Methods of Identifying Staphylococcus aureus Infections among Electronic Health Data to Inform Epidemiological Studies Open Access

Abstract

Background: Epidemiological studies utilize administrative discharge diagnosis codes to identify methicillin-resistant and methicillin-sensitive Staphylococcus aureus (MRSA, MSSA) infections, trends, and clinical outcomes, despite debate regarding their accuracy for these purposes. We aimed to evaluate the impact that method of identification may have on epidemiological studies. 

 

Methods: Clinical microbiology results and discharge data from U.S. hospitals participating in the Premier Healthcare Database from 2012 – 2017 were used in this analysis. Positive clinical cultures and/or a MRSA- or MSSA-specific International Classification of Diseases, Ninth/Tenth Revision, Clinical Modification (ICD-9/10-CM) diagnosis codes from adult inpatients were included as S. aureus hospitalizations; positive blood cultures or septicemia codes denoted a septicemia hospitalization. To calculate sensitivity and PPV for codes true infection was considered a positive clinical culture. Negative binomial regression was used to measure trends in code and culture rates per 1,000 discharges. Logistic regression was used to examine the impact of method of identification on the adjusted risk of in-hospital mortality.   

 

Results: Sensitivity of MRSA and MSSA codes was approximately 61% or less; results were similar when restricting to septicemia. MRSA trends in code and culture rates were not significantly different. However, MSSA code rates showed an increasing trend that was not observed among MSSA culture rates. Compared to hospitalizations with both a MRSA code and culture, code only hospitalizations had a decreased odds of in-hospital mortality (OR=0.90, 95% CI: (0.85, 0.94)); culture only hospitalizations had an increased odds of in-hospital mortality (OR=1.66, 95% CI: (1.59, 1.73)). MSSA culture only hospitalizations had an increased odds of in-hospital mortality compared with those identified by code and culture (OR=1.89, 95% CI: (1.81, 1.98)). However, there were no significant differences between code only and culture and code identified MSSA hospitalizations.             

 

Conclusion: ICD diagnosis code sensitivity in identifying infections remain consistently poor in recent years, and differing methods of identification may identify conflicting trends, risk factors, and associations with outcomes. Using diagnosis codes to identify S. aureus infections may not be appropriate for assessing trends and clinical outcomes due to significant misclassification.

Table of Contents

Introduction………………………………………………………………………….1

Methods……………………………………………………………………………...15

Study Design, Population, Data Source…………………………………........15

Exposure, Outcomes, and Covariates……………………………………........16

Analytic Approach…………………………………………………………….......17

Objective One………………………………………………………………….......17

Objective Two………………………………………………………………….......20

Objective Three………………………………………………………………........20

Ethics Approval................................................................................21

Results............................................................................................22

Characteristics of Hospitalizations.....................................................22

Sensitivity and PPV of ICD Codes………………………………………….......24

Trends in Culture and Code rates…………………………………………........25

Risk factors and In-hospital Mortality………….…………………………......25

Discussion…………………………………………………………………………….30

Sensitivity and PPV of ICD Codes…………………………………………........30

Trends in Culture and Code rates………………………………………….........31

Risk factors and In-hospital Mortality………….………………………….......32

Limitations……………………………………………………………………….......34

Strengths………………………………………………………………………….......35

Future Directions………………………………………………………………........35

Conclusion……………………………………………………………………………..37

References………………………………………………………………………………38

Tables and Figures…………………………………………………………………....45

Appendix…………………………………………………………………………………65

About this Master's Thesis

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School	Rollins School of Public Health
Department	Epidemiology
Degree	M.P.H.
Submission	Master's Thesis
Language	English
Research Field	Health Sciences, Epidemiology Health Sciences, Public Health
Keyword	Staphylococcus aureus Epidemiology Epidemiological methods
Committee Chair / Thesis Advisor	Fridkin, Scott, Emory University
Committee Members	Hatfield, Kelly, Centers for Disease Control and Prevention
Partnering Agencies	CDC

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