Sometimes in Microbial Life, Size Matters

10/16/23 I/O Magazine

The multi-institutional PreMiEr Engineering Research Center will rely on three life-sized test beds to examine how microbial communities affect human health in the places people live, work and play.

Sometimes in Microbial Life, Size Matters

When Duke University Hospital fully opened its 11-floor, 350-bed Central Tower to patients in late 2021, it represented a lot of things to a lot of people. For a hospital system still dealing with the peak waves of the pandemic, it meant more space and newer facilities to meet the unending demand. For Duke Children’s Hospital, it meant an upgraded home complete with larger rooms, transitional furniture, activity rooms and family zones. For the construction company Skanska, it meant the culmination of nearly five years’ worth of work, completing the $265 million project on time.

Duke Hospitals. Photo courtesy of Shawn Rocco and Duke Health
Photo courtesy of Duke Health

The tower came with all the bells and whistles. Rooms that were, on average, twice as big as other buildings in the complex. The surgical facilities featured the latest advances in technology to ensure a comfortable setting for care. The entrance and lobby area featured high ceilings, large waiting areas and a shiny new Starbucks.

Deverick Anderson couldn’t wait to see the bacteria move in. “With the opening of Duke Central Tower, our group saw an opportunity to characterize how bacterial communities change over time within the plumbing of the sinks, starting with a fresh slate,” said Anderson, professor of infectious diseases at the Duke University School of Medicine. “Within a year, almost 100% of them were contaminated with antibiotic-resistant pathogens.

“There’s a growing focus in the field on having water management plans in healthcare settings to mitigate these health threats. Not to make the bathrooms sterile, obviously, because that would be impossible. But trying to understand how to decrease or mitigate potential problems for patients.”

That, in a nutshell, is the overarching goal of the Engineering Research Center for Precision Microbiome Engineering, or PreMiEr for short. Funded by up to $52 million from the National Science Foundation (NSF), PreMiEr aims to develop diagnostic tools and engineering approaches that promote building designs for preventing the colonization of harmful bacteria, fungi or viruses, while encouraging beneficial microorganisms.

“There’s a growing focus in the field on having water management plans in healthcare settings to mitigate these health threats. Not to make the bathrooms sterile, obviously, because that would be impossible. But trying to understand how to decrease or mitigate potential problems for patients.”

Deverick Anderson
Professor of Infectious Diseases, School of Medicine

The hospital rooms in Duke Central Tower—and other facilities in the complex, featuring hardware and technology from different decades stretching back to the early 80s—are just one of three life-sized “test beds” that the research consortium will use to work toward this ambitious goal. A second test bed also resides on Duke’s campus in the form of a home originally built for faculty members back in the 1920s. And the third is both more expansive and varied than either of those found in North Carolina; a consortium of different buildings, both professional and residential, located throughout La Paz, Bolivia.

Together, along with smaller, tightly controlled experimental settings, the three real-world test beds offer researchers complementary opportunities. On various scales and with various controls, researchers will look to explore how microbes—both harmful and beneficial—are introduced to, expand through, interact across and share space with their human cohabitants.

“Even though we’re engineers, we usually work on widgets in the lab and don’t get opportunities to actually build at scale,” said Claudia Gunsch, professor of civil and environmental engineering at Duke and director of PreMiEr. “But one of the requirements of NSF’s Engineering Research Center system is to think about how findings will actually be deployed at scale, which forced us to think about how we’d take our work outside of the lab and push the envelope.”

Modeling Large Intestines

Another smaller-scale test bed resides in the laboratory of Lawrence David, associate professor of molecular genetics and microbiology at Duke. His setup features a set of eight replicate bioreactors; essentially one-liter fermentation vessels that allow researchers to replicate conditions and microbial communities found in the human large intestine. In this test bed, researchers can explore questions such as how bacteria might live or interact with bacteria typically found in the human gut, what sorts of pertubations in the human gut environment lead to changes in the microbiome, and what levels of bacterial exposure are required for different species to successfully colonize within the human gut.

