Characterizing Fungal Infections in the All of Us Research Program

Fungal infections, such as coccidioidomycosis, aspergillosis, and histoplasmosis, represent a growing public health concern in the United States. However, the actual burden of these infections is often underestimated by traditional surveillance methods. Therefore, this study characterizes these infections within the All of Us Research Program and evaluates the quality of related clinical data. We constructed three cohorts, coccidioidomycosis (n = 1,171), aspergillosis (n = 687), and histoplasmosis (n = 347), among 393,601 participants with electronic health record data. We analyzed geographic and sociodemographic distributions, disease reporting, and host factors, and performed a data quality assessment on 10 key laboratory biomarkers and organism-specific tests within 90 days of diagnosis. Our analysis confirmed known epidemiological patterns, including the geographic distributions of coccidioidomycosis in the Southwest and histoplasmosis in the Midwest. Aspergillosis is not routinely reportable, and 49.3% of histoplasmosis cases occurred in states without reporting mandates. Fungal infections disproportionately affected older adults and males relative to baseline, and 44.7% of aspergillosis cases were in immunocompromised patients. The data quality assessment showed high completeness for general hematology markers (e.g., hemoglobin > 70% in coccidioidomycosis and aspergillosis) but limited availability of organism-specific tests, such as Coccidioides serology (4.6% in coccidioidomycosis). Most coccidioidomycosis hemoglobin values (97.9%) were reported in g/L despite a g/dL label. In conclusion, the All of Us dataset is a valuable resource for characterizing fungal infections, but data quality issues related to completeness and conformance must be addressed to support robust clinical research.