[ { "phenotype_id": "PH795", "phenotype_version_id": 2219, "name": "Pneumonia Secondary care", "definition": "\n- Not found code search\n- The definition of pneumonia has not been validated.", "implementation": "\n\nThese codes will capture both community- and hospital-acquired pneumonia. These codes are not intended to be mandatory, but are to be used as a starting point for the identification of pneumonia in routine EHR. Each study may differ in the sensitivity and specificity of the coding required. \n\n \n\nDefining a community-acquired pneumonia occurrence in CPRD and HES, Millett et al. 2013 used the following algorithm:\n\n1) Pneumonia records wtihin 28 days of each other were considered to be separate consultations for the same illness\n\n2) First record of pneumonia was the index date\n\n3) End of a pneumonia occurrence was defined as 28 days after the last pneumonia code within the illness episode\n\n4) In HES, pneumonia coded as the primary diagnosis on the first day of a hospital admission\n\n \n\nDefining a hospital-acquired pneumonia occurrence in HES and CPRD, Millett et al. 2013 used the following algorithm:\n\n1) Pneumonia coded at any time beyond the first day of a hospital admission\n\n2) Using CPRD in conjunction with HES, pneumonia coded in CPRD within 14 days of a hospital admission (for any cause) was deemed hospital-acquired\n\n3) In CPRD, use of a hospital-acquired pneumonia code at any time during the pneumonia occurrence\n\n \n\nMillett, E. R., Quint, J. K., Smeeth, L., Daniel, R. M., & Thomas, S. L. (2013). Incidence of community-acquired lower respiratory tract infections and pneumonia among older adults in the United Kingdom: a population-based study. PLoS One, 8(9), e75131. doi:10.1371/journal.pone.0075131\n\n \n\nDefining a community-acquired pneumonia resulting in hospitalisation occurrence in HES, Hicks et al. 2016 used the following algorithm:\n\n1) In HES, hospital admission following A&E visit, where pneumonia was coded as the primary diagnosis within two days of admission\n\n \n\nDefining a hospital-acquired pneumonia occurrence in CPRD and HES, Hicks et al. 2016 used the following algorithm:\n\n1) Pneumonia diagnosis in HES >2 days after hospital admission\n\n2) Pneumonia diagnosed in CPRD within 7 days after hospital discharge\n\n \n\nHicks, B. M., Yin, H., Bladou, F., Ernst, P., & Azoulay, L. (2017). Androgen deprivation therapy for prostate cancer and the risk of hospitalisation for community-acquired pneumonia. Thorax, 72(7), 596-597. doi:10.1136/thoraxjnl-2016-209512\n\n \n\nDefining a hospital-acquired respiratory infection including pneumonia occcurence using ICD-10 codes, Timmers et al. 2020 used the following algorithm: \n\n1) The main diagnosis of acute hospital admission records, excluding any secondary diagnoses, was used to classify records into disease categories, which corresponded to disease blocks as described in the chapters of ICD-10.\n\n2) Mortality trends were modelled using morbidity trends: we first determined the major disease categories (ICD-10 blocks) associated with the most lives lost.\n\n \n\nTimmers PRHJ, Kerssens JJ, Minton J, Grant I, Wilson JF, Campbell H, Fischbacher CM, Joshi PK. Trends in disease incidence and survival and their effect on mortality in Scotland: nationwide cohort study of linked hospital admission and death records 2001-2016. BMJ Open. 2020 Mar 25;10(3):e034299. doi: 10.1136/bmjopen-2019-034299. PMID: 32217562; PMCID: PMC7170664.\n\n \n\nDefining a hospital-acquired respiratory infection including pneumonia occcurence using ICD-10 codes, Brunner-La Rocca et al. 2020 used the following algorithm:\n\n1) Both bespoke chronic diseases (ICD-classification) and Clinical Classification Software (CCS) codes were used to define bacterial pneumonia as index hospitalisation.\n\n \n\nBrunner-La Rocca HP, Peden CJ, Soong J, Holman PA, Bogdanovskaya M, Barclay L. Reasons for readmission after hospital discharge in patients with chronic diseases-Information from an international dataset. PLoS One. 2020 Jun 30;15(6):e0233457. doi: 10.1371/journal.pone.0233457. PMID: 32603361; PMCID: PMC7326238.\n\n \n\nDefining a hospital-acquired respiratory infection including pneumonia occcurence using ICD-10 codes, Reynurn et al. 2020 used the following algorithm:\n\n1) all-cause pneumonia (which is highly sensitive but not specific), and three clinical definitions based on WHO definitions of severe or very severe pneumonia, hypoxic pneumonia (which indicates severe disease and is the main cause for pneumonia-associated death), and radiological pneumonia\n\n2) All-cause pneumonia included ICD-10 codes J10·0–18·9, J21, and J22. Bronchiolitis (ICD-10 code J21) was included because clinicians in Fiji code pneumonia according to Integrated Management of Childhood Illnesses definitions (cough and breathing rate, according to age) and this includes bronchiolitis.\n\n3) Severe or very severe pneumonia was based on the WHO 2005 pneumonia case definitions10 with the addition of oxygen saturation of less than 90% in room air, or death due to pneumonia (confirmed by a pathologist at autopsy). \n\n4) Hypoxic pneumonia was defined as any child with pneumonia and oxygen saturation of less than 90% in room air, or death due to pneumonia.\n\n5) Radiological pneumonia was defined as primary endpoint consolidation according to the WHO 2005 standard case definition as re-read by a paediatric radiologist (MdC). Individuals with pneumonia who died from pneumonia before having a chest radiograph taken were also classified as having radiological pneumonia.\n\n \n\nReyburn R, Tuivaga E, Nguyen CD, Ratu FT, Nand D, Kado J, Tikoduadua L, Jenkins K, de Campo M, Kama M, Devi R, Rafai E, Weinberger DM, Mulholland EK, Russell FM. Effect of ten-valent pneumococcal conjugate vaccine introduction on pneumonia hospital admissions in Fiji: a time-series analysis. Lancet Glob Health. 2021 Jan;9(1):e91-e98. doi: 10.1016/S2214-109X(20)30421-6. Epub 2020 Nov 20. PMID: 33227258.\n\n \n\nDefining a community-acquired pneumonia resulting in hospitalisation occurrence, Lawrence et al. 2020 used the following algorithm:\n\n1) Cases were identified by participating institutions via ICD10 codes mapping to a primary discharge diagnosis of pneumonia (J12.0–J18.0) and selected for eligibility against inclusion criteria to confirm a clinical and radiographic diagnosis of Community-Acquired Pneumonia (CAP).