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Respiratory Tract Infection

Rebecca M Joseph, Mohammad Movahedi, William G Dixon, Deborah PM Symmons

Type
Disease or Syndrome
ID
PH488
Version ID
1521
Valid event data range
01/01/1998 - 10/01/2012
Sex
Female, Male
Agreement Date
2017-09-26
Coding system
ICD10 codes
Tags /Collections
ClinicalCodes Repository Phenotype Library

Definition

Objectives:

To investigate the associations between smoking status, smoking cessation and hospitalisations for cardiovascular events (CVE) and respiratory tract infections (RTI ) in an inception cohort of patients with rheumatoid arthritis (RA).

Methods:

The study was set within UK primary care electronic health records (the Clinical Practice Research Datalink) linked to hospital inpatient data (Hospital Episode Statistics). Patients with RA were followed from diagnosis to hospitalisation with a record of CVE or RTI , leaving their general practice, death, or 10 January 2012, whichever was earliest. Smoking status (never, current, former) was defined using primary care data and could vary over time. Survival analysis was performed using Cox regression (first event) and conditional risk set models (multiple RTI s).

Results:

5677 patients were included in the cohort: 68% female, median age 61 years. The age-adjusted and sexadjusted risks of hospitalisation for CVE or RTI were more than twice as high in current vs never smokers (CVE HR (95% CI) 2.19 (1.44 to 3.31); RTI 2.18 (1.71 to 2.78)). The risks for both outcomes were significantly higher in current compared with former smokers (CVE 1.51 (1.04 to 2.19), RTI 1.29 (1.04 to 1.61)). For each additional year of smoking cessation, the risk of first CVE and RTI hospitalisation fell significantly, approximately 25% and 15% respectively in the adjusted models.

Conclusions:

Patients with RA who smoke have an increased risk of hospitalisation with CVE or RTI compared with never and former smokers. The risk decreases for each additional year of smoking cessation. Patients with RA who smoke should be advised to stop smoking.

Publications

  • Rebecca M Joseph, Mohammad Movahedi, William G Dixon, Deborah PM Symmons, 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. RMD Open, 3(2), e000506, 2017.

