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Microbiologists Will Watch As Bacteria Take Over This Hospital
We often think of the world around us as sterile and static, especially when we are in a hospital. In reality, every surface on earth is literally teeming with millions of bacteria.
Jack Gilbert, a microbiologist from the University of Chicago, has spent his career investigating these invisible companions all around us. This year, Gilbert and a group of microbiologists will take over a brand new hospital in an experiment called the "Hospital Microbiome."
The goal of "Hospital Microbiome" is to try to see what microbes and viruses will move in to the hospital and how patients and hospital staff affect the variety of microbes that live in the hospital. Gilbert and his team will track the bacteria in the hospital before it opens and as it starts accepting staff and patients.
This data will help hospital administration, doctors, nurses, and researchers get a better understanding of how these bacteria and viruses make their way around a hospital, sometimes causing dangerous infections in the patients.
We asked Gilbert to explain the project and what they are hoping to find out from this hospital, below is an edited and condensed version of our conversation.
Business Insider: You've worked on multiple microbiome projects – Earth and Home — could you explain to me what microbiome is?
Jack Gilbert: A microbiome is the bacteria and other single celled organisms that live on and in whatever it is I'm studying. The home microbiome is the surfaces of your home, the kitchen counters, the doorknobs, and light fixtures and you, your hands, your feet and your nasal passages.
In the earth it's exactly what it sounds like, it's the entire planet. We have very ambitious goals of characterizing all microbial life on the planet.
BI: What kinds of microbes are you looking for in these projects?
JG: Um, all of them.
Essentially we want to uncover and identify the different types of bacteria that are present and associated with these kinds of environments.
In the home and the hospital it's obviously important to understand the pathogens, the bacteria that cause you to get sick. Where they come from, who brings them into those environments, how they develop and persist, and what that means.
It's shocking how little we actually understand about that after a century of work in microbiology. We have very little understanding of how these things move between surfaces and people.
BI: We think of the things around us as static, but these microbe communities change and evolve over time.
JG: Yeah, for example in the hospital microbiome project we have the unique opportunity to start exploring in detail the bacteria that live on the surfaces of the hospital, before all the patients move in.
We will be sampling the door handles, the floor, the toilets, showers and water in the incubators and the operating room.
When the patients and the staff move in there's a possibility they will bring with them less friendly bugs. They build up in the hospital environment and we don't know how they do that.
This causes people to get sick and even die in hospitals all over the United States and all over the world on a daily basis. These so-called healthcare acquired infections are very prevalent problem and we have very little understanding of how they get into the hospital, how they spread, what are the mechanisms of their development.
These so-called healthcare acquired infections are very prevalent problem and we have very little understanding of how they get into the hospital.
BI: So when a person leaves microbes behind in an environment, that's what's known as a "microbial footprint"?
JG: Exactly. In a home for example we've been able to show that the bacteria on your skin leaves an imprint on the home. When you move into your new house or your new apartment, it takes about four to six days for the bacteria on your skin to start making an imprint on the surfaces of your home.
It leaves a microbial fingerprint, which we can track. It's quite interesting.
BI: I feel like people often associate bacteria with BAD – but that's not really true is it?
JG: 99.9999999 percent of them are completely and utterly harmless to humans, and actually, as a good guy they are actually playing a fundamental role in protecting us from the bad guys.
There's circumstantial evidence that shows that when you are more susceptible to a severe pathogenic infection if you’ve taken a round of antibiotics. Obviously if you didn't take those antibiotics when you needed to take them you would die.
But if you were given antibiotics inappropriately and walked into a situation where a pathogen may be lurking, then that pathogen may be able to infect you more rapidly.
If you were given antibiotics inappropriately and walked into a situation where a pathogen may be lurking, then that pathogen may be able to infect you more rapidly.
It's a competitive environment in your body, all these bacteria fighting for space on to survive inside your gut and on your skin. If they are devastated by antibiotic regime and they can't form a defense, then a fresh pathogen may come in and it will take advantage of that and make you sick.
BI: So this is true of every environment, so why look at hospitals specifically?
