Since the inception of the pandemic in early 2020, laboratories such as the one at UC San Diego Health have been testing large numbers of samples for the virus that causes the disease COVID-19. Particularly early in the pandemic, there was significant concern that the virus may be harbored on laboratory surfaces and as such present an infection risk to the staff performing such tests. The early testing in this clinical laboratory took place before there was any mask mandate in the facility, and when the World Health Organization announced that the virus could be transmitted via an airborne fashion, there was a significant concern that such an airborne nature could result in a number of workplace exposures. While we had no reports of employees testing positive for SARS-CoV-2 during the sample collection for this study, there was still significant concern for workplace exposures. Some of the highest risk practices occurred when the facility was testing up to 4,500 specimens per day , which meant that not all samples could be handled in biosafety cabinets. The simple opening and closing of the caps in each tube promoted the risk of aerosolizing the live virus. It has been recently shown through RT-qPCR that SARS-CoV-2 RNA was present on surfaces of clinical microbiology laboratories indicating a possible role of environmental contamination . There was therefore a significant interest for us to perform such a study to identify where/if SARS-CoV-2 existed outside the collection tubes in the laboratory . The primary test used for detection of SARS-CoV-2 is a RT-qPCR test  to detect the presence of virus RNA. Our findings were largely reassuring that we could identify SARS-CoV-2 almost exclusively from the floors of the lab, but not from the sinks or the benches. We did, however, identify a single SARS-CoV-2 positive specimen from A-BN. All the specimens arrive in the laboratory through A-BN and occasionally these specimens leak when the caps are not sufficiently secured. It is possible that the positive A-BN specimen is the result of leakage, rather than A-BN serving as a persistent risk for SARS-CoV-2 transmission.
Bacterial alpha diversity on the floors of the clinical lab section was richer and more diverse (Fig. 2) than those detected on other surfaces. A prior study had also shown that indoor floor materials serve as microbial reservoirs, especially soil borne bacteria . Our finding of greater diversity on the floor surfaces is also supported by previous reports showing a significant correlation between the microbiome of shoe soles and floor surfaces [82, 83]. Floors come in direct contact with shoes which are typically contaminated with microbes from environmental sources such as soil and water. We found that there was no significant difference in alpha diversity among floor samples from all the lab sections (Fig S1). This could potentially be governed by the microbes tracked inside on the bottoms of shoes, combined with commensal microbes already living in these spaces, which may not lead to significant variation between different lab sections.
Significant proportions of potentially environmentally-derived bacteria were present on the floors, such as Actinobacteria and Nocardia (Fig. 6). The 16S rRNA amplicon sequencing analysis could not identify specific taxa, and these microbes are generally found in the environment. While taxa associated with Actinobacteria and Nocardia have been known to cause infections [84–87], there is no evidence to suggest the organisms identified posed any threat to healthcare workers. However, their presence does support the need to continue strict sterile techniques and to regularly sanitize testing areas. We believe that such sanitation practices account for the substantial differences in the representation of human skin-associated organisms between the bacteriology section and other parts of the laboratory. For example, Staphylococcus and Streptococcus were amongst the most abundant microbes identified in the bacteriology section (Fig. 5), indicating the substantial contribution that laboratory workers likely have to the BE microbiome. However, Staphylococcus and Streptococcus are also amongst the most common pathogens identified in patient cultures from this section of the laboratory, so it is not clear the extent to which patient cultures contribute to the BE microbiome in this section. Particularly, where Staphylococcus is so prevalent amongst the patient population and the Methicillin-resistant Staphylococcus aureus (MRSA) variant of Staphylococcus is known to colonize the skin of both patients and laboratory workers. Unfortunately, a much more detailed study examining the movements of Staphylococcus throughout the lab would be necessary to decipher the relative contributions of patients and lab workers to the representation of Staphylococcus. While Staphylococcus was found at high proportions in the bacteriology section, it was less prevalent in both the molecular and COVID overflow sections (Fig. 5). One potential explanation for this is that patient cultures (which do not take place in molecular and COVID overflow sections) may have been contributing to the proportion of Staphylococcus found in the bacteriology section. We were able to identify Staphylococcus and Streptococcus in the COVID overflow laboratory, but they were of relatively low proportion even compared to the molecular section. This difference may be due to the fact that the COVID overflow laboratory testing began after the beginning of this study and was largely unpopulated by workers for much of this time. Thus, we observed an increased proportion of environment-associated bacteria compared to human-associated bacteria in this section (Fig. 6).
