[ { "phenotype_id": "PH803", "phenotype_version_id": 2227, "name": "Empyema or pyothorax or purulent pleuritis Secondary care", "definition": "\n- Not found code search\n- Hamilton et al, 2020Clinical coding of pleural empyema was validated using coding data from three hospitals in England, UK. The coded diagnoses of pleural empyema is defined as J86-, also known as pyothorax. Empyema was considered as a pleural effusion that had a documented pH of less than 7.2, microscopic evidence of infection, or frank pus. If microscopic evidence was not available, then clear clinical management as empyema (supporting radiology, clinical progress, and biochemistry) was used.The clinical diagnosis of empyema was made on retrospective review of the notes, discharge summary, radiology, and microbiology available.Empyema was considered as a pleural effusion that had a documented pH of less than 7.2, microscopic evidence of infection, or frank pus. If microscopic evidence was not available, then clear clinical management as empyema (supporting radiology, clinical progress, and biochemistry) was used.Empyema coding was generally good (>85% accuracy), although some cases were miscoded. Using codes for elective admissions helped to differentiate post-operative from community acquired empyema. It is likely empyema is under rather than over-recorded in HES data.Using codes for elective admissions helped to differentiate post-operative from community acquired empyema. It is likely empyema is under rather than over-recorded in HES data.", "implementation": "\n\nThese codes are not intended to be mandatory, but are to be used as a starting point for the identification of empyema in routine Electronic Health Record (EHR). Each study may differ in the sensitivity and specificity of the coding required. \n\n \n\nAccording to the National Health Service (NHS), Empyema is defined as pocketcs of pus that have collected insided a body cavity. They can form if a bacterial infection is left untreated, or if it fails to fully respond to treatment. The term is most commonly used to refer to pus-filled pockets that develop in the pleural space.\n\nhttps://www.nhs.uk/conditions/empyema/\n\nNot found code search\n\n", "publications": [ { "doi": null, "details": "Publications in 2020-2021 identified in PubMed" }, { "doi": "10.1183/13993003.03546-2020", "details": "Arnold DT, Hamilton FW, Morris TT, Suri T, Morley A, Frost V, Vipond IB, Medford AR, Payne RA, Muir P, Maskell NA. Epidemiology of pleural empyema in English hospitals and the impact of influenza. Eur Respir J. 2021 Jun 17;57(6):2003546. doi: 10.1183/13993003.03546-2020. PMID: 33334937." }, { "doi": "10.1136/thoraxjnl-2020-216032", "details": "Strachan R, Homaira N, Beggs S, Bhuiyan MU, Gilbert GL, Lambert SB, Macartney K, Marshall H, Martin AC, McCallum GB, McCullagh A, McDonald T, McIntyre P, Oftadeh S, Ranganathan S, Suresh S, Wainwright CE, Wilson A, Wong M, Snelling T, Jaffé A. Assessing the impact of the 13 valent pneumococcal vaccine on childhood empyema in Australia. Thorax. 