{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:27:53Z","timestamp":1772173673870,"version":"3.50.1"},"reference-count":52,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2025,7,21]],"date-time":"2025-07-21T00:00:00Z","timestamp":1753056000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100018336","name":"National Institute for Health Research Health Protection Research Unit","doi-asserted-by":"publisher","award":["NIHR200915"],"award-info":[{"award-number":["NIHR200915"]}],"id":[{"id":"10.13039\/100018336","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100013373","name":"NIHR Oxford Biomedical Research Centre","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013373","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Robertson fellowship"},{"name":"NIHR Senior Investigator"}],"content-domain":{"domain":["www.plosdigitalhealth.org"],"crossmark-restriction":false},"short-container-title":["PLOS Digit Health"],"abstract":"<jats:p>Community-acquired pneumonia (CAP) is common and a significant cause of mortality. However, CAP surveillance commonly relies on diagnostic codes from electronic health records (EHRs), with imperfect accuracy. We used Bayesian latent class models with multiple imputation to assess the accuracy of CAP diagnostic codes in the absence of a gold standard and to explore the contribution of various EHR data sources in improving CAP identification. Using 491,681 hospital admissions in Oxfordshire, UK, from 2016 to 2023, we investigated four EHR-based algorithms for CAP detection based on 1) primary diagnostic codes, 2) clinician-documented indications for antibiotic prescriptions, 3) radiology free-text reports, and 4) vital signs and blood tests. The estimated prevalence of CAP as the reason for emergency hospital admission was 13.6% (95% credible interval 13.3-14.0%). Primary diagnostic codes had low sensitivity but a high specificity (best fitting model, 0.275 and 0.997 respectively), as did vital signs with blood tests (0.348 and 0.963). Antibiotic indication text had a higher sensitivity (0.590) but a lower specificity (0.982), with radiology reports intermediate (0.485 and 0.960). Defining CAP as present when detected by any algorithm produced sensitivity and specificity of 0.873 and 0.905 respectively. Results remained consistent using alternative priors and in sensitivity analyses. Relying solely on diagnostic codes for CAP surveillance leads to substantial under-detection; combining EHR data across multiple algorithms enhances identification accuracy. Bayesian latent class analysis-based approaches could improve CAP surveillance and epidemiological estimates by integrating multiple EHR sources, even without a gold standard for CAP diagnosis.<\/jats:p>","DOI":"10.1371\/journal.pdig.0000936","type":"journal-article","created":{"date-parts":[[2025,7,21]],"date-time":"2025-07-21T17:21:59Z","timestamp":1753118519000},"page":"e0000936","update-policy":"https:\/\/doi.org\/10.1371\/journal.pdig.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Community-acquired pneumonia identification from electronic health records in the absence of a gold standard: A Bayesian latent class analysis"],"prefix":"10.1371","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9621-529X","authenticated-orcid":true,"given":"Jia","family":"Wei","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kevin","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Augustine","family":"Luk","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A. Sarah","family":"Walker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David W.","family":"Eyre","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2025,7,21]]},"reference":[{"issue":"10159","key":"pdig.0000936.ref001","doi-asserted-by":"crossref","first-page":"1736","DOI":"10.1016\/S0140-6736(18)32203-7","article-title":"Global, regional, and national age-sex-specific mortality for 282 causes of death in 195 countries and territories, 1980-2017: a systematic analysis for the Global Burden of Disease Study 2017","volume":"392","author":"GA Roth","year":"2018","journal-title":"Lancet"},{"issue":"4","key":"pdig.0000936.ref002","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1016\/j.idc.2019.07.002","article-title":"Antibiotic-Resistant Community-Acquired Bacterial Pneumonia","volume":"33","author":"J Ho","year":"2019","journal-title":"Infectious Disease Clinics of North America"},{"issue":"1","key":"pdig.0000936.ref003","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1186\/s12931-018-0781-4","article-title":"Trends in mortality from pneumonia in the Europe union: a temporal analysis of the European detailed mortality database between 2001 and 2014","volume":"19","author":"DC Marshall","year":"2018","journal-title":"Respir Res"},{"issue":"6","key":"pdig.0000936.ref004","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1136\/thoraxjnl-2015-207688","article-title":"Increasing burden of community-acquired pneumonia leading to hospitalisation, 