Controlling for P(traps) in Bathrooms

When Anderson first began his career studying the spread of infectious diseases at Duke, the field was mostly focused on disinfecting surfaces and instruments throughout a hospital. And that makes sense. COVID taught us how easy it is for someone to inadvertently touch a contaminated desktop and then infect themselves by picking their nose. Extend that to a hospital setting where patients are constantly leaving pathogens behind on the surfaces and items in their rooms and in the hallways, and it’s easy to understand why that would be the priority.

But about a decade ago, a series of unfortunate events at Duke University Hospital put Anderson on to a slightly different scent. Not long after the 611,000-square-foot Duke Medicine Pavilion opened in 2013, doctors and staff were faced with a quickly spreading instance of Mycobacterium abscessus—a group of rapidly growing, multidrug-resistant bacteria that are responsible for a wide spectrum of skin and soft tissue diseases, central nervous system infections, and ocular and other infections.

After getting the issue under control and running downstream investigations, it was believed that the source of the problem was the building’s plumbing. More specifically, the P-traps found almost ubiquitously beneath sinks around the world. P-traps are the little squiggly bit of piping underneath sinks that dip down into a “U” shape before leveling out and connecting to the wall. The curve ensures that a little bit of water remains behind in the bend after the water has stopped flowing to prevent any gases from the downstream sewer lines and piping from coming back up.

That little bit of water, however, also creates an incredibly attractive environment for bacteria to grow. “Sinks in hospitals are used for more than just handwashing, and the P-trap components especially are prone to supporting microbial populations that we have no good way of eliminating,” Anderson said. “Even if you remove the sinks and wall plumbing, the biofilm can march back in. It takes time, but it does come back. It’s really difficult to irradicate.”

The incident started Anderson down a path of taking plumbing more seriously as a potential source of patient infection. Along with additional data and observations over the following two years to show the issue was not a singular event, the experience helped push plumbing issues to the same level as surface contamination in Anderson’s eyes and others throughout his field.

It’s a continuing issue that has yet to be solved in any meaningful way, other than to continuously pour disinfecting solutions through the systems. For several years, Anderson has been working with a biomedical engineer at Duke, Lingchong You, to see if they could introduce different, more beneficial species of bacteria into the equation to help keep the pathogens at bay. They are, in short, searching for a sort of P-trap probiotic.

“In the long term we hope we can get to the point where we can do experiments where we look at when people come into a space, how those individuals alter the microbiome in those spaces, how quickly that happens, and what the best practices are for minimizing the spread of particular organisms that we don’t want around.”

Claudia Gunsch
Professor and Director of PreMiEr, Civil & Environmental Engineering

But P-traps exist in most households, businesses and buildings in general throughout the world. Their potential to spread disease is not limited to hospital settings. Given the work that Anderson has put in on the topic, and that the second Duke-based test bed also has plenty of P-traps, it makes for a natural first topic of study for the new center.

Over the coming year, Gunsch plans to begin conducting experiments in the bathroom sinks of the old faculty housing. While the 100-year-old house isn’t a perfectly controlled environment, it has far fewer variables than the consistently occupied and busy hospital rooms Anderson tracks.

Their first experiments will try to get a better understanding of how the microbes aerosolize from the sink’s hardware into the surrounding indoor environment. Because nobody is actually living there, the researchers can simulate people washing their hands or brushing their teeth by adding mock microbial communities and simulating the activities people living in a space go through on a daily basis. Over time, the team can introduce variables, like different kinds of personal products and bathroom hardware, to see what effect those might have on the microbes and how they grow and spread.

On a smaller scale, the center will turn to another of its team members for more tightly controlled experiments. Barbara Turpin, professor of environmental sciences and engineering at the University of North Carolina at Chapel Hill (UNCChapel Hill), runs a laboratory with arm-sized cylinders that tightly control and measure how various liquids, microbes and chemicals mix together and aerosolize into potential human exposures. (More info in short sidebar.)

In the longer term, Gunsch hopes she can eventually turn the former faculty housing into an experimental system approaching that level of control; something similar to how the National Institute of Standards and Technology has a fully sealed, fully controlled, roomsized laboratory for measuring aerosols.

“In the long term, we hope we can get to the point where we can do experiments where we look at when people come into a space, how those individuals alter the microbiome in those spaces, how quickly that happens, and what the best practices are for minimizing the spread of particular organisms that we don’t want around,” Gunsch said.

