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Other or unspecified infectious organisms

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

Type
Disease or Syndrome
ID
PH230
Version ID
460
Valid event data range
01/01/1999 - 01/07/2016
Sex
Female, Male
Agreement Date
2019-05-20
Coding system
ICD10 codes
Tags /Collections
CALIBER Phenotype Library

Definition

At the specified date, a patient is defined as having had Diseases caused by Other or unspecified infectious organisms 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 Diseases caused by Other or unspecified infectious organisms or history of diagnosis during a hospitalization OR

  2. ALL possible diagnosis of Diseases caused by Other or unspecified infectious organisms during a hospitalization IF NO record satisfying criteria for Bacterial Diseases, Tuberculosis, Viral diseases, Chronic viral Hepatitis, HIV, Mycoses or Parasitic Infections 30 days before or 30 days after the first event date for Diseases caused by Other or unspecified infectious organisms.

Implementation


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

Rows: 91
Code Description Disease Category
A08.5 Other specified intestinal infections Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
A09 Other gastroenteritis and colitis of infectious and unspecified origin Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
A41.8 Other specified sepsis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
A41.9 Sepsis, unspecified Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
A63.8 Other specified predominantly sexually transmitted diseases Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
A64 Unspecified sexually transmitted disease Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
A81.0 Creutzfeldt-Jakob disease Other or unspecified infectious organisms Diagnosis of Other or unspecified infectious organisms
A81.8 Other atypical virus infections of central nervous system Other or unspecified infectious organisms Diagnosis of Other or unspecified infectious organisms
A81.9 Atypical virus infection of central nervous system, unspecified Other or unspecified infectious organisms Diagnosis of Other or unspecified infectious organisms
B94.8 Sequelae of other specified infectious and parasitic diseases Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
B94.9 Sequelae of unspecified infectious or parasitic disease Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
B99 Other and unspecified infectious diseases Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
G02.8 Meningitis in other specified infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
G04.8 Other encephalitis, myelitis and encephalomyelitis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
G04.9 Encephalitis, myelitis and encephalomyelitis, unspecified Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
G05.2 Encephalitis, myelitis and encephalomyelitis in other infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
G06 Intracranial and intraspinal abscess and granuloma Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
G07 Intracranial and intraspinal abscess and granuloma in diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
G08 Intracranial and intraspinal phlebitis and thrombophlebitis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
G53.1 Multiple cranial nerve palsies in infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
G63.0 Polyneuropathy in infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
G94.0 Hydrocephalus in infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
H10 Conjunctivitis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
H13.1 Conjunctivitis in infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
H19.2 Keratitis and keratoconjunctivitis in other infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
H60 Otitis externa Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
H62.3 Otitis externa in other infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
H62.4 Otitis externa in other diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
H65 Nonsuppurative otitis media Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
H66 Suppurative and unspecified otitis media Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
H67.8 Otitis media in other diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
H70 Mastoiditis and related conditions Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
H73.0 Acute myringitis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
H73.1 Chronic myringitis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
H75.0 Mastoiditis in infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
I30.1 Infective pericarditis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
I32.1 Pericarditis in other infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
I33.0 Acute and subacute infective endocarditis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
I40.0 Infective myocarditis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
I41.2 Myocarditis in other infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
I43.0 Cardiomyopathy in infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
I98.1 Cardiovascular disorders in other infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J00 Acute nasopharyngitis [common cold] Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J01 Acute sinusitis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J02.8 Acute pharyngitis due to other specified organisms Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J02.9 Acute pharyngitis, unspecified Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J03.8 Acute tonsillitis due to other specified organisms Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J03.9 Acute tonsillitis, unspecified Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J04 Acute laryngitis and tracheitis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J05 Acute obstructive laryngitis [croup] and epiglottitis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J06 Acute upper respiratory infections of multiple and unspecified sites Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J16.8 Pneumonia due to other specified infectious organisms Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J17.8 Pneumonia in other diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J18 Pneumonia, organism unspecified Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J20.8 Acute bronchitis due to other specified organisms Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J20.9 Acute bronchitis, unspecified Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J22 Unspecified acute lower respiratory infection Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J44.0 Chronic obstructive pulmonary disease with acute lower respiratory infection Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J44.1 Chronic obstructive pulmonary disease with acute exacerbation, unspecified Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
J85 Abscess of lung and mediastinum Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
K75.0 Abscess of liver Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
K77.0 Liver disorders in infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
L08.0 Pyoderma Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
L08.8 Other specified local infections of skin and subcutaneous tissue Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
L08.9 Local infection of skin and subcutaneous tissue, unspecified Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
L30.3 Infective dermatitis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
M01.8 Arthritis in other infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
M02 Reactive arthropathies Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
M03 Postinfective and reactive arthropathies in diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
M46.3 Infection of intervertebral disc (pyogenic) Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
M46.4 Discitis, unspecified Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
M46.5 Other infective spondylopathies Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
M49.3 Spondylopathy in other infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
M60.0 Infective myositis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
M63.2 Myositis in other infectious diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
N08.0 Glomerular disorders in infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
N10 Acute tubulo-interstitial nephritis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
N16.0 Renal tubulo-interstitial disorders in infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
N29.1 Other disorders of kidney and ureter in infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
N30.0 Acute cystitis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
N30.8 Other cystitis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
N30.9 Cystitis, unspecified Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
N34 Urethritis and urethral syndrome Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
N48.1 Balanoposthitis Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
N77.0 Ulceration of vulva in infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
N77.1 Vaginitis, vulvitis and vulvovaginitis in infectious and parasitic diseases classified elsewhere Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
P23.8 Congenital pneumonia due to other organisms Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
P23.9 Congenital pneumonia, unspecified Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
P37.8 Other specified congenital infectious and parasitic diseases Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
P37.9 Congenital infectious and parasitic disease, unspecified Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms
P39 Other infections specific to the perinatal period Other or unspecified infectious organisms Possible diagnosis of Other or unspecified infectious organisms

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH230/version/460/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH230/version/460/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('PH230', '460', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH230/version/460/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH230/version/460/export/codes/?format=json
CSV site_root/phenotypes/PH230/version/460/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('PH230', '460', api_client=client)

Version History

Version
ID
Name Owner Publish date
460 Other or unspecified infectious organisms 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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