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    Original Investigation
    Infectious Diseases
    July 22, 2020

    Assessment of the Accuracy of Using ICD-9 Diagnosis Codes to Identify Pneumonia Etiology in Patients Hospitalized With Pneumonia

    Author Affiliations
    • 1The Center for Case Management, Natick, Massachusetts
    • 2Department of Critical Care Medicine, University of Massachusetts Medical School-Baystate, Springfield
    • 3Center for Value-Based Care Research, Cleveland Clinic Community Care, Cleveland Clinic, Cleveland, Ohio
    • 4EviMed Research Group LLC, Goshen, Massachusetts
    • 5Institute for Healthcare Delivery and Population Science, Department of Medicine, University of Massachusetts Medical School-Baystate, Springfield
    • 6Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester
    • 7Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
    • 8Cleveland Clinic, Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio
    • 9Division of Infectious Diseases, Department of Medicine, University of Massachusetts Medical School-Baystate, Springfield
    • 10Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
    JAMA Netw Open. 2020;3(7):e207750. doi:10.1001/jamanetworkopen.2020.7750
    Key Points español 中文 (chinese)

    Question  Are organism-specific International Classification of Diseases, Ninth Revision (ICD-9) administrative codes for pneumonia valid measures in identifying pneumonia etiology?

    Findings  In this cross-sectional study of data from 161 529 patients hospitalized with pneumonia between 2010 and 2015, ICD-9 codes had generally low sensitivity but high specificity for pneumonia etiology identified by laboratory testing.

    Meaning  In this study, ICD-9 codes appeared to underestimate prevalence of specific organisms.


    Importance  Administrative databases may offer efficient clinical data collection for studying epidemiology, outcomes, and temporal trends in health care delivery. However, such data have seldom been validated against microbiological laboratory results.

    Objective  To assess the validity of International Classification of Diseases, Ninth Revision (ICD-9) organism-specific administrative codes for pneumonia using microbiological data (test results for blood or respiratory culture, urinary antigen, or polymerase chain reaction) as the criterion standard.

    Design, Setting, and Participants  Cross-sectional diagnostic accuracy study conducted between February 2017 and June 2019 using data from 178 US hospitals in the Premier Healthcare Database. Patients were aged 18 years or older admitted with pneumonia and discharged between July 1, 2010, and June 30, 2015. Data were analyzed from February 14, 2017, to June 27, 2019.

    Exposures  Organism-specific pneumonia identified from ICD-9 codes.

    Main Outcomes and Measures  Sensitivity, specificity, positive predictive value, and negative predictive value of ICD-9 codes using microbiological data as the criterion standard.

    Results  Of 161 529 patients meeting inclusion criteria (mean [SD] age, 69.5 [16.2] years; 51.2% women), 35 759 (22.1%) had an identified pathogen. ICD-9–coded organisms and laboratory findings differed notably: for example, ICD-9 codes identified only 14.2% and 17.3% of patients with laboratory-detected methicillin-sensitive Staphylococcus aureus and Escherichia coli, respectively. Although specificities and negative predictive values exceeded 95% for all codes, sensitivities ranged downward from 95.9% (95% CI, 95.3%-96.5%) for influenza virus to 14.0% (95% CI, 8.8%-20.8%) for parainfluenza virus, and positive predictive values ranged downward from 91.1% (95% CI, 89.5%-92.6%) for Staphylococcus aureus to 57.1% (95% CI, 39.4%-73.7%) for parainfluenza virus.

    Conclusions and Relevance  In this study, ICD-9 codes did not reliably capture pneumonia etiology identified by laboratory testing; because of the high specificities of ICD-9 codes, however, administrative data may be useful in identifying risk factors for resistant organisms. The low sensitivities of the diagnosis codes may limit the validity of organism-specific pneumonia prevalence estimates derived from administrative data.