1998-2014","volume":"71","author":"TP Quan","year":"2016","journal-title":"Thorax"},{"issue":"6","key":"pdig.0000936.ref005","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1177\/1062860605280358","article-title":"Accuracy of administrative data for identifying patients with pneumonia","volume":"20","author":"D Aronsky","year":"2005","journal-title":"Am J Med Qual"},{"issue":"8","key":"pdig.0000936.ref006","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1016\/j.jclinepi.2006.10.018","article-title":"International classification of diseases codes showed modest sensitivity for detecting community-acquired pneumonia","volume":"60","author":"EMW van de Garde","year":"2007","journal-title":"J Clin Epidemiol"},{"issue":"5","key":"pdig.0000936.ref007","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/j.annepidem.2013.02.005","article-title":"Accuracy of ICD-9-CM codes in identifying infections of pneumonia and herpes simplex virus in administrative data","volume":"23","author":"J Drahos","year":"2013","journal-title":"Ann Epidemiol"},{"issue":"9","key":"pdig.0000936.ref008","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1001\/jamapediatrics.2013.186","article-title":"Identifying pediatric community-acquired pneumonia hospitalizations: Accuracy of administrative billing codes","volume":"167","author":"DJ Williams","year":"2013","journal-title":"JAMA Pediatr"},{"issue":"8","key":"pdig.0000936.ref009","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0070944","article-title":"Using the electronic medical record to identify community-acquired pneumonia: toward a replicable automated strategy","volume":"8","author":"S DeLisle","year":"2013","journal-title":"PLoS One"},{"issue":"4","key":"pdig.0000936.ref010","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1136\/thoraxjnl-2016-209405","article-title":"Adults miscoded and misdiagnosed as having pneumonia: results from the British Thoracic Society pneumonia audit","volume":"72","author":"P Daniel","year":"2017","journal-title":"Thorax"},{"issue":"4","key":"pdig.0000936.ref011","doi-asserted-by":"crossref","first-page":"293","DOI":"10.4258\/hir.2017.23.4.293","article-title":"Validity of Principal Diagnoses in Discharge Summaries and ICD-10 Coding Assessments Based on National Health Data of Thailand","volume":"23","author":"C Sukanya","year":"2017","journal-title":"Healthc Inform Res"},{"issue":"1","key":"pdig.0000936.ref012","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/j.jhin.2018.01.017","article-title":"Should International Classification of Diseases codes be used to survey hospital-acquired pneumonia?","volume":"99","author":"A Wolfensberger","year":"2018","journal-title":"J Hosp Infect"},{"issue":"6","key":"pdig.0000936.ref013","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1038\/nrg3208","article-title":"Mining electronic health records: towards better research applications and clinical care","volume":"13","author":"PB Jensen","year":"2012","journal-title":"Nat Rev Genet"},{"key":"pdig.0000936.ref014","doi-asserted-by":"crossref","DOI":"10.1136\/bmj.c4226","article-title":"Importance of accurately identifying disease in studies using electronic health records","volume":"341","author":"DG Manuel","year":"2010","journal-title":"BMJ"},{"issue":"1","key":"pdig.0000936.ref015","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1186\/s12879-018-3515-9","article-title":"High heterogeneity in community-acquired pneumonia inclusion criteria: does this impact on the validity of the results of randomized controlled trials?","volume":"18","author":"C Flateau","year":"2018","journal-title":"BMC Infect Dis"},{"issue":"8","key":"pdig.0000936.ref016","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0011989","article-title":"A systematic review on the diagnosis of pediatric bacterial pneumonia: when gold is bronze","volume":"5","author":"T Lynch","year":"2010","journal-title":"PLoS One"},{"key":"pdig.0000936.ref017","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/s41479-016-0012-z","article-title":"The definition and classification of pneumonia","volume":"8","author":"G Mackenzie","year":"2016","journal-title":"Pneumonia (Nathan)"},{"key":"pdig.0000936.ref018"},{"issue":"1","key":"pdig.0000936.ref019","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/s43856-025-00790-1","article-title":"Transformers and large language models are efficient feature extractors for electronic health record studies.","volume":"5","author":"K Yuan","year":"2025","journal-title":"Commun Med (Lond)"},{"key":"pdig.0000936.ref020","doi-asserted-by":"crossref","DOI":"10.1136\/bmj.f2450","article-title":"Use of serum C reactive protein and procalcitonin concentrations in addition to symptoms and signs to predict pneumonia in patients presenting to primary care with acute cough: diagnostic study","volume":"346","author":"SF van Vugt","year":"2013","journal-title":"BMJ"},{"issue":"9","key":"pdig.0000936.ref021","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0239606","article-title":"Accuracy