UC San Diego

Clinical microbiology laboratories perform testing of patient samples, including bacterial and fungal cultures, and nucleic acid diagnostics for bacteria and viruses such as SARS-CoV-2. Even though such laboratories have been performing testing for many decades, it is unknown what microbes inhabit these laboratory surfaces. Particularly, in the setting of the COVID-19 pandemic, it is important to understand whether laboratory surfaces harbor pathogens such as SARS-CoV-2. Therefore, we characterized the microbiota present on different surfaces of the clinical microbiology laboratory using 16S rRNA amplicon sequencing to understand whether there were unique microbes associated with different surfaces that technicians commonly come in contact with. We also deciphered whether SARS-CoV-2 might also be harbored on these surfaces to further assess the potential risk for occupational exposures. We analyzed laboratory surfaces, including workbenches, floors, and sinks within the main bacteriology, molecular microbiology, and newly-established COVID-19 testing laboratory. We performed this study during the early COVID-19 pandemic time period from July to October 2020. RT-PCR testing found that SARS-CoV-2 was found primarily on the floors, which suggests that it may have been brought in on the shoes of laboratory employees or was the result of the aerosolization of the virus from processing the high numbers of SARS-CoV-2 PCR tests in the microbiology laboratory. Characterization of the bacteria on the clinical lab surfaces revealed distinct workbench, floor, and sink communities, colonized primarily with human-associated microbes. These data provide much needed insights into the complex microbial communities that make up the clinical microbiology laboratory.