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Bacterial Diseases (excl TB)

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
PH117
Version ID
234
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 'Bacterial Diseases (excl TB)' 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 Bacterial Diseases (excl TB) or history of diagnosis during a hospitalization

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: 153
Code Description Disease Category
A00 Cholera Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A01 Typhoid and paratyphoid fevers Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A02 Other salmonella infections Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A03 Shigellosis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A04 Other bacterial intestinal infections Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A05 Other bacterial foodborne intoxications, not elsewhere classified Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A20 Plague Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A21 Tularaemia Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A22 Anthrax Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A23 Brucellosis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A24 Glanders and melioidosis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A25 Rat-bite fevers Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A26 Erysipeloid Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A27 Leptospirosis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A28 Other zoonotic bacterial diseases, not elsewhere classified Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A30 Leprosy [Hansen's disease] Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A31 Infection due to other mycobacteria Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A32 Listeriosis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A35 Other tetanus Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A36 Diphtheria Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A37 Whooping cough Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A38 Scarlet fever Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A39 Meningococcal infection Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A40 Streptococcal sepsis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A41.0 Sepsis due to Staphylococcus aureus Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A41.1 Sepsis due to other specified staphylococcus Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A41.2 Sepsis due to unspecified staphylococcus Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A41.3 Sepsis due to Haemophilus influenzae Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A41.4 Sepsis due to anaerobes Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A41.5 Sepsis due to other Gram-negative organisms Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A42 Actinomycosis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A43 Nocardiosis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A44 Bartonellosis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A46 Erysipelas Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A48 Other bacterial diseases, not elsewhere classified Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A49 Bacterial infection of unspecified site Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A50 Congenital syphilis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A51 Early syphilis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A52 Late syphilis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A53 Other and unspecified syphilis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A54 Gonococcal infection Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A55 Chlamydial lymphogranuloma (venereum) Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A56 Other sexually transmitted chlamydial diseases Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A57 Chancroid Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A58 Granuloma inguinale Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A65 Nonvenereal syphilis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A66 Yaws Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A67 Pinta [carate] Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A68 Relapsing fevers Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A69 Other spirochaetal infections Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A70 Chlamydia psittaci infection Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A71 Trachoma Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A74 Other diseases caused by chlamydiae Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A75 Typhus fever Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A77 Spotted fever [tick-borne rickettsioses] Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A78 Q fever Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
A79 Other rickettsioses Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
B20.1 HIV disease resulting in other bacterial infections Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
B92 Sequelae of leprosy Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
B94.0 Sequelae of trachoma Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
B95 Streptococcus and staphylococcus as the cause of diseases classified to other chapters Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
B96 Other specified bacterial agents as the cause of diseases classified to other chapters Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
B98.0 Helicobacter pylori [H.pylori] as the cause of diseases classified to other chapters Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
B98.1 Vibrio vulnificus as the cause of diseases classified to other chapters Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
G00 Bacterial meningitis, not elsewhere classified Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
G01 Meningitis in bacterial diseases classified elsewhere Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
G04.2 Bacterial meningoencephalitis and meningomyelitis, not elsewhere classified Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
G05.0 Encephalitis, myelitis and encephalomyelitis in bacterial diseases classified elsewhere Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
H62.0 Otitis externa in bacterial diseases classified elsewhere Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
H67.0 Otitis media in bacterial diseases classified elsewhere Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
I00 Rheumatic fever without mention of heart involvement Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
I01 Rheumatic fever with heart involvement Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
I02 Rheumatic chorea Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
I05 Rheumatic mitral valve diseases Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
I06 Rheumatic aortic valve diseases Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
I07 Rheumatic tricuspid valve diseases Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
I09 Other rheumatic heart diseases Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
I32.0 Pericarditis in bacterial diseases classified elsewhere Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
I41.0 Myocarditis in bacterial diseases classified elsewhere Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
I98.0 Cardiovascular syphilis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