of C-reactive protein, procalcitonin, serum amyloid A and neopterin for low-dose CT-scan confirmed pneumonia in elderly patients: A prospective cohort study","volume":"15","author":"V Prendki","year":"2020","journal-title":"PLoS One"},{"issue":"4","key":"pdig.0000936.ref022","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1183\/09031936.03.00080203","article-title":"C-reactive protein levels in community-acquired pneumonia","volume":"21","author":"E Garc\u00eda V\u00e1zquez","year":"2003","journal-title":"Eur Respir J"},{"key":"pdig.0000936.ref023"},{"issue":"3","key":"pdig.0000936.ref024","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1093\/cid\/ciq076","article-title":"Oxygen saturations less than 92% are associated with major adverse events in outpatients with pneumonia: a population-based cohort study","volume":"52","author":"SR Majumdar","year":"2011","journal-title":"Clin Infect Dis"},{"key":"pdig.0000936.ref025","article-title":"Physiology, Respiratory Rate","author":"C Chourpiliadis","year":"2022","journal-title":"StatPearls"},{"issue":"6316","key":"pdig.0000936.ref026","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1136\/bmj.284.6316.626","article-title":"Raised respiratory rate in elderly patients: a valuable physical sign","volume":"284","author":"JP McFadden","year":"1982","journal-title":"Br Med J (Clin Res Ed)"},{"key":"pdig.0000936.ref027","first-page":"237","article-title":"C Reactive Protein","volume":"65","author":"SM Nehring","year":"2023","journal-title":"StatPearls"},{"key":"pdig.0000936.ref028"},{"issue":"2","key":"pdig.0000936.ref029","first-page":"211","article-title":"ATS\/ACCP Statement on cardiopulmonary exercise testing","volume":"167","author":"IM Weisman","year":"2012","journal-title":"Am J Respir Crit Care Med"},{"issue":"3","key":"pdig.0000936.ref030","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1093\/oxfordjournals.aje.a117428","article-title":"Bayesian estimation of disease prevalence and the parameters of diagnostic tests in the absence of a gold standard","volume":"141","author":"L Joseph","year":"1995","journal-title":"Am J Epidemiol"},{"issue":"3","key":"pdig.0000936.ref031","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1002\/pds.3870","article-title":"Bayesian estimation of the accuracy of ICD-9-CM- and CPT-4-based algorithms to identify cholecystectomy procedures in administrative data without a reference standard","volume":"25","author":"SR Jafarzadeh","year":"2016","journal-title":"Pharmacoepidemiol Drug Saf"},{"issue":"10","key":"pdig.0000936.ref032","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1016\/j.annepidem.2016.08.002","article-title":"Sepsis surveillance from administrative data in the absence of a perfect verification","volume":"26","author":"SR Jafarzadeh","year":"2016","journal-title":"Ann Epidemiol"},{"issue":"1","key":"pdig.0000936.ref033","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1111\/j.0006-341X.2001.00158.x","article-title":"Bayesian approaches to modeling the conditional dependence between multiple diagnostic tests","volume":"57","author":"N Dendukuri","year":"2001","journal-title":"Biometrics"},{"issue":"4","key":"pdig.0000936.ref034","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1111\/1467-9868.00353","article-title":"Bayesian Measures of Model Complexity and Fit","volume":"64","author":"DJ Spiegelhalter","year":"2002","journal-title":"Journal of the Royal Statistical Society Series B: Statistical Methodology"},{"issue":"2","key":"pdig.0000936.ref035","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1093\/pubmed\/fdv041","article-title":"Accuracy of clinician-clinical coder information handover following acute medical admissions: implication for using administrative datasets in clinical outcomes management","volume":"38","author":"SAR Nouraei","year":"2016","journal-title":"J Public Health (Oxf)"},{"issue":"6","key":"pdig.0000936.ref036","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1097\/EDE.0000000000000888","article-title":"Accuracy of Administrative Health Data for Surveillance of Traumatic Brain Injury: A Bayesian Latent Class Analysis","volume":"29","author":"O Lasry","year":"2018","journal-title":"Epidemiology"},{"issue":"1","key":"pdig.0000936.ref037","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1111\/j.1541-0420.2006.00665.x","article-title":"Robustness of prevalence estimates derived from misclassified data from administrative databases","volume":"63","author":"M Ladouceur","year":"2007","journal-title":"Biometrics"},{"issue":"4","key":"pdig.0000936.ref038","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1007\/s00296-010-1591-2","article-title":"Surveillance of systemic autoimmune rheumatic diseases using administrative data","volume":"31","author":"S Bernatsky","year":"2011","journal-title":"Rheumatol Int"},{"key":"pdig.0000936.ref039","doi-asserted-by":"crossref","first-page":"111267","DOI":"10.1016\/j.jclinepi.2024.111267","article-title":"Estimates