The distribution and dynamics of microbial populations on surfaces within a clinical microbiology lab during the COVID-19 pandemic

In a recent study posted to Research Square*, researchers evaluated the distribution of microbes on surfaces within a microbiology laboratory.

Study: Characterization of SARS-CoV-2 distribution and microbial succession in a clinical microbiology testing facility during the SARS-CoV-2 pandemic. Image Credit: Gorodenkoff/Shutterstock
Study: Characterization of SARS-CoV-2 distribution and microbial succession in a clinical microbiology testing facility during the SARS-CoV-2 pandemic. Image Credit: Gorodenkoff/Shutterstock

Background

As per estimates, around 500,000 people work in clinical labs across the United States (US). They, particularly those in the microbiology departments, are at an increased risk of infections. These employees might contract laboratory-acquired infections through contact with contaminated surfaces, improper use of personal protective equipment, or a lack of adherence to safety protocols.

Most viruses causing respiratory tract infections persist for days on surfaces and could spread unless disinfected. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of the coronavirus disease 2019 (COVID-19), is primarily transmitted via respiratory droplets. Studies have reported that SARS-CoV-2 could persist for hours to days on different surfaces.

Humans spend most of their time in the built environment (BE), and the microbiology of BE is shaped by the microbial profiles of people inhabiting the BE. Reports suggest that pathogen outbreaks could occur in clinical microbiology labs since employees cultivate or detect pathogens. However, the presence/distribution of microbes on laboratory surfaces has not been thoroughly defined.

About the study

In the present study, researchers investigated whether microbiology lab surfaces present a potential risk of microbial exposure. The core objectives were to examine the bacterial succession throughout the facility over time and identify surfaces/sites where SARS-CoV-2 could be present. They collected swab samples from the surface of accessioning bench (A-BN), floors, sinks, and benches.

Sampling was performed from molecular microbiology, bacteriology, and COVID-19 sections of the facility between July 7, 2020, and October 30, 2020. Nucleic acids were extracted and subject to amplification of the V3/V4 hypervariable region of the 16S ribosomal RNA (rRNA) gene by polymerase chain reaction (PCR), followed by sequencing.

Samples were tested for SARS-CoV-2 RNA using quantitative reverse-transcription PCR (RT-qPCR). The authors processed sequenced reads using quantitative insights into microbial ecology 2 (QIIME2). Alpha diversity was examined using Shannon Index, Faith’s phylogenetic diversity, observed amplicon sequence variants (ASVs), and Beta diversity using the Bray-Curtis diversity metric.

Findings

Sixteen floor samples (42.1%) from the molecular microbiology lab tested positive for SARS-CoV-2. Similarly, five floor samples from bacteriology and one from the COVID overflow lab were SARS-CoV-2-positive. In contrast, A-BN, the access point for all specimens entering the lab facility, had only one positive sample. Samples from other surfaces (sinks and benches) from each lab section were SARS-CoV-2-negative.

During the first week of the study, 46.6% of all floor samples were positive for the virus, which dropped to 16.6% by the third week and increased to 66.6% by the fifth week. They noted that most positive samples were from the molecular lab’s floor. Significant differences were observed in the Alpha diversity between the sampling surfaces in all lab sections. The microbial diversity of floor samples was consistently higher than other surface samples in each laboratory section.

Longitudinally, there was no significant variation in the Alpha diversity within individual laboratory sections. Although the Beta diversity was not significantly different between the laboratory sections, it differed substantially between the sampling surfaces. That is, the microbial diversity of the sink was different from other surfaces in the bacteriology section. Likewise, the microbial composition of the floor was distinct from other surfaces in COVID and molecular sections.

Further, the microbial diversity was mostly similar across surfaces of each section longitudinally, with slight variation for molecular and COVID sections. The researchers noted that the microbiota of the floor comprised chiefly of bacteria associated with natural environments. In contrast, benches had a higher prevalence of microbes associated with humans that might have originated from clinical samples or lab personnel.

Conclusions

The findings revealed that SARS-CoV-2 could be almost exclusively detected from the laboratory floor and not from other surfaces. Nonetheless, the authors found one A-BN sample positive for the virus, and because A-BN was the access point for all arriving clinical specimens, occasional sample leakage might occur. Therefore, they believed that SARS-CoV-2 might have been detected due to leakage.

Bacterial Alpha diversity was richer and more diverse on the floor than on other surfaces. There was no significant difference in the Alpha diversity between floor samples from different lab sections. Environmental bacteria such as Nocardia and Actinobacteria were most enriched in floor samples. Although these bacteria could cause infections, there was no evidence that these microbes could cause any health risk to lab personnel.

Moreover, Streptococcus and Staphylococcus were abundant in the bacteriology section. Because these microbes are also the common pathogens found in clinical samples, the degree to which clinical specimens contribute to the BE microbiota remains unclear. Besides, these bacteria were less prevalent in other sections (molecular or COVID).

In summary, the researchers comprehensively investigated the microbial composition of clinical laboratory surfaces. Although the microbiota source could not be determined, the study identified the different microbes that could inhabit lab surfaces.

*Important notice

Research Square publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Tarun Sai Lomte

Written by

Tarun Sai Lomte

Tarun is a writer based in Hyderabad, India. He has a Master’s degree in Biotechnology from the University of Hyderabad and is enthusiastic about scientific research. He enjoys reading research papers and literature reviews and is passionate about writing.

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