Phenotypes > Lower Respiratory Tract Infections

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Lower Respiratory Tract Infections

Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos C, Lumbers T, Mathur R, Sofat R, Casas JP, Wong I, Hemingway H, Hingorani A

ID
PH204
Version ID
408
Type
Disease or Syndrome
Data Sources
HES Admitted Patient Care data for CPRD GOLD
Valid event data range
01/01/1999 - 01/07/2016
Sex
♀  Female ♂  Male
Agreement Date
2019-05-20
Coding system
ICD10 codes
Collections
CALIBER Phenotype Library
Tags
No tags

Definition

At the specified date, a patient is defined as having had Lower Respiratory Tract Infections IF they meet the criteria for any of the following on or before the specified date. The earliest date on which the individual meets any of the following criteria on or before the specified date is defined as the first event date:

Secondary care

  1. ALL diagnoses of Lower Respiratory Tract Infections or history of diagnosis during a hospitalization

Implementation


https://kclhi.org/phenoflow/phenotype/download/589

Publications

  • Kuan V., Denaxas S., Gonzalez-Izquierdo A. et al. A chronological map of 308 physical and mental health conditions from 4 million individuals in the National Health Service. The Lancet Digital Health - DOI 10.1016/S2589-7500(19)30012-3

Clinical Code List

Expand All  /  Collapse All
Rows: 52
Code Description Disease Category
A06.5 Amoebic lung abscess Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
A15 Respiratory tuberculosis, bacteriologically and histologically confirmed Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
A16 Respiratory tuberculosis, not confirmed bacteriologically or histologically Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
A20.2 Pneumonic plague Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
A21.2 Pulmonary tularaemia Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
A22.1 Pulmonary Anthrax Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
A31.0 Pulmonary mycobacterial infection Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
A37 Whooping cough Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
A42.0 Pulmonary actinomycosis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
A43.0 Pulmonary nocardiosis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B01.2 Varicella pneumonia Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B05.2 Measles complicated by pneumonia Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B25.0 Cytomegaloviral pneumonitis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B37.1 Pulmonary candidiasis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B38.0 Acute pulmonary coccidioidomycosis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B38.1 Chronic pulmonary coccidioidomycosis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B38.2 Pulmonary coccidioidomycosis, unspecified Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B39.0 Acute pulmonary histoplasmosis capsulati Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B39.1 Chronic pulmonary histoplasmosis capsulati Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B39.2 Pulmonary histoplasmosis capsulati, unspecified Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B40.0 Acute pulmonary blastomycosis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B40.1 Chronic pulmonary blastomycosis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B40.2 Pulmonary blastomycosis, unspecified Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B41.0 Pulmonary paracoccidioidomycosis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B42.0 Pulmonary sporotrichosis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B44.0 Invasive pulmonary aspergillosis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B44.1 Other pulmonary aspergillosis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B45.0 Pulmonary cryptococcosis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B46.0 Pulmonary mucormycosis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B58.3 Pulmonary toxoplasmosis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B59 Pneumocystosis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
B67.1 Echinococcus granulosus infection of lung Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J10.0 Influenza with pneumonia, other influenza virus identified Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J11.0 Influenza with pneumonia, virus not identified Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J12 Viral pneumonia, not elsewhere classified Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J13 Pneumonia due to Streptococcus pneumoniae Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J14 Pneumonia due to Haemophilus influenzae Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J15 Bacterial pneumonia, not elsewhere classified Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J16 Pneumonia due to other infectious organisms, not elsewhere classified Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J17 Pneumonia in diseases classified elsewhere Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J18 Pneumonia, organism unspecified Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J20 Acute bronchitis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J21 Acute bronchiolitis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J22 Unspecified acute lower respiratory infection Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J44.0 Chronic obstructive pulmonary disease with acute lower respiratory infection Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J44.1 Chronic obstructive pulmonary disease with acute exacerbation, unspecified Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J65 Pneumoconiosis associated with tuberculosis Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J85.0 Gangrene and necrosis of lung Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J85.1 Abscess of lung with pneumonia Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J85.2 Abscess of lung without pneumonia Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
J86 Pyothorax Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections
P23 Congenital pneumonia Lower Respiratory Tract Infections Diagnosis of Lower Respiratory Tract Infections

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH204/version/408/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH204/version/408/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('PH204', '408', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH204/version/408/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH204/version/408/export/codes/?format=json
CSV site_root/phenotypes/PH204/version/408/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('PH204', '408', api_client=client)

Version History

Version
ID		 Name Owner Publish date
408 Lower Respiratory Tract Infections ieuan.scanlon 2021-10-06 currently shown

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

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