\n\n \n\nLawrence H, McKeever TM, Lim WS; British Thoracic Society. Admission to hospital in the UK at a weekend does not influence the prognosis of adults with community-acquired pneumonia. Thorax. 2020 Jul;75(7):594-596. doi: 10.1136/thoraxjnl-2019-214318. Epub 2020 Mar 31. PMID: 32234807.\n\nNot found code search\n\n", "publications": [ { "doi": null, "details": "Publications between 2013-2019 identifying pneumonia in CPRD and/or HES" }, { "doi": "10.1371/journal.pone.0075131", "details": "Millett, E. R., Quint, J. K., Smeeth, L., Daniel, R. M., & Thomas, S. L. (2013). Incidence of community-acquired lower respiratory tract infections and pneumonia among older adults in the United Kingdom: a population-based study. PLoS One, 8(9), e75131. doi:10.1371/journal.pone.0075131" }, { "doi": "10.2147/COPD.S138435", "details": "Braeken, D. C., Rohde, G. G., Franssen, F. M., Driessen, J. H., van Staa, T. P., Souverein, P. C., . . . de Vries, F. (2017). Risk of community-acquired pneumonia in chronic obstructive pulmonary disease stratified by smoking status: a population-based cohort study in the United Kingdom. Int J Chron Obstruct Pulmon Dis, 12, 2425-2432. doi:10.2147/COPD.S138435" }, { "doi": "10.1136/thoraxjnl-2016-209512", "details": "Hicks, B. M., Yin, H., Bladou, F., Ernst, P., & Azoulay, L. (2017). Androgen deprivation therapy for prostate cancer and the risk of hospitalisation for community-acquired pneumonia. Thorax, 72(7), 596-597. doi:10.1136/thoraxjnl-2016-209512" }, { "doi": "10.1017/S0950268819001559", "details": "Sun, X., Douiri, A., & Gulliford, M. (2019). Pneumonia incidence trends in UK primary care from 2002 to 2017: population-based cohort study. Epidemiol Infect, 147, e263. doi:10.1017/S0950268819001559" }, { "doi": null, "details": "Publications in 2020-2021 identified in PubMed" }, { "doi": "10.1136/bmjopen-2019-034299", "details": "Timmers PRHJ, Kerssens JJ, Minton J, et al. (2020). Trends in disease incidence and survival and their effect on mortality in Scotland: nationwide cohort study of linked hospital admission and death records 2001–2016. BMJ Open 2020;10:e034299. doi: 10.1136/bmjopen-2019-034299" }, { "doi": "10.1371/journal.pone.0233457", "details": "Brunner-La Rocca HP, Peden CJ, Soong J, Holman PA, Bogdanovskaya M, et al. (2020) Reasons for readmission after hospital discharge in patients with chronic diseases—Information from an international dataset. PLOS ONE 15(6): e0233457. https://doi.org/10.1371/journal.pone.0233457" }, { "doi": "10.1016/S2214-109X(20)30421-6", "details": "Reyburn R, Tuivaga E, Nguyen CD, Ratu FT, Nand D, Kado J, Tikoduadua L, Jenkins K, de Campo M, Kama M, Devi R, Rafai E, Weinberger DM, Mulholland EK, Russell FM. Effect of ten-valent pneumococcal conjugate vaccine introduction on pneumonia hospital admissions in Fiji: a time-series analysis. Lancet Glob Health. 2021 Jan;9(1):e91-e98. doi: 10.1016/S2214-109X(20)30421-6. Epub 2020 Nov 20. PMID: 33227258." }, { "doi": "10.1136/thoraxjnl-2019-214318", "details": "Lawrence H, McKeever TM, Lim WS; British Thoracic Society. Admission to hospital in the UK at a weekend does not influence the prognosis of adults with community-acquired pneumonia. Thorax. 2020 Jul;75(7):594-596. doi: 10.1136/thoraxjnl-2019-214318. Epub 2020 Mar 31. PMID: 32234807." }, { "doi": null, "details": "Mesalles-Naranjo O, Grant I, Wyper GMA, et al. Trends and inequalities in the burden of mortality in Scotland 2000–2015. PLoS One 2018" }, { "doi": null, "details": "Bennett JE, Pearson-Stuttard J, Kontis V, et al. Contributions of diseases and injuries to widening life expectancy inequalities in England from 2001 to 2016: a population-based analysis of vital registration data. Lancet Public Health 2018" }, { "doi": null, "details": ">Code repositories" }, { "doi": "10.1136/rmdopen-2017-000506", "details": "**ID**- Manchester Clinical Codes 52 \n- **Repository**- Manchester ClinicalCodes \n- **Description**- 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 \n- **Conditions**- Respiratory tract infection \n- **Publication**- https://doi.org/10.1136/rmdopen-2017-000506 \n- **Clinical codes**- ICD-10 " }, { "doi": "10.1002/acr.22882", "details": "**ID**- Manchester Clinical Codes 42 \n- **Repository**- Manchester ClinicalCodes \n- **Description**- Smoking-related mortality in patients with early rheumatoid arthritis – a retrospective cohort study using the Clinical Practice Research Datalink \n- **Conditions**- Respiratory tract infection \n- **Publication**- https://doi.org/10.1002/acr.22882 \n- **Clinical codes**- ICD-10 " }, { "doi": "10.1016/S2589-7500(19)30012-3", "details": "**ID**- HDR UK National Phenomics Resource Project (aspiration pneumonitis) \n- **Repository**- HDR UK National Phenomics Resource Project \n- **Description**- A chronological map of 308 physical and mental health conditions from 4 million individuals in the English National Health Service \n- **Conditions**- Aspiration pneumonitis \n- **Publication**- https://doi.org/10.1016/S2589-7500(19)30012-3 \n- **Clinical codes**- Read Version 2 & ICD-10 " }, { "doi": "10.1016/S2589-7500(19)30012-3", "details": "**ID**- HDR UK National Phenomics Resource Project (bacterial diseases, excl TB) \n- **Repository**- HDR UK National Phenomics Resource Project \n- **Description**- A chronological map of 308 physical and mental health conditions from 4 million individuals in the English National Health Service \n- **Conditions**- Bacterial diseases (excl TB) \n- **Publication**- https://doi.org/10.1016/S2589-7500(19)30012-3 \n- **Clinical codes**- ICD-10 " }, { "doi": "10.1016/S2589-7500(19)30012-3", "details": "**ID**- HDR UK National Phenomics Resource Project (LRTI) \n- **Repository**- HDR UK National Phenomics Resource Project \n- **Description**- A chronological map of 308 physical and mental health conditions from 4 million individuals in the English National Health Service \n- **Conditions**- Lower respiratory tract infections \n- **Publication**- https://doi.org/10.1016/S2589-7500(19)30012-3 \n- **Clinical codes**- ICD-10 " }, { "doi": "10.1016/S2589-7500(19)30012-3", "details": "**ID**- HDR UK National Phenomics Resource Project (other/unspecified infectious organisms) \n- **Repository**- HDR UK National Phenomics Resource Project \n- **Description**- A chronological map of 308 physical and mental health conditions from 4 million individuals in the English National Health Service \n- **Conditions**- Other or unspecified infectious organisms \n- **Publication**- https://doi.org/10.1016/S2589-7500(19)30012-3 \n- **Clinical codes**- ICD-10 " }, { "doi": "10.1016/S2589-7500(19)30012-3", "details": "**ID**- HDR UK National Phenomics Resource Project (TB) \n- **Repository**- HDR UK National Phenomics Resource Project \n- **Description**- A chronological map of 308 physical and mental health conditions from 4 million individuals in the English National Health Service \n- **Conditions**- TB \n- **Publication**- https://doi.org/10.1016/S2589-7500(19)30012-3 \n- **Clinical codes**- Read Version 2 & ICD-10 " }, { "doi": "10.1016/S2589-7500(19)30012-3", "details": "**ID**- HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV) \n- **Repository**- HDR UK National Phenomics Resource Project \n- **Description**- A chronological map of 308 physical and mental health conditions from 4 million individuals in the English National Health Service \n- **Conditions**- Viral diseases (excl chronic hepatitis/HIV) \n- **Publication**- https://doi.org/10.1016/S2589-7500(19)30012-3 \n- **Clinical codes**- ICD-10 " }, { "doi": "10.1371/journal.pone.0075131", "details": "**ID**- HDR UK National Phenomics Resource Project (pneumonia, 10.1371) \n- **Repository**- HDR UK National Phenomics Resource Project \n- **Description**- Incidence of Community-Acquired Lower Respiratory Tract Infections and Pneumonia among Older Adults in the United Kingdom: A Population-Based Study \n- **Conditions**- Pneumonia \n- **Publication**- https://doi.org/10.1371/journal.pone.0075131 \n- **Clinical codes**- Read Version 2\nSNOMED-CT\nICD-10\nICD-11\nUK Biobank " }, { "doi": "10.2147/COPD.S138435", "details": "**ID**- HDR UK National Phenomics Resource Project (pneumonia, 10.2147) \n- **Repository**- HDR UK National Phenomics Resource Project \n- **Description**- Risk of community-acquired pneumonia in chronic obstructive pulmonary disease stratified by smoking status: a population-based cohort study in the United Kingdom \n- **Conditions**- Pneumonia \n- **Publication**- https://doi.org/10.2147/COPD.S138435 \n- **Clinical codes**- " }, { "doi": "10.1136/thoraxjnl-2016-209512", "details": "**ID**- HDR UK National Phenomics Resource Project (pneumonia, 10.1136) \n- **Repository**- HDR UK National Phenomics Resource Project \n- **Description**- Androgen deprivation therapy for prostate cancer and the risk of hospitalisation for community-acquired pneumonia \n- **Conditions**- Pneumonia \n- **Publication**- http://dx.doi.org/10.1136/thoraxjnl-2016-209512 \n- **Clinical codes**- " }, { "doi": "10.1017/S0950268819001559", "details": "**ID**- HDR UK National Phenomics Resource Project (pneumonia, 10.1017) \n- **Repository**- HDR UK National Phenomics Resource Project \n- **Description**- Pneumonia incidence trends in UK primary care from 2002 to 2017: population-based cohort study \n- **Conditions**- Pneumonia \n- **Publication**- https://doi.org/10.1017/S0950268819001559 \n- **Clinical codes**- " }, { "doi": null, "details": "**ID**- OpenSAFELY (2020-05-18) \n- **Repository**- OpenSAFELY \n- **Description**- Codes indicating a diagnosis of influenza or influenza-like illness \n- **Conditions**- Documented influenza illness \n- **Publication**- \n- **Clinical codes**- CTV3 (Read V3) with TPP extensions " }, { "doi": null, "details": "**ID**- OpenSAFELY (2020-05-19) \n- **Repository**- OpenSAFELY \n- **Description**- Codes indicating a diagnosis of a lower respiratory tract infection excluding pneumonia \n- **Conditions**- Lower respiratory tract infection \n- **Publication**- \n- **Clinical codes**- CTV3 (Read V3) with TPP extensions " }, { "doi": null, "details": "**ID**- OpenSAFELY (2020-05-10) \n- **Repository**- OpenSAFELY \n- **Description**- Pneumonia ICD-10 codes \n- **Conditions**- Pneumonia secondary care \n- **Publication**- \n- **Clinical codes**- ICD-10 " }, { "doi": null, "details": "**ID**- OpenSAFELY (2020-07-16) \n- **Repository**- OpenSAFELY \n- **Description**- Codes indicating COVID-19 case (1 of 13 possible types of CTV3 codes that contain information related to COVID-19) \n- **Conditions**- COVID identification in primary care - probable covid - sequelae \n- **Publication**- \n- **Clinical codes**- CTV3 (Read V3) " }, { "doi": "10.17037/DATA.00002049", "details": "**ID**- LSHTM Data Compass (2049) \n- **Repository**- LSHTM Data Compass \n- **Description**- Read codes for lower respiratory tract infections \n- **Conditions**- Lower respiratory tract infection \n- **Publication**- https://doi.org/10.17037/DATA.00002049 \n- **Clinical codes**- CPRD GOLD Medcodes " }, { "doi": "10.17037/DATA.00002050", "details": "**ID**- LSHTM Data Compass (2050) \n- **Repository**- LSHTM Data Compass \n- **Description**- ICD-10 codes for lower respiratory tract infections \n- **Conditions**- Lower respiratory tract infection \n- **Publication**- https://doi.org/10.17037/DATA.00002050 \n- **Clinical codes**- ICD-10 " }, { "doi": "10.17037/DATA.00000847", "details": "**ID**- LSHTM Data Compass (0847) \n- **Repository**- LSHTM Data Compass \n- **Description**- ICD-10 codes for pneumonia \n- **Conditions**- Pneumonia \n- **Publication**- https://doi.org/10.17037/DATA.00000847 \n- **Clinical codes**- ICD-10 " }, { "doi": "10.17037/DATA.00001654", "details": "**ID**- LSHTM Data Compass (1654) \n- **Repository**- LSHTM Data Compass \n- **Description**- Read codes and terms used for pneumonia (CPRD) \n- **Conditions**- Pneumonia \n- **Publication**- https://doi.org/10.17037/DATA.00001654 \n- **Clinical codes**- Read Version 2 & CPRD GOLD Medcodes " }, { "doi": null, "details": "**ID**- Oxford-RCGP RSC \n- **Repository**- Oxford-RCGP RSC \n- **Description**- Surveillance & acute pathways of care theme \n- **Conditions**- PneumoniaOrPneumonitis-WRpt \n- **Publication**- \n- **Clinical codes**- " } ], "validation": "The definition of pneumonia has not