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Upper Respiratory Tract Infection

Jeremy I Hawker, Sue Smith, Gillian E Smith, Roger Morbey, Alan P Johnson, Douglas M Fleming, Laura Shallcross, Andrew C Hayward

Type
Disease or Syndrome
ID
PH478
Version ID
1519
Data Sources
The Health Improvement Network (THIN)
Valid event data range
1995 - 2011
Sex
Female
Agreement Date
2014-08-04
Coding system
Read codes v2
Tags /Collections
ClinicalCodes Repository Phenotype Library

Definition

This was an indication–prescription descriptive cross-sectional study using data from The Health Improvement Network (THIN), a computerized database of consultation data from 570 general practices that use the Vision practice software system, covering 3.8 million active patients (resulting in 68 million patient–years of data). The population covered has similar demographic characteristics to the national UK population,and the recording of consultations and prescriptions is comparable to national levels. Data are validated to ensure that they meet quality standards12 and data quality compliance dates are included to show when practices meet recording standards: practice data were only included in our analyses after the later of the acceptable mortality reporting date or the acceptable computer usage date, resulting in 537 practices being included in our study.

Diagnosis and prescribing data at the individual (anonymized) patient level were linked to determine the condition for which the antimicrobial was prescribed. For each clinical syndrome a list of search terms (keywords and synonyms) was produced and used to search the descriptions in the Read code dictionary. In the resulting Read code list, code stems were searched to include all codes containing the specified sequence of characters. This list was then pruned by two medical epidemiologists (J. I. H. and G. E. S.) to decide on the codes to be included for each condition and were checked by A. C. H., A. P. J. and D. M. F. Code lists were constructed for specificity rather than sensitivity (e.g. tonsillitis, but not influenza, was included in the sore throat list) and codes were excluded if they were likely to contain a significant number of consultations for which the relevant SMAC/PHLS recommendation was likely to be inappropriate: for example, those sore throats that were recorded as ‘bacterial’ or ‘streptococcal’ were excluded fromthe sore throat code list, and the UTI code list did not include chronic or recurring infections, kidney infections or conditions related to pregnancy (the code lists are available in Table S1, available as Supplementary data at JACOnline). The drug code list included all antibiotics in Chapter 5.1 of the British National Formulary, excluding antituberculosis drugs and antileprotic drugs. A prescription was linked to a consultation if both occurred on the same date. An episode of acute infection was defined as a newly recorded diagnosis that was not preceded by a consultation for the same diagnosis reported in the previous 14 days.

Stata v12 survival analysis commands were used to obtain overall incidence rates for each clinical condition in total and those cases prescribed an antibiotic. Yearly changes were assessed by calculating CIs reflecting the average change in percentiles year on year within practices, thereby removing the effect of between-practice variation. Variation by practice was illustrated by a funnel plot, which allowed an inspection of random variation according to practice size and was presented as a range from the 10th percentile to the 90th percentile (TNPR) or IQR to exclude outlying practices that might be atypical. The variation in the proportion of patients prescribed antibiotics was analysed by age group (0–4, 5–14, 15–24, 25–54, 55–64, 65–74, 75–84 and 85–94 years) and, for the cough/cold indicator, by socioeconomic status, using quintiles of increasing deprivation provided in the THIN database (derived from Townsend scores based on patients’ postcodes). For UTI, only women aged 16–74 years were included, and for trimethoprim and nitrofurantoin prescriptions the course length was calculated by dividing the ‘quantity prescribed’ field by the ‘calculated daily dosage’ field. The protocol for this work was approved by the THIN Scientific Review Committee (SRC ref 12-002). No patient-identifiable data were used and no new information was collected for this project.

Publications

  • Jeremy I Hawker, Sue Smith, Gillian E Smith, Roger Morbey, Alan P Johnson, Douglas M Fleming, Laura Shallcross, Andrew C Hayward, Trends in antibiotic prescribing in primary care for clinical syndromes subject to national recommendations to reduce antibiotic resistance, UK 1995–2011: analysis of a large database of primary care consultations. J Antimicrob Chemother, 69(3423-3430), 2014.

