiograph taken were also classified as having radiological pneumonia.

    Reyburn R, Tuivaga E, Nguyen CD, Ratu FT, Nand D, Kado J, Tikoduadua L, Jenkins K, de Campo M, Kama M, Devi R, Rafai E, Weinberger DM, Mulholland EK, Russell FM. Effect of ten-valent pneumococcal conjugate vaccine introduction on pneumonia hospital admissions in Fiji: a time-series analysis. Lancet Glob Health. 2021 Jan;9(1):e91-e98. doi: 10.1016/S2214-109X(20)30421-6. Epub 2020 Nov 20. PMID: 33227258.

    Defining a community-acquired pneumonia resulting in hospitalisation occurrence, Lawrence et al. 2020 used the following algorithm:

    1) Cases were identified by participating institutions via ICD10 codes mapping to a primary discharge diagnosis of pneumonia (J12.0–J18.0) and selected for eligibility against inclusion criteria to confirm a clinical and radiographic diagnosis of Community-Acquired Pneumonia (CAP).

    Lawrence H, McKeever TM, Lim WS; British Thoracic Society. Admission to hospital in the UK at a weekend does not influence the prognosis of adults with community-acquired pneumonia. Thorax. 2020 Jul;75(7):594-596. doi: 10.1136/thoraxjnl-2019-214318. Epub 2020 Mar 31. PMID: 32234807.

    Not found code search

  4. Clinical Code List

  5. Publication

    • Publications between 2013-2019 identifying pneumonia in CPRD and/or HES

    • Millett, E. R., Quint, J. K., Smeeth, L., Daniel, R. M., & Thomas, S. L. (2013). Incidence of community-acquired lower respiratory tract infections and pneumonia among older adults in the United Kingdom: a population-based study. PLoS One, 8(9), e75131. doi:10.1371/journal.pone.0075131

      (DOI:10.1371/journal.pone.0075131)

    • Braeken, D. C., Rohde, G. G., Franssen, F. M., Driessen, J. H., van Staa, T. P., Souverein, P. C., . . . de Vries, F. (2017). Risk of community-acquired pneumonia in chronic obstructive pulmonary disease stratified by smoking status: a population-based cohort study in the United Kingdom. Int J Chron Obstruct Pulmon Dis, 12, 2425-2432. doi:10.2147/COPD.S138435

      (DOI:10.2147/COPD.S138435)

    • Hicks, B. M., Yin, H., Bladou, F., Ernst, P., & Azoulay, L. (2017). Androgen deprivation therapy for prostate cancer and the risk of hospitalisation for community-acquired pneumonia. Thorax, 72(7), 596-597. doi:10.1136/thoraxjnl-2016-209512

      (DOI:10.1136/thoraxjnl-2016-209512)

    • Sun, X., Douiri, A., & Gulliford, M. (2019). Pneumonia incidence trends in UK primary care from 2002 to 2017: population-based cohort study. Epidemiol Infect, 147, e263. doi:10.1017/S0950268819001559

      (DOI:10.1017/S0950268819001559)

    • Publications in 2020-2021 identified in PubMed

    • Timmers PRHJ, Kerssens JJ, Minton J, et al. (2020). Trends in disease incidence and survival and their effect on mortality in Scotland: nationwide cohort study of linked hospital admission and death records 2001–2016. BMJ Open 2020;10:e034299. doi: 10.1136/bmjopen-2019-034299

      (DOI:10.1136/bmjopen-2019-034299)

    • Brunner-La Rocca HP, Peden CJ, Soong J, Holman PA, Bogdanovskaya M, et al. (2020) Reasons for readmission after hospital discharge in patients with chronic diseases—Information from an international dataset. PLOS ONE 15(6): e0233457. https://doi.org/10.1371/journal.pone.0233457

      (DOI:10.1371/journal.pone.0233457)

    • Reyburn R, Tuivaga E, Nguyen CD, Ratu FT, Nand D, Kado J, Tikoduadua L, Jenkins K, de Campo M, Kama M, Devi R, Rafai E, Weinberger DM, Mulholland EK, Russell FM. Effect of ten-valent pneumococcal conjugate vaccine introduction on pneumonia hospital admissions in Fiji: a time-series analysis. Lancet Glob Health. 2021 Jan;9(1):e91-e98. doi: 10.1016/S2214-109X(20)30421-6. Epub 2020 Nov 20. PMID: 33227258.

