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Factors associated with SARS-CoV-2 test positivity in long-term care homes: a population-based cohort analysis using machine learning

Lee DS, Wang CX, McAlister FA, Ma S, Chu A, Rochon PA, Kaul P, Austin PC, Wang X, Kalmady SV, Udell JA, Schull MJ, Rubin BB, Wang B. Lancet Reg Health Am. 2022; 6:100146. Epub 2022 Jan 17. DOI: https://doi.org/10.1016/j.lana.2021.100146


Background — SARS-Cov-2 infection rates are high among residents of long-term care (LTC) homes. We used machine learning to identify resident and community characteristics predictive of SARS-Cov-2 infection.

Methods — We linked 26 population-based health and administrative databases to identify the population of all LTC residents tested for SARS-Cov-2 infection in Ontario, Canada. Using ensemble-based algorithms, we examined 484 factors, including individual-level demographics, healthcare use, comorbidities, functional status, and laboratory results; and community-level characteristics to identify factors predictive of infection. Analyses were performed separately for January to April (early wave 1) and May to August (late wave 1).

Findings — Among 80,784 LTC residents, 64,757 (80.2%) were tested for SARS-Cov-2 (median age 86 (78–91) years, 30.6% male), of whom 10.2% of 33,519 and 5.2% of 31,238 tested positive in early and late wave 1, respectively. In the late phase (when restriction of visitors, closure of communal spaces, and universal masking in LTC were routine), regional-level characteristics comprised 33 of the top 50 factors associated with testing positive, while laboratory values and comorbidities were also predictive. The c-index of the final model was 0.934, and sensitivity was 0.887. In the highest versus lowest risk quartiles, the odds ratio for infection was 114.3 (95% CI 38.6–557.3). LTC-related geographic variations existed in the distribution of observed infection rates and the proportion of residents at highest risk.

Interpretation — Machine learning informed evaluation of predicted and observed risks of SARS-CoV-2 infection at the resident and LTC levels, and may inform initiatives to improve care quality in this setting.

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