Clinical Code List

Rows: 57
Code Description Category Coding System (Read) Entity type
16L..00 Influenza-like symptoms diagnostic Read res20: URTI
1J72.00 Suspected swine influenza diagnostic Read res20: URTI
H0...00 Acute respiratory infections diagnostic Read res20: URTI
H00..00 Acute nasopharyngitis diagnostic Read res20: URTI
H00..11 Common cold diagnostic Read res20: URTI
H00..12 Coryza - acute diagnostic Read res20: URTI
H00..13 Febrile cold diagnostic Read res20: URTI
H00..14 Nasal catarrh - acute diagnostic Read res20: URTI
H00..15 Pyrexial cold diagnostic Read res20: URTI
H00..16 Rhinitis - acute diagnostic Read res20: URTI
H023z00 Acute bacterial pharyngitis NOS diagnostic Read res20: URTI
H024.00 Acute viral pharyngitis diagnostic Read res20: URTI
H02z.00 Acute pharyngitis NOS diagnostic Read res20: URTI
H03..00 Acute tonsillitis diagnostic Read res20: URTI
H03..11 Throat infection - tonsillitis diagnostic Read res20: URTI
H036.00 Acute viral tonsillitis diagnostic Read res20: URTI
H03z.00 Acute tonsillitis NOS diagnostic Read res20: URTI
H04..00 Acute laryngitis and tracheitis diagnostic Read res20: URTI
H040.00 Acute laryngitis diagnostic Read res20: URTI
H040w00 Acute viral laryngitis unspecified diagnostic Read res20: URTI
H040z00 Acute laryngitis NOS diagnostic Read res20: URTI
H041.00 Acute tracheitis diagnostic Read res20: URTI
H041000 Acute tracheitis without obstruction diagnostic Read res20: URTI
H041100 Acute tracheitis with obstruction diagnostic Read res20: URTI
H041z00 Acute tracheitis NOS diagnostic Read res20: URTI
H042.00 Acute laryngotracheitis diagnostic Read res20: URTI
H042.11 Laryngotracheitis diagnostic Read res20: URTI
H042000 Acute laryngotracheitis without obstruction diagnostic Read res20: URTI
H042100 Acute laryngotracheitis with obstruction diagnostic Read res20: URTI
H042z00 Acute laryngotracheitis NOS diagnostic Read res20: URTI
H04z.00 Acute laryngitis and tracheitis NOS diagnostic Read res20: URTI
H05..00 Other acute upper respiratory infections diagnostic Read res20: URTI
H050.00 Acute laryngopharyngitis diagnostic Read res20: URTI
H051.00 Acute upper respiratory tract infection diagnostic Read res20: URTI
H052.00 Pharyngotracheitis diagnostic Read res20: URTI
H054.00 Recurrent upper respiratory tract infection diagnostic Read res20: URTI
H055.00 Pharyngolaryngitis diagnostic Read res20: URTI
H05y.00 Other upper respiratory infections of multiple sites diagnostic Read res20: URTI
H05z.00 Upper respiratory infection NOS diagnostic Read res20: URTI
H05z.11 Upper respiratory tract infection NOS diagnostic Read res20: URTI
H05z.12 Viral upper respiratory tract infection NOS diagnostic Read res20: URTI
H06z111 Respiratory tract infection diagnostic Read res20: URTI
H0z..00 Acute respiratory infection NOS diagnostic Read res20: URTI
H27..00 Influenza diagnostic Read res20: URTI
H271.00 Influenza with other respiratory manifestation diagnostic Read res20: URTI
H271000 Influenza with laryngitis diagnostic Read res20: URTI
H271100 Influenza with pharyngitis diagnostic Read res20: URTI
H271z00 Influenza with respiratory manifestations NOS diagnostic Read res20: URTI
H27yz00 Influenza with other manifestations NOS diagnostic Read res20: URTI
H27z.00 Influenza NOS diagnostic Read res20: URTI
H27z.11 Flu like illness diagnostic Read res20: URTI
H27z.12 Influenza like illness diagnostic Read res20: URTI
H29..00 Avian influenza diagnostic Read res20: URTI
H2A.. Influenza A (H1N1) swine flu diagnostic Read res20: URTI
H5yy.11 Respiratory infection NOS diagnostic Read res20: URTI
Hyu0.00 [X]Acute upper respiratory infections diagnostic Read res20: URTI
Hyu0300 [X]Other acute upper respiratory infections/multiple sites diagnostic Read res20: URTI

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH478/version/1519/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH478/version/1519/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('PH478', '1519', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH478/version/1519/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH478/version/1519/export/codes/?format=json
CSV site_root/phenotypes/PH478/version/1519/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('PH478', '1519', api_client=client)

Version History

Version
ID
Name Owner Publish date
1519 Upper 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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