Clinical Code List

Rows: 85
Code Description Category Coding System (ICD-10) Entity type
A15 Respiratory tuberculosis, bacteriologically and histologically confirmed diagnostic ICD-10 res52: respiratory tract infection ICD-10
A15.0 Tuberculosis of lung, confirmed by sputum microscopy with or without culture diagnostic ICD-10 res52: respiratory tract infection ICD-10
A15.1 Tuberculosis of lung, confirmed by culture only diagnostic ICD-10 res52: respiratory tract infection ICD-10
A15.2 Tuberculosis of lung, confirmed histologically diagnostic ICD-10 res52: respiratory tract infection ICD-10
A15.3 Tuberculosis of lung, confirmed by unspecified means diagnostic ICD-10 res52: respiratory tract infection ICD-10
A15.4 Tuberculosis of intrathoracic lymph nodes, confirmed bacteriologically and histologically diagnostic ICD-10 res52: respiratory tract infection ICD-10
A15.5 Tuberculosis of larynx, trachea and bronchus, confirmed bacteriologically and histologically diagnostic ICD-10 res52: respiratory tract infection ICD-10
A15.6 Tuberculous pleurisy, confirmed bacteriologically and histologically diagnostic ICD-10 res52: respiratory tract infection ICD-10
A15.7 Primary respiratory tuberculosis, confirmed bacteriologically and histologically diagnostic ICD-10 res52: respiratory tract infection ICD-10
A15.8 Other respiratory tuberculosis, confirmed bacteriologically and histologically diagnostic ICD-10 res52: respiratory tract infection ICD-10
A15.9 Respiratory tuberculosis unspecified, confirmed bacteriologically and histologically diagnostic ICD-10 res52: respiratory tract infection ICD-10
A16 Respiratory tuberculosis, not confirmed bacteriologically or histologically diagnostic ICD-10 res52: respiratory tract infection ICD-10
A16.0 Tuberculosis of lung, bacteriologically and histologically negative diagnostic ICD-10 res52: respiratory tract infection ICD-10
A16.1 Tuberculosis of lung, bacteriological and histological examination not done diagnostic ICD-10 res52: respiratory tract infection ICD-10
A16.2 Tuberculosis of lung, without mention of bacteriological or histological confirmation diagnostic ICD-10 res52: respiratory tract infection ICD-10
A16.3 Tuberculosis of intrathoracic lymph nodes, without mention of bacteriological or histological confir diagnostic ICD-10 res52: respiratory tract infection ICD-10
A16.4 Tuberculosis of larynx, trachea and bronchus, without mention of bacteriological or histological con diagnostic ICD-10 res52: respiratory tract infection ICD-10
A16.5 Tuberculous pleurisy, without mention of bacteriological or histological confirmation diagnostic ICD-10 res52: respiratory tract infection ICD-10
A16.7 Primary respiratory tuberculosis without mention of bacteriological or histological confirmation diagnostic ICD-10 res52: respiratory tract infection ICD-10
A16.8 Other respiratory tuberculosis, without mention of bacteriological or histological confirmation diagnostic ICD-10 res52: respiratory tract infection ICD-10
A16.9 Respiratory tuberculosis unspecified, without mention of bacteriological or histological confirmatio diagnostic ICD-10 res52: respiratory tract infection ICD-10
A48.1 Legionnaires disease diagnostic ICD-10 res52: respiratory tract infection ICD-10
J12 Viral pneumonia, not elsewhere classified diagnostic ICD-10 res52: respiratory tract infection ICD-10
J12.0 Adenoviral pneumonia diagnostic ICD-10 res52: respiratory tract infection ICD-10
J12.1 Respiratory syncytial virus pneumonia diagnostic ICD-10 res52: respiratory tract infection ICD-10
J12.2 Parainfluenza virus pneumonia diagnostic ICD-10 res52: respiratory tract infection ICD-10
J12.3 Human metapneumovirus pneumonia diagnostic ICD-10 res52: respiratory tract infection ICD-10
J12.8 Other viral pneumonia diagnostic ICD-10 res52: respiratory tract infection ICD-10
J12.9 Viral pneumonia, unspecified diagnostic ICD-10 res52: respiratory tract infection ICD-10
J13 Pneumonia due to Streptococcus pneumoniae diagnostic ICD-10 res52: respiratory tract infection ICD-10
J14 Pneumonia due to Haemophilus influenzae diagnostic ICD-10 res52: respiratory tract infection ICD-10
J15 Bacterial pneumonia, not elsewhere classified diagnostic ICD-10 res52: respiratory tract infection ICD-10
J15.0 Pneumonia due to Klebsiella pneumoniae diagnostic ICD-10 res52: respiratory tract infection ICD-10
J15.1 Pneumonia due to Pseudomonas diagnostic ICD-10 res52: respiratory tract infection ICD-10
J15.2 Pneumonia due to staphylococcus diagnostic ICD-10 res52: respiratory tract infection ICD-10
J15.3 Pneumonia due to streptococcus, group B diagnostic ICD-10 res52: respiratory tract infection ICD-10
J15.4 Pneumonia due to other streptococci diagnostic ICD-10 res52: respiratory tract infection ICD-10
J15.5 Pneumonia due to Escherichia coli diagnostic ICD-10 res52: respiratory tract infection ICD-10
J15.6 Pneumonia due to other aerobic Gram-negative bacteria diagnostic ICD-10 res52: respiratory tract infection ICD-10
J15.7 Pneumonia due to Mycoplasma pneumoniae diagnostic ICD-10 res52: respiratory tract infection ICD-10
J15.8 Other bacterial pneumonia diagnostic ICD-10 res52: respiratory tract infection ICD-10
J15.9 Bacterial pneumonia, unspecified diagnostic ICD-10 res52: respiratory tract infection ICD-10