Studies suggest that human skin, respiratory tract, gastrointestinal/urogenital associated bacteria, as well as those originating from water and soil habitats are the primary contributors to microbial diversity in many indoor BEs, such as restrooms [88, 89], offices [88, 89], kitchens , child-care facilities , and airplanes . Interestingly, the microbiota of health-care facilities, including hospitals [49, 92–94], and ICUs [44, 47, 95] is remarkably similar to every other built environment. It has been reported that the most common bacteria associated with indoor surfaces belong to Corynebacterium, Staphylococcus, Streptococcus, Lactobacillus, Mycobacterium, Bacillus, Pseudomonas, Acinetobacter, Sphingomonas, Methylobacterium and other members of the Enterobacteriaceae family [34, 96, 97]. Like other BEs and health care facilities, we found that the most common bacteria colonizing surfaces in a clinical diagnostic laboratory primarily belong to the genera Dickeya, Staphylococcus, Streptococcus, Lactobacillus, Nocardia, Comamonas, Clostridium, and to members of Actinobacteria, Lachnospiraceae and gamma-proteobacteria phyla and families. Clinical laboratories are a specialized BE that house trained medical staff and are exposed to a plethora of human commensal and pathogenic microbes. Surfaces in the clinical laboratory, particularly the floors, come in direct contact with shoes that bring a rich source of environmental microbes into the facility. This study provides a glimpse into the complex microbiota of an important and often neglected healthcare-associated facility.
In this study, we characterized the complex bacterial communities inhabiting the inanimate surfaces in a diagnostic clinical laboratory during the period of SARS-CoV-2 pandemic. While the 16S rRNA gene sequencing method is the most widely used technique to explore the microbial diversity that could otherwise go unrecognized by culture alone, there are some inherent limitations. For example, variation in 16S copy number and primer binding and amplification efficiencies can limit the accuracy in bacterial abundance and diversity estimations [98–102]. Similarly, this technique without modification does not inform about the viability and infectivity of the microbes being assessed. Another important limitation is that the technique based on a small segment of 16S rRNA (V3-V4 hypervariable region) often cannot resolve taxonomic classification for some medically important bacteria. A study utilizing metagenomic sequencing and classification of the bacteria on the laboratory surfaces could potentially resolve taxonomic classifications that were limited in this study.
As far as we can tell, the study described here is the first comprehensive survey of the microbiome of a clinical microbiology laboratory. BEs such as this one likely have not previously been described because the connection between hospital infections and laboratory infections are not always obvious. For example, there have been well documented outbreaks of pathogen infections such as Salmonella and Shigella in clinical laboratories before and pinpointing the source of these infections back to an individual patient is usually obvious. However, when dealing with other more pervasive pathogens such as MRSA, where the source could be a myriad of patients, and the laboratory workers who acquire MRSA infections could have been infected through another means, can be quite difficult. While our analysis here will not pinpoint 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. What is most favorable about this study is that it took place during a surge in the SARS-CoV-2 pandemic when the laboratory was testing thousands of specimens per day. We had no reports of SARS-CoV-2 LAIs during this period, we do note that along with potential pathogens colonizing laboratory surfaces, there was also SARS-CoV-2 on some surfaces in the lab. This study illuminates that we did not find SARS-CoV-2 on the benches (with 1 exception) or in the sinks of the lab, but instead found it largely on the floors. We believe that the virus arrived on the floors largely through droplets that settled to the ground and were captured by our swabs. Because of the techniques used to identify the presence of this virus, we cannot determine whether the virus from the floors was still infectious. The relative lack of SARS-CoV-2 on the working benches suggests that basic laboratory sanitary practices can help to prevent exposures.