Comprehensive Profiling of Hospital Air and Surface Microbial Communities Using Integrated Metagenomics and Metatranscriptomics Analyses

Description

People who live in metropolises spend up to 90% of their time in built environments (BEs). Therefore, in-depth knowledge of the microbial community (or microbiome) of a BE is required to understand its influence on the health of occupants. Recent advances in culture-independent sequencing technologies have enabled comprehensive analyses of indoor microbiomes. To date, the microbiomes of various BEs have been characterized, and different environmental, geographical, operational, and anthropogenic factors that influence these microbiomes have been identified. Among the BEs, hospitals are specialized environments that house patients who are vulnerable to infection and are often administered antimicrobial compounds. The global incidence of morbidity and mortality due to hospital-acquired infections underscores the importance of understanding the microbiology of hospital environments. Recently, the global COVID-19 pandemic has further underscored the need to minimize virus transmission in hospitals, and increasing antimicrobial resistance is an urgent hospital-related health threat that warrants attention. In a hospital environment, the key biological components to monitor include bacterial, fungal, and viral communities (i.e., virome). Additionally, surveillance of the hospital environment for antimicrobial resistance genes (ARGs; i.e., resistome) is an important component of antimicrobial stewardship in the fight against antimicrobial resistance. Although culture-independent approaches have been applied to study the BE microbiomes of a few hospitals worldwide, similar data from hospitals in Hong Kong are unavailable. Therefore, in this proposed study, the overarching objective is to characterize the spatial and temporal profiles of the microbiomes, resistomes, transcriptomes, and viromes in the air and on surfaces at a hospital in Hong Kong, using metagenomics and metatranscriptomics sequencing. We will aim to establish differences between the microbiological features of the hospital from those of other Hong Kong BEs and to demonstrate that hospital microbial communities harbor unique biological features. For this purpose, we will investigate the influences of different building, environmental, and anthropogenic factors on the hospital microbiology. We will use bioaerosol cytometry and quantitative PCR to determine the airborne microbial concentrations and their dynamics in real-time. We will identify the ARGs of concern and infer the potential transmission of microbiomes, resistomes, and viromes within the hospital environment from the data. By examining both DNA and RNA, we will attempt to identify the microbial members that are both present and metabolically active and the expressed metabolic functions. Overall, the findings from this proposed study will inform and improve strategies for managing the hospital environment to safeguard the well-being of occupants.