J02.0 Streptococcal pharyngitis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
J03.0 Streptococcal tonsillitis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
J13 Pneumonia due to Streptococcus pneumoniae Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
J14 Pneumonia due to Haemophilus influenzae Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
J15 Bacterial pneumonia, not elsewhere classified Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
J16.0 Chlamydial pneumonia Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
J17.0 Pneumonia in bacterial diseases classified elsewhere Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
J20.0 Acute bronchitis due to Mycoplasma pneumoniae Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
J20.1 Acute bronchitis due to Haemophilus influenzae Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
J20.2 Acute bronchitis due to streptococcus Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
J34.0 Abscess, furuncle and carbuncle of nose Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
J36 Peritonsillar abscess Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
J39.0 Retropharyngeal and parapharyngeal abscess Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
J39.1 Other abscess of pharynx Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
J86 Pyothorax Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
K61 Abscess of anal and rectal regions Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
K63.0 Abscess of intestine Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
K67.0 Chlamydial peritonitis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
K67.1 Gonococcal peritonitis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
L00 Staphylococcal scalded skin syndrome Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
L01 Impetigo Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
L02 Cutaneous abscess, furuncle and carbuncle Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
L03 Cellulitis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
L05.0 Pilonidal cyst with abscess Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
L08.1 Erythrasma Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M00.0 Staphylococcal arthritis and polyarthritis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M00.1 Pneumococcal arthritis and polyarthritis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M00.2 Other streptococcal arthritis and polyarthritis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M00.8 Arthritis and polyarthritis due to other specified bacterial agents Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M00.9 Pyogenic arthritis, unspecified Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M01.0 Meningococcal arthritis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M01.2 Arthritis in Lyme disease Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M01.3 Arthritis in other bacterial diseases classified elsewhere Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M03.0 Postmeningococcal arthritis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M03.1 Postinfective arthropathy in syphilis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M49.1 Brucella spondylitis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M49.2 Enterobacterial spondylitis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M63.0 Myositis in bacterial diseases classified elsewhere Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M65.0 Abscess of tendon sheath Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M65.1 Other infective (teno)synovitis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M68.0 Synovitis and tenosynovitis in bacterial diseases classified elsewhere Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M71.0 Abscess of bursa Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M71.1 Other infective bursitis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M72.6 Necrotizing fasciitis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M73.1 Syphilitic bursitis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M86 Osteomyelitis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M90.1 Periostitis in other infectious diseases classified elsewhere Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
M90.2 Osteopathy in other infectious diseases classified elsewhere Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N13.6 Pyonephrosis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N15.1 Renal and perinephric abscess Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N29.0 Late syphilis of kidney Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N39.0 Urinary tract infection, site not specified Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N41.0 Acute prostatitis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N41.2 Abscess of prostate Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N41.3 Prostatocystitis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N43.1 Infected hydrocele Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N45 Orchitis and epididymitis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N70 Salpingitis and oophoritis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N71 Inflammatory disease of uterus, except cervix Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N72 Inflammatory disease of cervix uteri Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N73 Other female pelvic inflammatory diseases Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N74.3 Female gonococcal pelvic inflammatory disease Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N74.4 Female chlamydial pelvic inflammatory disease Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N74.8 Female pelvic inflammatory disorders in other diseases classified elsewhere Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
N75.1 Abscess of Bartholin's gland Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
P23.1 Congenital pneumonia due to Chlamydia Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
P23.2 Congenital pneumonia due to staphylococcus Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
P23.3 Congenital pneumonia due to streptococcus, group B Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
P23.4 Congenital pneumonia due to Escherichia coli Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
P23.5 Congenital pneumonia due to Pseudomonas Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
P23.6 Congenital pneumonia due to other bacterial agents Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
P36 Bacterial sepsis of newborn Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)
P37.2 Neonatal (disseminated) listeriosis Bacterial Diseases (excl TB) Diagnosis of Bacterial Diseases (excl TB)

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH117/version/234/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH117/version/234/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('PH117', '234', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH117/version/234/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH117/version/234/export/codes/?format=json
CSV site_root/phenotypes/PH117/version/234/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('PH117', '234', api_client=client)

Version History

Version
ID
Name Owner Publish date
234 Bacterial Diseases (excl TB) ieuan.scanlon 2021-10-06 currently shown

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

Print - Print page.