National incidence of coccidioidomycosis in the United States estimated through machine learning integration of epidemiological, veterinary, and socioecological data
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Key points
Question
In the absence of nationwide reporting for coccidioidomycosis, can alternative data sources be integrated to enable estimates of monthly, county-level incidence across the US?
Findings
In this cross-sectional study of 3,108 counties, the model identified 60 counties in non-reporting states with predicted incidence ≥2 cases per 100,000 population (considered moderate to high incidence). In states with mandatory reporting outside of Arizona and California, the model’s predicted county-level incidence rates were, on average, 28% higher than those captured in national surveillance.
Meaning
Our predictions highlight the extent of case under-ascertainment for coccidioidomycosis relative to Arizona and California, both in states with mandatory reporting and in non-reporting states.
Importance
Coccidioidomycosis, also known as Valley fever, is a serious fungal disease caused by inhaling Coccidioides spores aerosolized from the soil. Despite rising public health concern, the distribution and incidence of coccidioidomycosis in the US remain poorly characterized as not all states are required to report cases, and case under-ascertainment is presumed to be high, particularly outside of the endemic region.
Objective
To estimate monthly, county-level coccidioidomycosis incidence across the US while accounting for widespread under-ascertainment.
Design, Setting, and Participants
We integrated multisource data, including human cases diagnosed in electronic health records, serological testing of dogs, and ecological and sociodemographic predictors, in a machine learning model estimating monthly, county-level coccidioidomycosis incidence. The model was trained on surveillance data from Arizona and California from 2013 to 2023, then applied to predict incidence in states across the contiguous US over the same time period.
Main Outcomes and Measures
Incidence of coccidioidomycosis at the monthly county level.
Results
The model predicted coccidioidomycosis incidence from 2013 to 2023 for 3,108 counties from all states in the contiguous US. The model identified 60 counties in non-reporting states where predicted incidence was ≥2 cases per 100,000 population (considered moderate to high incidence). In states with mandatory reporting outside of Arizona and California, the model predicted county-level incidence rates that were 28% higher (95% bootstrap interval, 0.1%–69.8%) than those captured in national surveillance, equating to a total of 608 potentially missed cases per year (95% bootstrap interval, 340–964).
Conclusions and Relevance
In this cross-sectional study, the model quantified case under-ascertainment for coccidioidomycosis relative to Arizona and California, and highlighted the potential for alternative data sources to fill in gaps in mandatory reporting. Estimating incidence while accounting for under-ascertainment and non-reporting may help efforts to improve public and physician awareness and to detect emergence in new regions.