been validated", "citation_requirements": "", "created": "2022-01-17T14:00:02.301331Z", "author": "Eleftheria Vasileiou, Chukwuma Iwundu, Alex Williams, Clare MacRae", "collections": [ { "name": "BREATHE", "value": 19 }, { "name": "Phenotype Library", "value": 18 } ], "tags": null, "organisation": null, "world_access": 2, "updated": "2022-08-04T18:38:20.670611Z", "sex": [ { "name": "Both", "value": "3" } ], "type": [ { "name": "Disease or syndrome", "value": "2" } ], "ontology": null, "phenoflowid": "", "data_sources": [ { "name": "Hospital Episode Statistics Admitted Patient Care", "value": 2, "uid": "6599230a-df54-4615-937c-d724d239491f", "url": "https://healthdatagateway.org/en/dataset/875", "datasource_id": 875 }, { "name": "Patient Episode Dataset for Wales (PEDW)", "value": 379, "uid": "4c33a5d2-164c-41d7-9797-dc2b008cc852", "url": "https://healthdatagateway.org/en/dataset/318", "datasource_id": 318 }, { "name": "Annual District Death Extract (ADDE)", "value": 50, "uid": "15cf4241-abad-4dcc-95b0-8cd7c02be999", "url": "https://healthdatagateway.org/en/dataset/316", "datasource_id": 316 }, { "name": "Civil Registration - Deaths", "value": 3, "uid": "b9009bc5-b7a6-4036-9d4b-a5133c0b14a3", "url": "https://healthdatagateway.org/en/dataset/877", "datasource_id": 877 } ], "coding_system": [ { "name": "ICD10 codes", "value": 4 }, { "name": "ICD9 codes", "value": 17 }, { "name": "ICD11 codes", "value": 18 } ], "event_date_range": "01/01/2001 to 31/01/2021", "concept_information": [ { "concept_id": 2475, "concept_version_id": 6350, "concept_name": "Pneumonia Secondary care - 3", "coding_system": { "id": 18, "name": "ICD11 codes", "description": "ICD11 codes" }, "phenotype_id": "PH795", "phenotype_version_id": 2219, "phenotype_name": "Pneumonia Secondary care", "code_attribute_header": [ "BREATHE recommended", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)" ], "codes": [ { "code": "CA40", "description": "Pneumonia", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "Y" } }, { "code": "CA40.0", "description": "Bacterial pneumonia", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.00", "description": "Pneumonia due to Chlamydophila pneumoniae", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.01", "description": "Pneumonia due to Escherichia coli", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.02", "description": "Pneumonia due to Haemophilus influenzae", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.03", "description": "Pneumonia due to Klebsiella pneumoniae", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.04", "description": "Pneumonia due to Mycoplasma pneumoniae", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.05", "description": "Pneumonia due to Pseudomonas aeruginosa", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.06", "description": "Pneumonia due to Staphylococcus", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.07", "description": "Pneumonia due to Streptococcus pneumoniae", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.08", "description": "Pneumonia due to Beta-haemolytic streptococcus", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.0Y", "description": "Pneumonia due to other specified bacteria", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.0Z", "description": "Bacterial pneumonia, unspecified", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.1", "description": "Viral pneumonia", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.10", "description": "Pneumonia due to Adenovirus", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.11", "description": "Pneumonia due to Respiratory syncytial virus", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.12", "description": "Pneumonia due to parainfluenza virus", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.13", "description": "Pneumonia due to Human metapneumovirus", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.1Y", "description": "Pneumonia due to other specified virus", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.1Z", "description": "Viral pneumonia, unspecified", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.2Z", "description": "Fungal pneumonia, unspecified", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } }, { "code": "CA40.Z", "description": "Pneumonia, organism unspecified", "attributes": { "BREATHE recommended": "Y", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "" } } ] }, { "concept_id": 2474, "concept_version_id": 6348, "concept_name": "Pneumonia Secondary care - 2", "coding_system": { "id": 4, "name": "ICD10 codes", "description": "ICD10 Codes" }, "phenotype_id": "PH795", "phenotype_version_id": 2219, "phenotype_name": "Pneumonia Secondary care", "code_attribute_header": [ "BREATHE recommended", "Reyburn et al. 2021", "Brunner-La Rocca et al. 2020", "Lawrence et al. 2020", "Timmers et al. 2020", "Sun et al. 2019", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)", "Braeken et al. 2017", "Hicks et al. 2017", "Diaz et al. 2016 (cited by Reyburn et al. 2021)", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)", 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"OpenSAFELY (2020-05-10)": "", "LSHTM Data Compass (2050)": "", "LSHTM Data Compass (0847)": "" } }, { "code": "A42.0", "description": "Pulmonary actinomycosis", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "", "Brunner-La Rocca et al. 2020": "Y", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "", "Manchester 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(2020-05-10)": "", "LSHTM Data Compass (2050)": "", "LSHTM Data Compass (0847)": "" } }, { "code": "A78", "description": "Q fever", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "", "Brunner-La Rocca et al. 2020": "Y", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "", "Manchester Clinical Codes 42": "", "HDR UK 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Data Compass (2050)": "Y", "LSHTM Data Compass (0847)": "Y" } }, { "code": "B25.0", "description": "Cytomegaloviral pneumonitis", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "", "Brunner-La Rocca et al. 2020": "Y", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "", "Manchester Clinical Codes 42": "", "HDR UK 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"Afonso