      (DOI:10.1016/S2214-109X(20)30421-6)

    • Lawrence H, McKeever TM, Lim WS; British Thoracic Society. Admission to hospital in the UK at a weekend does not influence the prognosis of adults with community-acquired pneumonia. Thorax. 2020 Jul;75(7):594-596. doi: 10.1136/thoraxjnl-2019-214318. Epub 2020 Mar 31. PMID: 32234807.

      (DOI:10.1136/thoraxjnl-2019-214318)

    • Mesalles-Naranjo O, Grant I, Wyper GMA, et al. Trends and inequalities in the burden of mortality in Scotland 2000–2015. PLoS One 2018

    • Bennett JE, Pearson-Stuttard J, Kontis V, et al. Contributions of diseases and injuries to widening life expectancy inequalities in England from 2001 to 2016: a population-based analysis of vital registration data. Lancet Public Health 2018

    • Code repositories

    • ID- Manchester Clinical Codes 52 - Repository- Manchester ClinicalCodes - Description- Risks of smoking and benefits of smoking cessation on hospitalisations for cardiovascular events and respiratory infection in patients with rheumatoid arthritis: a retrospective cohort study using the Clinical Practice Research Datalink - Conditions- Respiratory tract infection - Publication- https://doi.org/10.1136/rmdopen-2017-000506 - Clinical codes- ICD-10

      (DOI:10.1136/rmdopen-2017-000506)

    • ID- Manchester Clinical Codes 42 - Repository- Manchester ClinicalCodes - Description- Smoking-related mortality in patients with early rheumatoid arthritis – a retrospective cohort study using the Clinical Practice Research Datalink - Conditions- Respiratory tract infection - Publication- https://doi.org/10.1002/acr.22882 - Clinical codes- ICD-10

      (DOI:10.1002/acr.22882)

    • ID- HDR UK National Phenomics Resource Project (aspiration pneumonitis) - 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- Aspiration pneumonitis - Publication- https://doi.org/10.1016/S2589-7500(19)30012-3 - Clinical codes- Read Version 2 & ICD-10

      (DOI:10.1016/S2589-7500(19)30012-3)

    • ID- HDR UK National Phenomics Resource Project (bacterial diseases, excl TB) - 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- HDR UK National Phenomics Resource Project (LRTI) - 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-10

      (DOI:10.1016/S2589-7500(19)30012-3)

    • ID- HDR UK National Phenomics Resource Project (other/unspecified infectious organisms) - 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- Other or unspecified infectious organisms - Publication- https://doi.org/10.1016/S2589-7500(19)30012-3 - Clinical codes- ICD-10

      (DOI:10.1016/S2589-7500(19)30012-3)

    • ID- HDR UK National Phenomics Resource Project (TB) - 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- TB - Publication- https://doi.org/10.1016/S2589-7500(19)30012-3 - Clinical codes- Read Version 2 & ICD-10

      (DOI:10.1016/S2589-7500(19)30012-3)

    • ID- HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV) - 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- Viral diseases (excl chronic hepatitis/HIV) - Publication- https://doi.org/10.1016/S2589-7500(19)30012-3 - Clinical codes- ICD-10

      (DOI:10.1016/S2589-7500(19)30012-3)

    • ID- HDR UK National Phenomics Resource Project (pneumonia, 10.1371) - 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 UK Biobank

      (DOI:10.1371/journal.pone.0075131)

    • ID- HDR UK National Phenomics Resource Project (pneumonia, 10.2147) - Repository- HDR UK National Phenomics Resource Project - Description- Risk of community-acquired pneumonia in chronic obstructive pulmonary disease stratified by smoking status: a population-based cohort study in the United Kingdom - Conditions- Pneumonia - Publication- https://doi.org/10.2147/COPD.S138435 - Clinical codes-

      (DOI:10.2147/COPD.S138435)