JG: Protecting humanity, protecting people from sickness and disease, it doesn't just end and begin with your doctor it also ends with the people studying the bacteria in the environment and on your bodies. These microbiologists, you may never see them, but they are vitally important for protecting the people of this country and every country from disease.
It's also an interesting ecological problem to understand how bacteria move between your skin and in your body and onto surfaces.
We know people are getting sick, we just don’t know how and this is the only way we can really find out.
We know people are getting sick, we just don’t know how and this is the only way we can really find out.
BI: Can you describe the project to me?
JG: We are studying two floors of this new hospital. We will be looking at five patient rooms in the cancer ward and the nursing station. We will be sampling the patients and the nurses and the surfaces of the rooms and the nursing station daily for a year.
We are creating, quite honestly, one of the largest microbial surveys ever undertaken.
Then we will do the floor directly below that, this is the surgery ward. And these people coming in for a very short period of time because they are having their appendix removed, or some form of elective surgery.
These two environments are quite different, but they are set within this identical architecture. The rooms and the nursing stations are identical. The only difference is the patients and how long they spend in those rooms. So this is fundamental to the design of the experiment.
We want to know, if you are only in a room for two days, do you leave behind a very significant microbial signature? And how does that effect the next patient that walks into that room?
We will also be understanding how cleaning affects each of the rooms and what cleaning regimes are most appropriate. And how we can better inform cleaning strategies in hospitals to better remove or prevent future infections.
All of these aspects come together in this beautiful scenario.
BI: What's the timeline for the Hospital Microbiome Project?
JG: Patients start showing up in February and we will continue for a year after they start showing up.
BI: What's already been done?
JG: The status right now is, the project is warming up. We've just got the funding in. We are doing training for nurses and residents. We are getting all the equipment in place that can tell us about the physical and chemical environment in the air and on the surfaces.
In the meantime, we have done some quick and interesting explorations of the empty hospital and you can see that at the hospital microbiombe website under findings.
BI: What will we be seeing coming out of it in the next few years?
JG: There are 13,000 individual Q-tips that will be swabbed on surfaces and noses and hands, and what we will see over the next 8 to 9 months is data coming out, which we will process and post in this public forum before we publish it.
The data that will be coming out of this project will be the types of bacterial species we are finding, their abundances, how their abundances change over time, how their abundances are affected by different patients, by different staff interactions with those patients and what all this means in terms of the distribution of the bacteria around the hospital.
If all of these sick people are coming in, are we suddenly going to see an increase in known pathogenic organisms in that environment?
If all of these sick people are coming in, are we suddenly going to see an increase in known pathogenic organisms in that environment?
BI: Based on previous projects, do you have any predictions or ideas of what you'll find?
JG: We have an understanding of the types of bacteria we might find.
On the whole we find a lot of bacteria that look like human skin bacteria on door handles and railings and sink taps, and anywhere where people are touching. That will give us a very good indication of how much people are using certain facets of the building structure.
BI: How will this project help us treat and prevent hospital-acquired infections?
JG: We will be trying to say: when a new patient moves into this particular room, these are the surfaces they interact with most, and it's these surfaces that contain the highest probability of generating a reservoir of organisms that somebody else could pick up.
Now, without very much understanding with what surfaces people interacted with, just how that transmission occurred, this will give us, over a very long time scale, it will give us rich, high resolution contextual data of how that happens.
And because we are looking at it every day for a year we will see many of those occurrences happening. We can build up a probability matrix that tells us that this is the most likely route the disease will take as it moves through the hospital.
BI: Will it give us any insight into antibiotic resistant microbes and how they evolve?
JG: We are working with the department of defense, using a specific technology they developed to track the development of antibiotic resistance markers within community populations.
And because we have lots of different patients and we have these two different time frames — monthly patients in the cancer wards and daily patients in the surgery wards — we will be able to use that to see when the patients arrive to see if when the patients arrive we suddenly see an increase in antibiotic resistance markers, or whether it takes months for the community that already exists there to start developing resistance to antibiotics.
So, if all these patients move into this hospital and the bacteria that were already living there respond to the use of antibiotics in the environment, then there is a possibility that the bacteria in that environment may adopt antibiotic resistance as a method to move between surfaces and people.
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