The SARS-CoV-2 pandemic has resulted in considerable mortality in hospital settings. Built environment surveillance can provide a non-invasive indicator of SARS-CoV-2 status in hospitals, but we have a limited understanding of SARS-CoV-2's microbial co-associations in the built environment, including any potential co-occurrence dynamics with pathogenic and antimicrobial-resistant microorganisms. Here we examine the microbial communities on floors and elevator buttons across several locations in two major tertiary-care Ontario hospitals during a surge in SARS-CoV-2 cases in 2020. Total microbial community composition, prevalence and type of detected antimicrobial resistance genes, and virulence factor distributions were governed by sample source rather than SARS-CoV-2 detection status. Fifteen microorganisms were identified as indicator species associated with positive SARS-CoV-2 signal, including three opportunistic pathogens (i.e., two Corynebacterium sp. and a Sutterella sp). Key clinically relevant antimicrobial resistance genes showed varying prevalence across sites within the hospital, suggesting that our workflow could inform resistance burden in hospitals. Overall, these results indicate limited or only weak interactions between microbiome composition and SARS-CoV-2 detection status in the hospital built environment.

ED works for DNA Genotek that provided sampling swabs in-kind for this study in an unrestricted fashion. DNA Genotek had no control over the findings, interpretations, or conclusions published in this paper. MF was a consultant for ProofDx, a start up company creating a point of care diagnostic test for COVID-19 is an advisor for SIGNAL1, a start-up company deploying machine learned models to improve inpatient care and has been an expert witness on content unrelated to this work. He also holds a provisional patent for a model that predicts acute dialysis needs.

This work was supported by The Ottawa Hospital Academic Medical Organization (TOHAMO), Alliance Grant # 554478 - 20 from the Natural Sciences and Engineering Research Council (NSERC), funding from the University of Ottawa COVID-19 Reintegration Taskforce, and a Carleton University Rapid Response Research Grant. LAH was supported by a Tier II Canada Research Chair.

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