et al. 2013 (cited by Reyburn et al. 2021)": "", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "", "Manchester Clinical Codes 42": "", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics Resource Project (LRTI)": "", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "", "OpenSAFELY (2020-05-10)": "", "LSHTM Data Compass (2050)": "", "LSHTM Data Compass (0847)": "" } }, { "code": "B58.3", "description": "Pulmonary toxoplasmosis", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "", "Brunner-La Rocca et al. 2020": "Y", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 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Compass (2050)": "", "LSHTM Data Compass (0847)": "" } }, { "code": "B59", "description": "Pneumocystosis", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "", "Brunner-La Rocca et al. 2020": "Y", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "", "Manchester Clinical Codes 42": "", "HDR UK National Phenomics 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"LSHTM Data Compass (2050)": "Y", "LSHTM Data Compass (0847)": "" } }, { "code": "J12.2", "description": "Parainfluenza virus pneumonia", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "Y", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "Y", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", 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(2020-05-10)": "", "LSHTM Data Compass (2050)": "Y", "LSHTM Data Compass (0847)": "" } }, { "code": "J12.9", "description": "Viral pneumonia, unspecified", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "Y", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "Y", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics Resource Project (LRTI)": "", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "", "OpenSAFELY (2020-05-10)": "", "LSHTM Data Compass (2050)": "Y", "LSHTM Data Compass (0847)": "" } }, { "code": "J13", "description": "Pneumonia due to Streptococcus pneumoniae", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "Y", "Lawrence et al. 2020": "Y", "Timmers et al. 2020": "Y", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "Y", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "Y", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "Y", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "Y", "HDR UK National Phenomics Resource Project (LRTI)": "Y", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "Y", "OpenSAFELY (2020-05-10)": "Y", "LSHTM Data Compass (2050)": "Y", "LSHTM Data Compass (0847)": "Y" } }, { "code": "J14", "description": "Pneumonia due to Haemophilus influenzae", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "Y", "Lawrence et al. 2020": "Y", "Timmers et al. 2020": "Y", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "Y", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "Y", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "Y", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "Y", "HDR UK National Phenomics Resource Project (LRTI)": "Y", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "Y", "OpenSAFELY (2020-05-10)": "Y", "LSHTM Data Compass (2050)": "Y", "LSHTM Data Compass (0847)": "Y" } }, { "code": "J15", "description": "Bacterial pneumonia, not elsewhere classified", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "Y", "Lawrence et al. 2020": "Y", "Timmers et al. 2020": "Y", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "Y", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "Y", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "Y", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "Y", "HDR UK National Phenomics Resource Project (LRTI)": "Y", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "Y", "OpenSAFELY (2020-05-10)": "Y", "LSHTM Data Compass (2050)": "Y", "LSHTM Data Compass (0847)": "Y" } }, { "code": "J15.0", "description": "Pneumonia due to Klebsiella pneumoniae", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "Y", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "Y", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics Resource Project (LRTI)": "", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "", "OpenSAFELY (2020-05-10)": "", "LSHTM Data Compass (2050)": "Y", "LSHTM Data Compass (0847)": "" } }, { "code": "J15.1", "description": "Pneumonia due to Pseudomonas", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "Y", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "Y", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics Resource Project (LRTI)": "", "HDR UK National Phenomics Resource Project (viral diseases, excl 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Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics Resource Project (LRTI)": "", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "", "OpenSAFELY (2020-05-10)": "", "LSHTM Data Compass (2050)": "Y", "LSHTM Data Compass (0847)": "" } }, { "code": "J15.3", "description": "Pneumonia due to streptococcus, group B", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "Y", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "Y", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics Resource Project (LRTI)": "", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "", "OpenSAFELY (2020-05-10)": "", "LSHTM Data Compass (2050)": "Y", "LSHTM Data Compass (0847)": "" } }, { "code": "J15.4", "description": "Pneumonia due to other streptococci", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "Y", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "Y", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics Resource Project (LRTI)": "", "HDR UK National 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et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics Resource Project (LRTI)": "", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "", "OpenSAFELY (2020-05-10)": "", "LSHTM Data Compass (2050)": "Y", "LSHTM Data Compass (0847)": "" } }, { "code": "J15.6", "description": "Pneumonia due to other Gram-negative bacteria", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 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due to Mycoplasma pneumoniae", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "Y", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "Y", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics 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"Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics Resource Project (LRTI)": "", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "", "OpenSAFELY (2020-05-10)": "", "LSHTM Data Compass (2050)": "Y", "LSHTM Data Compass (0847)": "" } }, { "code": "J15.9", "description": "Bacterial pneumonia, unspecified", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et 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"J16", "description": "Pneumonia due to other infectious organisms, not elsewhere classified", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "Y", "Lawrence et al. 2020": "Y", "Timmers et al. 2020": "Y", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "Y", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "Y", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "Y", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics Resource Project (LRTI)": "Y", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "Y", "OpenSAFELY (2020-05-10)": "Y", "LSHTM Data Compass (2050)": "", "LSHTM Data Compass (0847)": "Y" } }, { "code": "J16.0", "description": "Chlamydial pneumonia", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "Y", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "", "Afonso et al. 2013 (cited 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Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "Y", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "Y", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics Resource Project (LRTI)": "", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": 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2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics Resource Project (LRTI)": "Y", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "Y", "OpenSAFELY (2020-05-10)": "Y", "LSHTM Data Compass (2050)": "", "LSHTM Data Compass (0847)": "Y" } }, { "code": "J18.0", "description": "Bronchopneumonia, unspecified", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et 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2021": "Y", "Brunner-La Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "Y", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "Y", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics Resource Project (LRTI)": "", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "", "OpenSAFELY (2020-05-10)": "", "LSHTM Data Compass (2050)": "Y", "LSHTM Data Compass (0847)": "" } }, { "code": "J18.2", "description": "Hypostatic pneumonia, unspecified", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et al. 2016 (cited by Reyburn et al. 2021)": "Y", "Uematsu et al. 2016 (cited by Lawrence et al. 2020)": "Y", "Nimptsch. 2016 (cited by Brunner-La Rocca et al. 2020)": "", "Afonso et al. 2013 (cited by Reyburn et al. 2021)": "Y", "Millett et al. 2013": "", "Mesalles-Naranjo O et al. 2018 (cited by Timmers et al. 2020)": "", "Bennett JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics Resource Project (LRTI)": "", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "", "OpenSAFELY (2020-05-10)": "", "LSHTM Data Compass (2050)": "Y", "LSHTM Data Compass (0847)": "" } }, { "code": "J18.8", "description": "Other pneumonia, organism unspecified", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "Y", "de Oliveira et 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(cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "Y", "HDR UK National Phenomics Resource Project (LRTI)": "", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "", "OpenSAFELY (2020-05-10)": "", "LSHTM Data Compass (2050)": "Y", "LSHTM Data Compass (0847)": "" } }, { "code": "J21", "description": "Acute bronchiolitis", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "Y", "Brunner-La Rocca et al. 2020": "", "Lawrence et al. 2020": "", "Timmers et al. 2020": "Y", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "", "de Oliveira et al. 2016 (cited by 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JE et al. 2018 (cited by Timmers et al. 2020)\n": "", "Timmers PRHJ et al. 2020": "Y", "Manchester Clinical Codes 52": "Y", "Manchester Clinical Codes 42": "Y", "HDR UK National Phenomics Resource Project (bacterial diseases, excl TB)": "", "HDR UK National Phenomics Resource Project (LRTI)": "", "HDR UK National Phenomics Resource Project (viral diseases, excl hepatitis/HIV)": "", "HDR UK National Phenomics Resource Project (pneumonia, 10.1371 to 10.1017)": "", "OpenSAFELY (2020-05-10)": "", "LSHTM Data Compass (2050)": "", "LSHTM Data Compass (0847)": "" } }, { "code": "J85.1", "description": "Abscess of lung with pneumonia", "attributes": { "BREATHE recommended": "Y", "Reyburn et al. 2021": "", "Brunner-La Rocca et al. 2020": "Y", "Lawrence et al. 2020": "", "Timmers et al. 2020": "", "Sun et al. 2019": "", "Mpabalwani et al. 2019 (cited by Reyburn et al.2021)": "", "Braeken et al. 2017": "", "Hicks et al. 2017": "", "Diaz et al. 2016 (cited by Reyburn et al. 2021)": "", "de 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Secondary care - 1", "coding_system": { "id": 17, "name": "ICD9 codes", "description": "ICD9 codes" }, "phenotype_id": "PH795", "phenotype_version_id": 2219, "phenotype_name": "Pneumonia Secondary care", "code_attribute_header": [ "BREATHE recommended", "Manchester Clinical Codes 42" ], "codes": [ { "code": "115.9", "description": "HISTOPLASMOSIS PNEUMONIA UNSPECIFIED", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "116.0", "description": "TB PNEUMONIA UNSP", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "116.1", "description": "TB PNEUMONIA W/O EXAM", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "116.2", "description": "TB PNEUMONIA EXAM UNKNOWN", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "116.3", "description": "TB PNEUMONIA MICRO DX", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "116.4", "description": "TB PNEUMONIA CULT DX", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "116.5", "description": "TB PNEUMONIA HISTO DX", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "116.6", "description": "TB PNEUMONIA OTH", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "117.0", "description": "TB PNEUMOTHORAX