2021 May;76(5):487-493. doi: 10.1136/thoraxjnl-2020-216032. Epub 2021 Jan 27. PMID: 33504566." }, { "doi": null, "details": ">Code repositories" }, { "doi": null, "details": "**ID**- 1 \n- **Repository**- Manchester ClinicalCodes \n- **Description**- The association between smoking and 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**- Unpublished \n- **Clinical codes**- ICD-10 " }, { "doi": "10.1002/acr.22882", "details": "**ID**- 2 \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": "10.1093/jac/dkz163", "details": "**ID**- 3 \n- **Repository**- Manchester ClinicalCodes \n- **Description**- Antibiotic prescribing for common infections in UK general practice: variability and drivers \n- **Conditions**- LRTI \n- **Publication**- https://doi.org/10.1093/jac/dkz163 \n- **Clinical codes**- Read Version 2 " }, { "doi": null, "details": "**ID**- 4 \n- **Repository**- HDR UK National Phenomics Resource Project \n- **Description**- \n- **Conditions**- Bacterial diseases (excl TB) \n- **Publication**- \n- **Clinical codes**- ICD-10 " }, { "doi": null, "details": "**ID**- 5 \n- **Repository**- HDR UK National Phenomics Resource Project \n- **Description**- \n- **Conditions**- Lower respiratory tract infections \n- **Publication**- \n- **Clinical codes**- ICD-10 " } ], "validation": "Hamilton et al, 2020Clinical coding of pleural empyema was validated using coding data from three hospitals in England, UK. The coded diagnoses of pleural empyema is defined as J86-, also known as pyothorax. Empyema was considered as a pleural effusion that had a documented pH of less than 7.2, microscopic evidence of infection, or frank pus. If microscopic evidence was not available, then clear clinical management as empyema (supporting radiology, clinical progress, and biochemistry) was used.The clinical diagnosis of empyema was made on retrospective review of the notes, discharge summary, radiology, and microbiology available.Empyema was considered as a pleural effusion that had a documented pH of less than 7.2, microscopic evidence of infection, or frank pus. If microscopic evidence was not available, then clear clinical management as empyema (supporting radiology, clinical progress, and biochemistry) was used.Empyema coding was generally good (>85% accuracy), although some cases were miscoded. Using codes for elective admissions helped to differentiate post-operative from community acquired empyema. It is likely empyema is under rather than over-recorded in HES data.Using codes for elective admissions helped to differentiate post-operative from community acquired empyema. It is likely empyema is under rather than over-recorded in HES data.", "citation_requirements": "", "created": "2022-01-17T14:00:50.851712Z", "author": "Chukwuma Iwundu, Clare MacRae, Eleftheria Vasileiou", "collections": [ { "name": "BREATHE", "value": 19 }, { "name": "Phenotype Library", "value": 18 } ], "tags": null, "organisation": null, "world_access": 2, "updated": "2022-08-04T18:39:05.726551Z", "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 } ], "event_date_range": "01/01/2001 to 31/01/2021", "concept_information": [ { "concept_id": 2508, "concept_version_id": 6416, "concept_name": "Empyema or pyothorax or purulent pleuritis Secondary care - 2", "coding_system": { "id": 17, "name": "ICD9 codes", "description": "ICD9 codes" }, "phenotype_id": "PH803", "phenotype_version_id": 2227, "phenotype_name": "Empyema or pyothorax or purulent pleuritis Secondary care", "code_attribute_header": [ "BREATHE recommended", "Wiese et al, 2016", "Nath et al, 2015", "Grijalva et al, 2011", "Ampofo et al, 2010", "Bender et al, 2009", "Strachan et al, 2009", "Farjah et al, 2007", "Byington et al, 2006", "Roxburgh et al, 2006", "Manchester Clinical Codes 2" ], "codes": [ { "code": "510", "description": "Empyema", "attributes": { "BREATHE recommended": "Y", "Wiese et al, 2016": "Y", "Nath et al, 2015": "", "Grijalva et al, 2011": "Y", "Ampofo et al, 2010": "Y", "Bender et al, 2009": "", "Strachan et al, 2009": "Y", "Farjah et al, 2007": "", "Byington et al, 