of sensitivity and specificity of serological tests for SARS-CoV-2 specific antibodies using a Bayesian latent class model approach","volume":"168","author":"JP Costa","year":"2024","journal-title":"J Clin Epidemiol"},{"issue":"8","key":"pdig.0000936.ref040","doi-asserted-by":"crossref","first-page":"1689","DOI":"10.1093\/aje\/kwab093","article-title":"Diagnostic Accuracy Estimates for COVID-19 Real-Time Polymerase Chain Reaction and Lateral Flow Immunoassay Tests With Bayesian Latent-Class Models","volume":"190","author":"P Kostoulas","year":"2021","journal-title":"Am J Epidemiol"},{"issue":"7","key":"pdig.0000936.ref041","doi-asserted-by":"crossref","DOI":"10.1001\/jamanetworkopen.2020.7750","article-title":"Assessment of the Accuracy of Using ICD-9 Diagnosis Codes to Identify Pneumonia Etiology in Patients Hospitalized With Pneumonia","volume":"3","author":"TL Higgins","year":"2020","journal-title":"JAMA Netw Open"},{"issue":"1","key":"pdig.0000936.ref042","doi-asserted-by":"crossref","DOI":"10.1017\/ash.2024.41","article-title":"Electronic health record-based identification of inpatients receiving antibiotic treatment for community-acquired pneumonia","volume":"4","author":"D Yang","year":"2024","journal-title":"Antimicrob Steward Healthc Epidemiol"},{"key":"pdig.0000936.ref043","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.intimp.2018.08.022","article-title":"Diagnostic value of blood parameters for community-acquired pneumonia","volume":"64","author":"Y Huang","year":"2018","journal-title":"Int Immunopharmacol"},{"issue":"9","key":"pdig.0000936.ref044","doi-asserted-by":"crossref","first-page":"609","DOI":"10.21037\/atm.2020.02.182","article-title":"Diagnostic markers for community-acquired pneumonia","volume":"8","author":"A Ito","year":"2020","journal-title":"Ann Transl Med"},{"issue":"9","key":"pdig.0000936.ref045","doi-asserted-by":"crossref","first-page":"1296","DOI":"10.1017\/S0950268810002529","article-title":"Classification algorithms to improve the accuracy of identifying patients hospitalized with community-acquired pneumonia using administrative data","volume":"139","author":"O Yu","year":"2011","journal-title":"Epidemiol Infect"},{"issue":"120","key":"pdig.0000936.ref046","doi-asserted-by":"crossref","first-page":"20160266","DOI":"10.1098\/rsif.2016.0266","article-title":"The power of data mining in diagnosis of childhood pneumonia","volume":"13","author":"E Naydenova","year":"2016","journal-title":"J R Soc Interface"},{"issue":"9","key":"pdig.0000936.ref047","doi-asserted-by":"crossref","DOI":"10.1590\/1806-9282.20240381","article-title":"Investigating artificial intelligence models for predicting joint pain from serum biochemistry","volume":"70","author":"S Shahid","year":"2024","journal-title":"Rev Assoc Med Bras (1992)"},{"issue":"18","key":"pdig.0000936.ref048","doi-asserted-by":"crossref","DOI":"10.1016\/j.heliyon.2024.e37743","article-title":"Computational imaging for rapid detection of grade-I cerebral small vessel disease (cSVD)","volume":"10","author":"S Shahid","year":"2024","journal-title":"Heliyon"},{"key":"pdig.0000936.ref049","first-page":"172","article-title":"NLP-based identification of pneumonia cases from free-text radiological reports","author":"PL Elkin","year":"2008","journal-title":"AMIA Annu Symp Proc"},{"key":"pdig.0000936.ref050","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/1472-6947-13-90","article-title":"Automated identification of pneumonia in chest radiograph reports in critically ill patients","volume":"13","author":"V Liu","year":"2013","journal-title":"BMC Med Inform Decis Mak"},{"issue":"8","key":"pdig.0000936.ref051","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1002\/pds.3418","article-title":"Natural Language Processing to identify pneumonia from radiology reports","volume":"22","author":"S Dublin","year":"2013","journal-title":"Pharmacoepidemiol Drug Saf"},{"issue":"3","key":"pdig.0000936.ref052","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1111\/j.1541-0420.2009.01330.x","article-title":"Identifiability of models for multiple diagnostic testing in the absence of a gold standard","volume":"66","author":"G Jones","year":"2010","journal-title":"Biometrics"}],"container-title":["PLOS Digital Health"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pdig.0000936","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,21]],"date-time":"2025-07-21T17:22:08Z","timestamp":1753118528000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pdig.0000936"}},"subtitle":[],"editor":[{"given":"David Fraile","family":"Navarro","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2025,7,21]]},"references-count":52,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2025,7,21]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pdig.0000936","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.02.03.25321566","asserted-by":"object"}]},"ISSN":["2767-3170"],"issn-type":[{"value":"2767-3170","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7,21]]}}}