    • ID- HDR UK National Phenomics Resource Project (pneumonia, 10.1136) - Repository- HDR UK National Phenomics Resource Project - Description- Androgen deprivation therapy for prostate cancer and the risk of hospitalisation for community-acquired pneumonia - Conditions- Pneumonia - Publication- http://dx.doi.org/10.1136/thoraxjnl-2016-209512 - Clinical codes-

      (DOI:10.1136/thoraxjnl-2016-209512)

    • ID- HDR UK National Phenomics Resource Project (pneumonia, 10.1017) - Repository- HDR UK National Phenomics Resource Project - Description- Pneumonia incidence trends in UK primary care from 2002 to 2017: population-based cohort study - Conditions- Pneumonia - Publication- https://doi.org/10.1017/S0950268819001559 - Clinical codes-

      (DOI:10.1017/S0950268819001559)

    • ID- OpenSAFELY (2020-05-18) - Repository- OpenSAFELY - Description- Codes indicating a diagnosis of influenza or influenza-like illness - Conditions- Documented influenza illness - Publication- - Clinical codes- CTV3 (Read V3) with TPP extensions

    • ID- OpenSAFELY (2020-05-19) - Repository- OpenSAFELY - Description- Codes indicating a diagnosis of a lower respiratory tract infection excluding pneumonia - Conditions- Lower respiratory tract infection - Publication- - Clinical codes- CTV3 (Read V3) with TPP extensions

    • ID- OpenSAFELY (2020-05-10) - Repository- OpenSAFELY - Description- Pneumonia ICD-10 codes - Conditions- Pneumonia secondary care - Publication- - Clinical codes- ICD-10

    • ID- OpenSAFELY (2020-07-16) - Repository- OpenSAFELY - Description- Codes indicating COVID-19 case (1 of 13 possible types of CTV3 codes that contain information related to COVID-19) - Conditions- COVID identification in primary care - probable covid - sequelae - Publication- - Clinical codes- CTV3 (Read V3)

    • ID- LSHTM Data Compass (2049) - Repository- LSHTM Data Compass - Description- Read codes for lower respiratory tract infections - Conditions- Lower respiratory tract infection - Publication- https://doi.org/10.17037/DATA.00002049 - Clinical codes- CPRD GOLD Medcodes

      (DOI:10.17037/DATA.00002049)

    • ID- LSHTM Data Compass (2050) - Repository- LSHTM Data Compass - Description- ICD-10 codes for lower respiratory tract infections - Conditions- Lower respiratory tract infection - Publication- https://doi.org/10.17037/DATA.00002050 - Clinical codes- ICD-10

      (DOI:10.17037/DATA.00002050)

    • ID- LSHTM Data Compass (0847) - Repository- LSHTM Data Compass - Description- ICD-10 codes for pneumonia - Conditions- Pneumonia - Publication- https://doi.org/10.17037/DATA.00000847 - Clinical codes- ICD-10

      (DOI:10.17037/DATA.00000847)

    • ID- LSHTM Data Compass (1654) - Repository- LSHTM Data Compass - Description- Read codes and terms used for pneumonia (CPRD) - Conditions- Pneumonia - Publication- https://doi.org/10.17037/DATA.00001654 - Clinical codes- Read Version 2 & CPRD GOLD Medcodes

      (DOI:10.17037/DATA.00001654)

    • ID- Oxford-RCGP RSC - Repository- Oxford-RCGP RSC - Description- Surveillance & acute pathways of care theme - Conditions- PneumoniaOrPneumonitis-WRpt - Publication- - Clinical codes-

    Citation Example

    Eleftheria Vasileiou, Chukwuma Iwundu, Alex Williams, Clare MacRae. PH796 / 1671 - Pneumonia Biobank. Phenotype Library [Online]. 17 January 2022. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH796/version/1671/detail/. [Accessed 23 November 2024]

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH796/version/1671/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(
     'PH796',
     version_id=1671
    )

    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(
     'PH796',
     version_id=1671
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH796/version/1671/export/codes/?format=json
    CSV site_root/phenotypes/PH796/version/1671/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(
     'PH796',
     version_id=1671
    )

    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(
     'PH796',
     version_id=1671
    )

  7. Version History

    Version IDNameOwnerPublish date
    2220 Pneumonia Biobank zinnurar2022-08-08
    1671 Pneumonia Biobank zinnurar2022-01-17currently shown