2006": "", "Roxburgh et al, 2006": "", "Manchester Clinical Codes 2": "Y" } }, { "code": "510.0", "description": "Empyema with fistula", "attributes": { "BREATHE recommended": "Y", "Wiese et al, 2016": "", "Nath et al, 2015": "Y", "Grijalva et al, 2011": "", "Ampofo et al, 2010": "", "Bender et al, 2009": "", "Strachan et al, 2009": "Y", "Farjah et al, 2007": "Y", "Byington et al, 2006": "", "Roxburgh et al, 2006": "Y", "Manchester Clinical Codes 2": "" } }, { "code": "510.9", "description": "Empyema without fistula", "attributes": { "BREATHE recommended": "Y", "Wiese et al, 2016": "", "Nath et al, 2015": "", "Grijalva et al, 2011": "", "Ampofo et al, 2010": "", "Bender et al, 2009": "Y", "Strachan et al, 2009": "Y", "Farjah et al, 2007": "Y", "Byington et al, 2006": "Y", "Roxburgh et al, 2006": "Y", "Manchester Clinical Codes 2": "Y" } } ] }, { "concept_id": 2507, "concept_version_id": 6414, "concept_name": "Empyema or pyothorax or purulent pleuritis Secondary care - 1", "coding_system": { "id": 4, "name": "ICD10 codes", "description": "ICD10 Codes" }, "phenotype_id": "PH803", "phenotype_version_id": 2227, "phenotype_name": "Empyema or pyothorax or purulent pleuritis Secondary care", "code_attribute_header": [ "BREATHE recommended", "Arnold et al, 2021", "Strachan et al, 2021", "Hamilton et al, 2020", "National thoracic surgery report activity, 2018", "Nath et al, 2015", "Lindstrand et al, 2014", "Sogaard et al, 2014", "Strachan et al, 2013", "Bender et al, 2009", "Strachan et al, 2009", "Roxburgh et al, 2006", "Manchester Clinical Codes 1", "Manchester Clinical Codes 2", "HDR UK National Phenomics Resource Project 4", "HDR UK National Phenomics Resource Project 5" ], "codes": [ { "code": "A15.6", "description": "Tuberculous pleurisy, confirmed bacteriologically and histologically", "attributes": { "BREATHE recommended": "Y", "Arnold et al, 2021": "", "Strachan et al, 2021": "", "Hamilton et al, 2020": "", "National thoracic surgery report activity, 2018": "", "Nath et al, 2015": "Y", "Lindstrand et al, 2014": "", "Sogaard et al, 2014": "", "Strachan et al, 2013": "", "Bender et al, 2009": "", "Strachan et al, 2009": "", "Roxburgh et al, 2006": "", "Manchester Clinical Codes 1": "Y", "Manchester Clinical Codes 2": "Y", "HDR UK National Phenomics Resource Project 4": "", "HDR UK National Phenomics Resource Project 5": "" } }, { "code": "A16.5", "description": "Tuberculous pleurisy, without mention of bacteriological or histological confirmation", "attributes": { "BREATHE recommended": "Y", "Arnold et al, 2021": "", "Strachan et al, 2021": "", "Hamilton et al, 2020": "", "National thoracic surgery report activity, 2018": "", "Nath et al, 2015": "Y", "Lindstrand et al, 2014": "", "Sogaard et al, 2014": "", "Strachan et al, 2013": "", "Bender et al, 2009": "", "Strachan et al, 2009": "", "Roxburgh et al, 2006": "", "Manchester Clinical Codes 1": "Y", "Manchester Clinical Codes 2": "Y", "HDR UK National Phenomics Resource Project 4": "", "HDR UK National Phenomics Resource Project 5": "" } }, { "code": "J86", "description": "Pyothorax", "attributes": { "BREATHE recommended": "Y", "Arnold et al, 2021": "Y", "Strachan et al, 2021": "", "Hamilton et al, 2020": "Y", "National thoracic surgery report activity, 2018": "Y", "Nath et al, 2015": "", "Lindstrand et al, 2014": "Y", "Sogaard et al, 2014": "", "Strachan et al, 2013": "Y", "Bender et al, 2009": "", "Strachan et al, 2009": "Y", "Roxburgh et al, 2006": "", "Manchester Clinical Codes 1": "", "Manchester Clinical Codes 2": "Y", "HDR UK National Phenomics Resource Project 