Characterization of SARS-CoV-2 distribution and microbial succession in a clinical microbiology testing facility during the SARS-CoV-2 pandemic

Abstract

Background The exchange of microbes between humans and the built environment is a bidirectional and dynamic process that has significant impact on health. Most studies exploring the microbiome of the built environment have been predicated on improving our understanding of pathogen emergence, persistence, and transmission. Previous studies have demonstrated that SARS-CoV-2 presence significantly correlates with the proportional abundance of specific bacteria on surfaces in the built environment. However, in these studies, SARS-CoV-2 originated from infected patients. Here we perform a similar assessment for a clinical microbiology lab while staff were handling SARS-CoV-2 infected swab samples for RT-qPCR analysis. The goal of this study was to understand the distribution and dynamics of microbial population on various surfaces within different sections of a clinical microbiology lab during a short period of 2020 Coronavirus disease (COVID-19) pandemic. Results We sampled floors, benches and sinks in three sections of an active clinical microbiology lab (bacteriology, molecular microbiology, and COVID) over a 3-month period. Although floor samples harbored SARS-CoV-2, it was rarely identified on other surfaces, and bacterial diversity was significantly greater in floor samples than sinks and benches. The floor-associated microbiota comprised greater proportions of bacteria commonly associated with natural environments (e.g., soils), and benchtops harbored a greater proportion of human-associated microbes, including Staphylococcus and Streptococcus, which may have originated from either laboratory staff or clinical samples. Finally, we show that the microbial composition of these surfaces did not change over time and remained stable. Conclusion Despite of finding viruses on the floors, no lab-acquired infections were reported during the study period, which suggests that lab safety protocols and sanitation practices were sufficient to prevent pathogen exposures. Like other BEs and health care facilities the most common bacteria colonizing the surfaces in a clinical microbiology lab primarily consist of bacterial taxa of environmental and human origin. Although our analysis here does not identify the source of infection in any given case, it does help to elucidate microbes that colonize these surfaces and have the potential to cause LAIs.