Replicating Conditions

Along with the three large test beds being used in PreMiEr is a set of smaller test beds found in the laboratory of Barbara Turpin, professor of environmental sciences and engineering at UNC-Chapel Hill. Her lab features a continuously stirred tank reactor that can generate aerosols under various environmental conditions like relative humidity and mixes of gases for long periods of times to investigate how microbes behave when aerosolized. Her lab also features long flow reactors where researchers can insert surfaces from the real world, like pieces of walls or windows that have been soiled authentically, to see how they interact with the air and the environment. A third setup features a cylindrical reactor that can introduce variables like ultraviolet light or oxidizing radicals. Between the three, her lab can study processes in a controlled setting to understand how microbes behave in simpler environments than a complex test bed.

The Other End of the Control Spectrum

While the testbeds at Duke Hospital and Duke University represent one side of the control spectrum, the buildings and structures in Bolivia occupy the complete opposite. Hospital rooms have tight air filtration requirements and specialized HVAC units, while occupants and staff are constantly cleaning and sanitizing everything within sight. While the campus test bed may be an aging home, the number of people visiting, the products being used and the air conditioning systems can still be accounted for.

None of those situations apply to Bolivia. “The big idea around the test bed in Bolivia is to understand environments that are very different from those in the U.S. and, indeed, in the rest of PreMiEr,” said Joe Brown, associate professor of environmental sciences and engineering at UNC-Chapel Hill. “It’s an opportunity to study some aspects of this work in a place where the stakes are lot higher because there are more pathogens and a greater threat of emergence.”

For starters, Brown explains, buildings generally don’t have central HVAC, so they’re more open to the outside. Rural areas have larger influences from animals, both wild and domestic. There are also many places that have a relatively high pathogenic burden compared to the U.S., leading to a much higher potential for antibiotic resistance to grow and spread.

Brown already has a strong track record in the area, having worked on NSF-sponsored projects for the past seven years along with local partners in Universidad Católica Boliviana and Universidad Mayor de San Andrés. Through those collaborations, he’s been taking microbial samples across different types of buildings—urban versus rural, households versus institutional—to begin the process of generating hypotheses to refine the questions PreMiEr wants to ask going forward.

“The big idea around the test bed in Bolivia is to understand environments that are very different from those in the U.S. and, indeed, in the rest of PreMiEr. It’s an opportunity to study some aspects of this work in a place where the stakes are lot higher because there are more pathogens and a greater threat of emergence.”

Joe Brown
Associate Professor of Environmental Sciences and Engineering, UNC Chapel Hill

To understand why this baseline of inquiry is needed, it’s useful to look at some of Brown’s work that was published in 2021. It showed that microbes that cause many waste-borne diseases with the potential to spread into the surrounding environment are present in air particles around areas that have open sewers, which are prevalent in many Bolivian cities.

For example, he found that 25% of samples from La Paz were positive for culturable E. coli, indicating that at least some may have been capable of infecting people when sampled. In contrast, when conducting similar studies in Atlanta, which is comparable in population density, no pathogens found in aerosol particles were accompanied by culturable E. coli.

These differences, according to Gunsch, are critical to PreMiEr’s mission for several reasons. For one, the researchers recognize that different places in the world face different challenges than those in the United States, and they want to produce results that will benefit people across the entire world. But the higher rate of pathogenic exposure is also critical to what PreMiEr is trying to accomplish.

“It’s difficult to create computational models of how aerosolized pathogens travel into and through our buildings and homes because the numbers in the United States are so small,” Gunsch said. “Working in Bolivia can actually help us develop a better model because of their higher burdens. We can then test those models in our test bed house with its lower burden to see if they still hold.”

That computational work should, in theory, then have a large impact on the recommendations that PreMiEr is able to generate for anybody living anywhere in any situation.

“We’re focused on ensuring we translate this fundamental research into practical applications for how we design buildings, that’s the central point of the center,” said Brown. “While some of the work is a bit theoretical to start, we’re engineers, and we want to affect the real world. These test beds are our greatest tools to make sure we achieve the most impact that we possibly can.

PreMiEr

The National Science Funded Engineering Research Center for Precision Microbiome Engineering studies and improves the microbiomes of the built environment.

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