4": "Y", "HDR UK National Phenomics Resource Project 5": "Y" } }, { "code": "J86.0", "description": "Pyothorax with fistula", "attributes": { "BREATHE recommended": "Y", "Arnold et al, 2021": "", "Strachan et al, 2021": "Y", "Hamilton et al, 2020": "", "National thoracic surgery report activity, 2018": "", "Nath et al, 2015": "", "Lindstrand et al, 2014": "", "Sogaard et al, 2014": "Y", "Strachan et al, 2013": "Y", "Bender et al, 2009": "", "Strachan et al, 2009": "Y", "Roxburgh et al, 2006": "", "Manchester Clinical Codes 1": "", "Manchester Clinical Codes 2": "Y", "HDR UK National Phenomics Resource Project 4": "", "HDR UK National Phenomics Resource Project 5": "" } }, { "code": "J86.9", "description": "Pyothorax without fistula", "attributes": { "BREATHE recommended": "Y", "Arnold et al, 2021": "", "Strachan et al, 2021": "Y", "Hamilton et al, 2020": "", "National thoracic surgery report activity, 2018": "", "Nath et al, 2015": "Y", "Lindstrand et al, 2014": "", "Sogaard et al, 2014": "Y", "Strachan et al, 2013": "Y", "Bender et al, 2009": "Y", "Strachan et al, 2009": "Y", "Roxburgh et al, 2006": "Y", "Manchester Clinical Codes 1": "", "Manchester Clinical Codes 2": "Y", "HDR UK National Phenomics Resource Project 4": "", "HDR UK National Phenomics Resource Project 5": "" } } ] }, { "concept_id": 2506, "concept_version_id": 6412, "concept_name": "Empyema or pyothorax or purulent pleuritis Secondary care - BREATHE recommended - 2", "coding_system": { "id": 17, "name": "ICD9 codes", "description": "ICD9 codes" }, "phenotype_id": "PH803", "phenotype_version_id": 2227, "phenotype_name": "Empyema or pyothorax or purulent pleuritis Secondary care", "code_attribute_header": [], "codes": [ { "code": "510", "description": "Empyema", "attributes": {} }, { "code": "510.0", "description": "Empyema with fistula", "attributes": {} }, { "code": "510.9", "description": "Empyema without fistula", "attributes": {} } ] }, { "concept_id": 2505, "concept_version_id": 6410, "concept_name": "Empyema or pyothorax or purulent pleuritis Secondary care - BREATHE recommended - 1", "coding_system": { "id": 4, "name": "ICD10 codes", "description": "ICD10 Codes" }, "phenotype_id": "PH803", "phenotype_version_id": 2227, "phenotype_name": "Empyema or pyothorax or purulent pleuritis Secondary care", "code_attribute_header": [], "codes": [ { "code": "A15.6", "description": "Tuberculous pleurisy, confirmed bacteriologically and histologically", "attributes": {} }, { "code": "A16.5", "description": "Tuberculous pleurisy, without mention of bacteriological or histological confirmation", "attributes": {} }, { "code": "J86", "description": "Pyothorax", "attributes": {} }, { "code": "J86.0", "description": "Pyothorax with fistula", "attributes": {} }, { "code": "J86.9", "description": "Pyothorax without fistula", "attributes": {} } ] } ], "status": 2, "doi": "https://doi.org/10.48533/6f7z-qm33", "is_deleted": null, "publish_status": 2, "owner": "zinnurar", "template": { "id": 1, "name": "Clinical-Coded Phenotype", "description": "Phenotype definitions that are based on lists of clinical codes, or algorithms using clinical codes.", "version_id": 1 }, "versions": [ { "version_id": 2227, "version_name": "Empyema or pyothorax or purulent pleuritis Secondary care", "version_date": "2022-08-04T18:39:06.007846Z", "is_published": true, "is_latest": true }, { "version_id": 1685, "version_name": "Empyema or pyothorax or purulent pleuritis Secondary care", "version_date": "2022-01-17T14:00:50.902139Z", "is_published": true, "is_latest": false } ] } ]