Swabbing toilet seats and air vents for science

A few weeks ago Sophie told us all about the Home Microbiome Project, where scientists are studying the microbes that live on you, your spouse, and the house you just moved into. Each of those things – you, spouse and house – hosts a unique microbial community,  and scientists want to understand how those microbial communities change as they come into more contact with each other. Does the home microbiome start mirroring that of your own personal community of wee beasties, or do you add some new microbes from the house to your collection (or maybe a combo of the two)?

That same research group has expanded this concept to understand how microbes are spread in hospitals in the Hospital Microbiome Project. Dr. Jack Gilbert, Assistant Professor of Ecology and Evolution at the University of Chicago and environmental microbiologist at Argonne National Laboratory, has undertaken the Hospital Microbiome Project with a team of researchers interested in the changing microbiome of hospital environments.This research hopes to discover how potential pathogens spread in a hospital. Hospital acquired infections (HAIs) are a serious challenge in medicine and are the 6th leading cause of death in the United States (a ranking that completely shocked me, as it beats out diabetes and inluenza/pneumonia). From the project website:

Contrary to public expectation, the potential for contracting a microbial pathogen is highest within a hospital environment, and these infections are much more likely to be fatal. The Centers for Disease Control and Prevention identified 1.5 million cases of environmentally-contracted notifiable diseases in the United States for 2002 [1], 15,743 of which resulted in death (1 %) [2]. In comparison, during the same year, estimates of healthcare associated infections (HAI) in the United States was 1.7 million, a rate of 4.5 infections per 100 hospital admissions, which contributed to an astonishing 99,000 deaths (6%) [3]. This sobering statistic places HAIs as the 6th leading cause of death, ahead of diabetes, influenza/pneumonia, and Alzheimer’s [4]. Circumstantial evidence suggests that agent transfer between surfaces and humans is the most important transmission route, and therefore, hospitals are likely to be the foremost ecosystem for studying the transfer of microorganisms between humans and a built environment.

Just like the microbiome of homes changes when a new couple moves in, so can the microbiome of hospitals as patients, doctors and visitors interact with each other and the actual building. This study is the first of its kind to examine how microbial communities develop in a hospital. Researchers hope to determine which environmental parameters have the greatest influence on the development of microbial communities within a hospital – patient/staff microflora, building material, climate control like temperature/humidity, light level/source, and exposure (staff vs. patient area, high vs. low traffic areas) will all be studied. Every day for a full year, one lucky scientist will be swabbing nearly all the surfaces of two floors of a newly built University of Chicago hospital, where it is possible to sample the hospital before and after it is occupied:

 Currently there is a lot of misinformation about the whole idea of where infection comes from in the hospital setting, i.e. infected instruments, water supply, keyboards, human hands, noses, sheets, etc. The real question to ask is geo-spatially how does the microbiome of a hospital organize? The only way to know that is to study it before patients and personnel are there, and then to track how the structure (and key elements that it houses) become colonized, and from where the infection originates.

The building has only recently been completed, so the team has samples of the unoccupied building to establish a baseline of the microbes. Researchers are sampling patient areas with swabs – taking samples from bed rails, floors, sinks, light switches, monitor touch screens, tap water, nasal swabs from patients and doctors, public restroom surfaces, front desk surfaces and floors. Doctors will move in one to two months before patients begin being admitted, so the team will have samples of the microbial community from the empty hospital, from the hospital occupied by doctors, and from the hospital occupied by both doctors and patients.

The researchers will study how abundant different species of microbes are, how resistant they are to antibiotics, and will sequence the microbial DNA to understand how closely related the microbes are to understand how microbes colonize a built environment. Initial findings are already up for all to see on their site from the construction phase of the hospital. By sequencing DNA from microbial samples, the team can study how genetically different or similar samples are and see how many species are in each sample. Below, the microbe communities on everyone’s shoes grouped together on the top-left corner of the plot (the more similar the communities are, the closer they appear to each other on the plot). The operating room floor, table tops and lobby floor all have similar communities (bottom left) – remember this is the CONSTRUCTION phase, BEFORE antiseptic protocols have begun, so it makes sense that all these surfaces house similar microbe communities.

Principal Coordinate Analysis (PCA). A PCA plot shows how closely related different samples are. Samples from similar types of surfaces have more similar microbial communities and group together. From the Hospital Microbiome Project site.

In a bar graph of the number of species observed in microbe communities from different samples during the construction phase, the shoes from the scientists who went on the sampling tour (top 4 bars) have 10 times as many species as the hospital showerheads (bottom-most bar)!

Alpha Diversity Plots. This figure shows the calculated number of observed species in each sample. The bottom of shoes before the tour had approximately 10 times as many different types of bacteria than the shower head. From the Hospital Microbiome Project site.

I am really keen to see how the microbial communities change once the hospital is up and running with doctors, patients and full antiseptic protocols. The project is going to shed some major insight into the ways microbes colonize built environments.


  1. Groseclose SL, Brathwaite WS, Hall PA, Connor FJ, Sharp P, et al. (2004) Summary of Notifiable Diseases — United States, 2002. MMWR Morb Mortal Wkly Rep 51: 1–84.
  2. Hall-Baker PA, Nieves E, Jajosky RA, Adams DA, Sharp P, et al. (2010) Summary of Notifiable Diseases — United States, 2008. MMWR Morb Mortal Wkly Rep 57: 1–100.
  3. Klevens RM, Edwards JR, Richards CL Jr, Horan TC, Gaynes RP, et al. (2007) Estimating health care-associated infections and deaths in U.S. hospitals, 2002. Public Health Rep 122: 160–166.
  4. Anderson RN, Smith BL (2005) Deaths: leading causes for 2002. Natl Vital Stat Rep 53: 1–89

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