Pneumonia
Eleanor L Axson, Jennifer K Quint
PH15 / 30 Clinical-Coded Phenotype
Overview
Phenotype TypeDisease or syndromeSexBothValid Event Date Range01/01/2001 - 31/12/2019Coding SystemICD10 codesRead codes v2SNOMED CT codesICD11 codesCollectionsPhenotype LibraryTagsNo dataDefinition
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
Implementation
Phenoflow ID
No dataImplementation
Clinical Code List
PUBLISHED - 88 Codes
PUBLISHED - 58 Codes
PUBLISHED - 88 Codes
PUBLISHED - 58 Codes
PUBLISHED - 10 Codes
PUBLISHED - 10 Codes
PUBLISHED - 1 Codes
Publication
Publications 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)
Citation Example
Eleanor L Axson, Jennifer K Quint. PH15 / 30 - Pneumonia. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH15/version/30/detail/. [Accessed 20 September 2024]
API
To Export Phenotype Details:
Format API JSON site_root/api/v1/phenotypes/PH15/version/30/detail/?format=json R Package library(ConceptLibraryClient)
# Connect to API
client = ConceptLibraryClient::Connection$new(public=TRUE)
# Get details of phenotype
phenotype_details = client$phenotypes$get_detail(
'PH15',
version_id=30
)Py Package from pyconceptlibraryclient import Client
# Connect to API
client = Client(public=True)
# Get codelist of phenotype
phenotype_codelist = client.phenotypes.get_detail(
'PH15',
version_id=30
)To Export Phenotype Code List:
Format API JSON site_root/api/v1/phenotypes/PH15/version/30/export/codes/?format=json CSV site_root/phenotypes/PH15/version/30/export/codes/ R Package library(ConceptLibraryClient)
# Connect to API
client = ConceptLibraryClient::Connection$new(public=TRUE)
# Get codelist of phenotype
phenotype_codelist = client$phenotypes$get_codelist(
'PH15',
version_id=30
)Py Package from pyconceptlibraryclient import Client
# Connect to API
client = Client(public=True)
# Get codelist of phenotype
phenotype_codelist = client.phenotypes.get_codelist(
'PH15',
version_id=30
)Version History