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

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.

Feasibility of SARS-CoV-2 virus detection from consumer-grade cotton swabs (preprint)

BackgroundDetermining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to ease COVID-19 public health restrictions and attempt to safely reopen economies. Expanding COVID-19 testing to include environmental surfaces would ideally be performed with inexpensive swabs that could be transported safely without concern of being a source of new infections. However, CDC-approved clinical-grade sampling supplies and techniques using a polyester swab are expensive, potentially expose laboratory workers to viable virus and prohibit analysis of the microbiome due to the presence of antibiotics in viral transport media (VTM). To this end, we performed a series of experiments comparing the diagnostic yield using five consumer-grade swabs (including plastic and wood shafts and various head materials including cotton, polyester, and foam) and one clinical grade swab for inhibition to RNA. For three of these swabs, we evaluated performance to detect SARS-CoV-2 in twenty intensive care unit (ICU) hospital rooms of patients with 16 COVID-19+. All swabs were placed in 95% ethanol and further evaluated in terms of RNase activity. SARS-CoV-2 was measured both directly from the swab and from the swab eluent. ResultsCompared to samples collected in VTM, 95% ethanol demonstrated significant inhibition properties against RNases. When extracting directly from the swab head as opposed to the eluent, RNA recovery was approximately 2-4x higher from all six swab types tested as compared to the clinical standard of testing the eluent from a CDC-approved polyester swab. The limit of detection (LoD) of SARs-CoV-2 from floor samples collected using the CGp or TMI swabs was similar or better than the CDC standard, further suggesting that swab type does not impact RNA recovery as measured by SARs-CoV-2. The LoD for TMI was between 0-362.5 viral particles while PE and CGp were both between 725-1450 particles. Lastly microbiome analyses (16S rRNA) of paired samples (e.g., environment to host) collected using different swab types in triplicate indicated that microbial communities were not impacted by swab type but instead driven by the patient and sample type (floor or nasal). ConclusionsCompared to using a clinical-grade polyester swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer grade swabs, stored in 95% ethanol. The yield was best from the swab head rather than the eluent and the low level of RNase activity in these samples makes it possible to perform concomitant microbiome analysis.