UNSP", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "117.1", "description": "TB PNEUMOTHORAX W/O EXAM", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "117.2", "description": "TB PNEUMOTHORAX EXAM UNKNOWN", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "117.3", "description": "TB PNEUMOTHORAX MICRO DX", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "117.4", "description": "TB PNEUMOTHORAX CULT DX", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "117.5", "description": "TB PNEUMOTHORAX HISTO DX", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "117.6", "description": "TB PNEUMOTHORAX OTH", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "182.8", "description": "PNEUMONIA DUE TO OTHER SPECIFIED BACTERIA", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "480.0", "description": "PNEUMONIA DUE TO ADENOVIRUS", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "480.1", "description": "PNEUMONIA DUE TO RESPIRATORY SYNCYTIAL VIRUS", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "480.2", "description": "PNEUMONIA DUE TO PARAINFLUENZA VIRUS", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "480.3", "description": "PNEUMONIA DUE TO SARS-ASSOCIATED CORONAVIRUS", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "480.8", "description": "PNEUMONIA DUE TO OTHER VIRUS NOT ELSEWHERE CLASSIFIED", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "480.9", "description": "VIRAL PNEUMONIA UNSPECIFIED", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "481.0", "description": "PNEUMOCOCCAL PNEUMONIA [STREPTOCOCCUS PNEUMONIAE PNEUMONIA]", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "482.0", "description": "PNEUMONIA DUE TO KLEBSIELLA PNEUMONIAE", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "482.1", "description": "PNEUMONIA DUE TO PSEUDOMONAS", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } }, { "code": "482.2", "description": "PNEUMONIA DUE TO HEMOPHILUS INFLUENZAE [H. 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Clinical Codes 42": "Y" } }, { "code": "517.0", "description": "RHEUMATIC PNEUMONIA", "attributes": { "BREATHE recommended": "", "Manchester Clinical Codes 42": "Y" } }, { "code": "730.0", "description": "ORNITHOSIS WITH PNEUMONIA", "attributes": { "BREATHE recommended": "Y", "Manchester Clinical Codes 42": "Y" } } ] }, { "concept_id": 2472, "concept_version_id": 6344, "concept_name": "Pneumonia Secondary care - BREATHE recommended - 3", "coding_system": { "id": 18, "name": "ICD11 codes", "description": "ICD11 codes" }, "phenotype_id": "PH795", "phenotype_version_id": 2219, "phenotype_name": "Pneumonia Secondary care", "code_attribute_header": [], "codes": [ { "code": "CA40", "description": "Pneumonia", "attributes": {} }, { "code": "CA40.0", "description": "Bacterial pneumonia", "attributes": {} }, { "code": "CA40.00", "description": "Pneumonia due to Chlamydophila pneumoniae", "attributes": {} }, { "code": "CA40.01", "description": "Pneumonia due to Escherichia coli", "attributes": {} }, { "code": "CA40.02", "description": "Pneumonia due to Haemophilus influenzae", "attributes": {} }, { "code": "CA40.03", "description": "Pneumonia due to Klebsiella pneumoniae", "attributes": {} }, { "code": "CA40.04", "description": "Pneumonia due to Mycoplasma pneumoniae", "attributes": {} }, { "code": "CA40.05", "description": "Pneumonia due to Pseudomonas aeruginosa", "attributes": {} }, { "code": "CA40.06", "description": "Pneumonia due to Staphylococcus", "attributes": {} }, { "code": "CA40.07", "description": "Pneumonia due to Streptococcus pneumoniae", "attributes": {} }, { "code": "CA40.08", "description": "Pneumonia due to Beta-haemolytic streptococcus", "attributes": {} }, { "code": "CA40.0Y", "description": "Pneumonia due to other specified bacteria", "attributes": {} }, { "code": "CA40.0Z", "description": "Bacterial pneumonia, unspecified", "attributes": {} }, { "code": "CA40.1", "description": "Viral pneumonia", "attributes": {} }, { "code": "CA40.10", "description": "Pneumonia due to Adenovirus", "attributes": {} }, { "code": "CA40.11", "description": "Pneumonia due to Respiratory syncytial virus", "attributes": {} }, { "code": "CA40.12", "description": "Pneumonia due to parainfluenza virus", "attributes": {} }, { "code": "CA40.13", "description": "Pneumonia due to Human metapneumovirus", "attributes": {} }, { "code": "CA40.1Y", "description": "Pneumonia due to other specified virus", "attributes": {} }, { "code": "CA40.1Z", "description": "Viral pneumonia, unspecified", "attributes": {} }, { "code": "CA40.2Z", "description": "Fungal pneumonia, unspecified", "attributes": {} }, { "code": "CA40.Z", "description": "Pneumonia, organism unspecified", "attributes": {} } ] }, { "concept_id": 2471, "concept_version_id": 6342, "concept_name": "Pneumonia Secondary care - BREATHE recommended - 2", "coding_system": { "id": 4, "name": "ICD10 codes", "description": "ICD10 Codes" }, "phenotype_id": "PH795", "phenotype_version_id": 2219, "phenotype_name": "Pneumonia Secondary care", "code_attribute_header": [], "codes": [ { "code": "A20.2", "description": "Pneumonic plague", "attributes": {} }, { "code": "A21.2", "description": "Pulmonary tularaemia", "attributes": {} }, { "code": "A22.1", "description": "Pulmonary anthrax", "attributes": {} }, { "code": "A31.0", "description": "Pulmonary mycobacterial infection", "attributes": {} }, { "code": "A42.0", "description": "Pulmonary actinomycosis", "attributes": {} }, { "code": "A43.0", "description": "Pulmonary nocardiosis", "attributes": {} }, { "code": "A48.1", "description": "Legionnaires disease", "attributes": {} }, { "code": "A78", "description": "Q fever", "attributes": {} }, { "code": "B01.2", "description": "Varicella pneumonia", "attributes": {} }, { "code": "B05.2", "description": "Measles complicated by pneumonia", "attributes": {} }, { "code": "B25.0", "description": "Cytomegaloviral pneumonitis", "attributes": {} }, { "code": "B37.1", "description": "Pulmonary candidiasis", "attributes": {} }, { "code": "B58.3", "description": "Pulmonary toxoplasmosis", "attributes": {} }, { "code": "B59", "description": "Pneumocystosis", "attributes": {} }, { "code": "B67.1", "description": "Echinococcus granulosus infection of