J16 Pneumonia due to other infectious organisms, not elsewhere classified diagnostic ICD-10 res52: respiratory tract infection ICD-10
J16.0 Chlamydial pneumonia diagnostic ICD-10 res52: respiratory tract infection ICD-10
J16.8 Pneumonia due to other specified infectious organisms diagnostic ICD-10 res52: respiratory tract infection ICD-10
J17 Pneumonia in diseases classified elsewhere diagnostic ICD-10 res52: respiratory tract infection ICD-10
J17.0 Pneumonia in bacterial diseases classified elsewhere diagnostic ICD-10 res52: respiratory tract infection ICD-10
J17.1 Pneumonia in viral diseases classified elsewhere diagnostic ICD-10 res52: respiratory tract infection ICD-10
J17.2 Pneumonia in mycoses diagnostic ICD-10 res52: respiratory tract infection ICD-10
J17.3 Pneumonia in parasitic diseases diagnostic ICD-10 res52: respiratory tract infection ICD-10
J17.8 Pneumonia in other diseases classified elsewhere diagnostic ICD-10 res52: respiratory tract infection ICD-10
J18 Pneumonia, organism unspecified diagnostic ICD-10 res52: respiratory tract infection ICD-10
J18.0 Bronchopneumonia, unspecified diagnostic ICD-10 res52: respiratory tract infection ICD-10
J18.1 Lobar pneumonia, unspecified diagnostic ICD-10 res52: respiratory tract infection ICD-10
J18.2 Hypostatic pneumonia, unspecified diagnostic ICD-10 res52: respiratory tract infection ICD-10
J18.8 Other pneumonia, organism unspecified diagnostic ICD-10 res52: respiratory tract infection ICD-10
J18.9 Pneumonia, unspecified diagnostic ICD-10 res52: respiratory tract infection ICD-10
J20 Acute bronchitis diagnostic ICD-10 res52: respiratory tract infection ICD-10
J20.0 Acute bronchitis due to Mycoplasma pneumoniae diagnostic ICD-10 res52: respiratory tract infection ICD-10
J20.1 Acute bronchitis due to Haemophilus influenzae diagnostic ICD-10 res52: respiratory tract infection ICD-10
J20.2 Acute bronchitis due to streptococcus diagnostic ICD-10 res52: respiratory tract infection ICD-10
J20.3 Acute bronchitis due to coxsackievirus diagnostic ICD-10 res52: respiratory tract infection ICD-10
J20.4 Acute bronchitis due to parainfluenza virus diagnostic ICD-10 res52: respiratory tract infection ICD-10
J20.5 Acute bronchitis due to respiratory syncytial virus diagnostic ICD-10 res52: respiratory tract infection ICD-10
J20.6 Acute bronchitis due to rhinovirus diagnostic ICD-10 res52: respiratory tract infection ICD-10
J20.7 Acute bronchitis due to echovirus diagnostic ICD-10 res52: respiratory tract infection ICD-10
J20.8 Acute bronchitis due to other specified organisms diagnostic ICD-10 res52: respiratory tract infection ICD-10
J20.9 Acute bronchitis, unspecified diagnostic ICD-10 res52: respiratory tract infection ICD-10
J21 Acute bronchiolitis diagnostic ICD-10 res52: respiratory tract infection ICD-10
J21.0 Acute bronchiolitis due to respiratory syncytial virus diagnostic ICD-10 res52: respiratory tract infection ICD-10
J21.1 Acute bronchiolitis due to human metapneumovirus diagnostic ICD-10 res52: respiratory tract infection ICD-10
J21.8 Acute bronchiolitis due to other specified organisms diagnostic ICD-10 res52: respiratory tract infection ICD-10
J21.9 Acute bronchiolitis, unspecified diagnostic ICD-10 res52: respiratory tract infection ICD-10
J22 Unspecified acute lower respiratory infection diagnostic ICD-10 res52: respiratory tract infection ICD-10
J40 Bronchitis, not specified as acute or chronic diagnostic ICD-10 res52: respiratory tract infection ICD-10
J44.0 Chronic obstructive pulmonary disease with acute lower respiratory infection diagnostic ICD-10 res52: respiratory tract infection ICD-10
J44.1 Chronic obstructive pulmonary disease with acute exacerbation, unspecified diagnostic ICD-10 res52: respiratory tract infection ICD-10
J85 Abscess of lung and mediastinum diagnostic ICD-10 res52: respiratory tract infection ICD-10
J85.0 Gangrene and necrosis of lung diagnostic ICD-10 res52: respiratory tract infection ICD-10
J85.1 Abscess of lung with pneumonia diagnostic ICD-10 res52: respiratory tract infection ICD-10
J85.2 Abscess of lung without pneumonia diagnostic ICD-10 res52: respiratory tract infection ICD-10
J85.3 Abscess of mediastinum diagnostic ICD-10 res52: respiratory tract infection ICD-10
J86 Pyothorax diagnostic ICD-10 res52: respiratory tract infection ICD-10
J86.0 Pyothorax with fistula diagnostic ICD-10 res52: respiratory tract infection ICD-10
J86.9 Pyothorax without fistula diagnostic ICD-10 res52: respiratory tract infection ICD-10

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH488/version/1521/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH488/version/1521/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('PH488', '1521', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH488/version/1521/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH488/version/1521/export/codes/?format=json
CSV site_root/phenotypes/PH488/version/1521/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('PH488', '1521', api_client=client)

Version History

Version
ID
Name Owner Publish date
1521 Respiratory Tract Infection ieuan.scanlon 2021-10-26 currently shown

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

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