Microbiota Evolution and Interactions of Surfaces and Employees Within a Newly Opened Skilled Nursing Facility

Abstract

The microbiota of assisted living facilities potentially influences the health outcomes of its inhabitants. Understanding the microbial composition of these environments is critical for the characterization of pathogen reservoirs and pathways. Despite increased efforts in infection control and intervention strategies within healthcare settings, Healthcare-associated infections (HAIs) continue to be a significant burden in assisted living facilities, and environmental surfaces have been implicated in the spread of nosocomial pathogens. Patients, healthcare workers and their families may also be exposed to HAI- associated pathogens through various routes, as microbial exchange between people and their environments has been well documented. The overarching goal of this study was to identify potential patient and healthcare worker exposure to pathogens capable of causing HAIs by identifying reservoirs and pathways. Surface swab samples were collected over the course of 127 days, spanning pre-opening of a skilled nursing facility (SNF) through its first few weeks of patient occupation. In addition, samples were collected from SNF employees’ bodies, cell phones, and homes pre- and post- facility opening. Samples were processed via 16S rRNA sequencing and culture-based methods. Microbiota composition of samples taken from a pre-opening SNF was significantly different from samples taken after patients were admitted into the facility. Overall, across different SNF surfaces, the greatest observed microbial diversity and most frequent detection of Coagulase-negative Staphylococci and S.aureus was within low-touch environmental surfaces. The admission of a patient with a MRSA infection was associated overall increased relative abundance of Staphylococcus and detection of viable S.aureus in three different locations of the SNF (dresser top, and supply air register, and the arm of a chair in the communal dining room on a single sampling day). Microbiota diversity was found to decrease significantly in rooms in which viable pathogen were recovered (Faith’s PD, Kruskal-Wallis, P < 0.05). Surfaces within the SNF employees’ homes and SNF surfaces were not significantly different prior to the facility opening, but they were significantly different after the facility opened and began to be occupied (weighted UniFrac, PERMANOVA, P < 0.05). The pooled samples taken from the SNF employee’s cell phones were not significantly different from any of the samples taken from any of the homes or healthcare worker’s bodies (weighted UniFrac, PERMANOVA, P >0.05). The microbial diversity and community relationships in a human-home-workplace system were characterized, and results support findings of relatedness of occupants to their personal homes, but also elucidate the relationship humans have to their places of work. Low-touch environmental surfaces were identified as reservoirs and increased attention to these surfaces in disinfection practices may mitigate HAI risk. Pathogen presence was found to be associated with decreased microbial diversity, indicating future research should focus on determining causality to determine if reduced diversity could be a risk factor for environmental contamination. Cell phones were found to be highly related to both the work and home environment, suggesting their role in serving as a transporter of microbes between these two environments, which may have consequences for employees of healthcare facilities. Understanding how work environments influence human microbiota and the microbial ecosystem of their homes is an important foundation in discerning how unfavorable exposures may be mitigated.