lung", "attributes": {} }, { "code": "J09", "description": "Influenza due to identified zoonotic or pandemic influenza virus", "attributes": {} }, { "code": "J10", "description": "Influenza due to identified seasonal influenza virus", "attributes": {} }, { "code": "J10.0", "description": "Influenza with pneumonia, seasonal influenza virus identified", "attributes": {} }, { "code": "J10.1", "description": "Influenza with other respiratory manifestations, seasonal influenza virus identified", "attributes": {} }, { "code": "J10.8", "description": "Influenza with other manifestations, seasonal influenza virus identified", "attributes": {} }, { "code": "J11", "description": "Influenza, virus not identified", "attributes": {} }, { "code": "J11.0", "description": "Influenza with pneumonia, virus not identified", "attributes": {} }, { "code": "J11.1", "description": "Influenza with other respiratory manifestations, virus not identified", "attributes": {} }, { "code": "J11.8", "description": "Influenza with other manifestations, virus not identified", "attributes": {} }, { "code": "J12", "description": "Viral pneumonia, not elsewhere classified", "attributes": {} }, { "code": "J12.0", "description": "Adenoviral pneumonia", "attributes": {} }, { "code": "J12.1", "description": "Respiratory syncytial virus pneumonia", "attributes": {} }, { "code": "J12.2", "description": "Parainfluenza virus pneumonia", "attributes": {} }, { "code": "J12.3", "description": "Human metapneumovirus pneumonia", "attributes": {} }, { "code": "J12.8", "description": "Other viral pneumonia", "attributes": {} }, { "code": "J12.9", "description": "Viral pneumonia, unspecified", "attributes": {} }, { "code": "J13", "description": "Pneumonia due to 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"code": "J15.8", "description": "Other bacterial pneumonia", "attributes": {} }, { "code": "J15.9", "description": "Bacterial pneumonia, unspecified", "attributes": {} }, { "code": "J16", "description": "Pneumonia due to other infectious organisms, not elsewhere classified", "attributes": {} }, { "code": "J16.0", "description": "Chlamydial pneumonia", "attributes": {} }, { "code": "J16.8", "description": "Pneumonia due to other specified infectious organisms", "attributes": {} }, { "code": "J17.0", "description": "Pneumonia in bacterial diseases classified elsewhere", "attributes": {} }, { "code": "J17.1", "description": "Pneumonia in viral diseases classified elsewhere", "attributes": {} }, { "code": "J17.2", "description": "Pneumonia in mycoses", "attributes": {} }, { "code": "J17.3", "description": "Pneumonia in parasitic diseases", "attributes": {} }, { "code": "J17.8", "description": "Pneumonia in other diseases classified elsewhere", "attributes": {} }, { "code": "J18", "description": "Pneumonia, organism unspecified", "attributes": {} }, { "code": "J18.0", "description": "Bronchopneumonia, unspecified", "attributes": {} }, { "code": "J18.1", "description": "Lobar pneumonia, unspecified", "attributes": {} }, { "code": "J18.2", "description": "Hypostatic pneumonia, unspecified", "attributes": {} }, { "code": "J18.8", "description": "Other pneumonia, organism unspecified", "attributes": {} }, { "code": "J18.9", "description": "Pneumonia, unspecified", "attributes": {} }, { "code": "J20", "description": "Acute bronchitis", "attributes": {} }, { "code": "J21", "description": "Acute bronchiolitis", "attributes": {} }, { "code": "J22", "description": "Unspecified acute lower respiratory infection", "attributes": {} }, { "code": "J85.1", "description": "Abscess of lung with pneumonia", "attributes": {} } ] }, { "concept_id": 2470, "concept_version_id": 6340, "concept_name": "Pneumonia Secondary care - BREATHE recommended - 1", "coding_system": { "id": 17, "name": "ICD9 codes", "description": "ICD9 codes" }, "phenotype_id": "PH795", "phenotype_version_id": 2219, "phenotype_name": "Pneumonia Secondary care", "code_attribute_header": [], "codes": [ { "code": "115.9", "description": "HISTOPLASMOSIS PNEUMONIA UNSPECIFIED", "attributes": {} }, { "code": "116.0", "description": "TB PNEUMONIA UNSP", "attributes": {} }, { "code": "116.1", "description": "TB PNEUMONIA W/O EXAM", "attributes": {} }, { "code": "116.2", "description": "TB PNEUMONIA EXAM UNKNOWN", "attributes": {} }, { "code": "116.3", "description": "TB PNEUMONIA MICRO DX", "attributes": {} }, { "code": "116.4", "description": "TB PNEUMONIA CULT DX", "attributes": {} }, { "code": "116.5", "description": "TB PNEUMONIA HISTO DX", "attributes": {} }, { "code": "116.6", "description": "TB PNEUMONIA OTH", "attributes": {} }, { "code": "117.0", "description": "TB PNEUMOTHORAX UNSP", "attributes": {} }, { "code": "117.1", "description": "TB PNEUMOTHORAX W/O EXAM", "attributes": {} }, { "code": "117.2", "description": "TB PNEUMOTHORAX EXAM UNKNOWN", "attributes": {} }, { "code": "117.3", "description": "TB PNEUMOTHORAX MICRO DX", "attributes": {} }, { "code": "117.4", "description": "TB PNEUMOTHORAX CULT DX", "attributes": {} }, { "code": "117.5", "description": "TB PNEUMOTHORAX HISTO DX", "attributes": {} }, { "code": "117.6", "description": "TB PNEUMOTHORAX OTH", "attributes": {} }, { "code": "182.8", "description": "PNEUMONIA DUE TO OTHER SPECIFIED BACTERIA", "attributes": {} }, { "code": "480.0", "description": "PNEUMONIA DUE TO ADENOVIRUS", "attributes": {} }, { "code": "480.1", "description": "PNEUMONIA DUE TO RESPIRATORY SYNCYTIAL VIRUS", "attributes": {} }, { "code": "480.2", "description": "PNEUMONIA DUE TO PARAINFLUENZA VIRUS", "attributes": {} }, { "code": "480.3", "description": "PNEUMONIA DUE TO SARS-ASSOCIATED CORONAVIRUS", "attributes": {} }, { "code": "480.8", "description": "PNEUMONIA DUE TO OTHER VIRUS NOT ELSEWHERE CLASSIFIED", "attributes": {} }, { "code": "480.9", "description": "VIRAL PNEUMONIA UNSPECIFIED", "attributes": {} }, { "code": "481.0", "description": "PNEUMOCOCCAL PNEUMONIA [STREPTOCOCCUS PNEUMONIAE PNEUMONIA]", "attributes": {} }, { "code": "482.0", "description": "PNEUMONIA DUE TO KLEBSIELLA PNEUMONIAE", "attributes": {} }, { "code": "482.1", "description": "PNEUMONIA DUE TO PSEUDOMONAS", "attributes": {} }, { "code": "482.2", "description": "PNEUMONIA DUE TO HEMOPHILUS INFLUENZAE [H. 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