Hospital microbe project—Tracking deadly bacteria

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CHICAGO, Ill. (Ivanhoe Newswire) – 48,000 Americans die each year from infections contracted in hospitals. Now, researchers are tracking these deadly bugs from your home to the hospital and back again. What they find could end up saving millions of lives.

It's been six days in the hospital for Rochelle Speller. That's five more than she'd hoped

“If you're in the hospital, as soon as you can get out,” Rochelle told Ivanhoe.

With a struggling immune system, Rochelle says she doesn't want to become one of the thousands of people who die due to hospital acquired bacterial infections.

“I have been lucky not to have gotten sick,” Rochelle said.

Each person has 100 trillion bacterial cells in our bodies. That out numbers our human cells ten to one.

“The bacteria that are inside you come from the places you live, work, and visit,” Jack Gilbert, PhD, Environmental Microbiologist and Associate Professor, the University of Chicago, told Ivanhoe.

University of Chicago researchers are looking at what makes up the hospital's microbial jungle and how it grows, changes, and transmits from surface to person over a year.

Researchers swab surfaces and patients to gather samples on a daily basis.

“People are very interested in it,” Kristen Starkey, Hospital Microbiome Project Research Assistant, told Ivanhoe.

With over 10,000 samples, researchers and doctors hope to eventually find a way to prevent hospital born infections.

“One thing to do might be to provide more good bacteria to counteract the bad bacteria as opposed to just giving more antibiotics that will wipe out everybody,” John C. Alverdy, MD, Professor of Surgery, Executive Vice Chairman of Department of Surgery, The University of Chicago Medicine, told Ivanhoe.

This is the first time a private hospital has enabled anybody to analyze the bacteria in their building using these techniques. This is the most comprehensive assessment of a hospital microbiome ever performed.

In the University of Chicago Hospital Microbe Project, researchers hope other hospitals will begin to investigate the potential of building bacteria and the influence it has on patient outcomes.

BACKGROUND: Being in the hospital can expose patients to the myriad of bacteria that live in the environment. Often, people can get sick from these bacteria, and these are called hospital acquired infections, or healthcare-associated infections (HAIs). Every day, about one in every 20 patients contracts an HAI from receiving healthcare in a hospital. Sometimes, these infections can be deadly for patients, and often HAIs can be even more serious than a “normal” virus or infection. This is because the bacteria often have become drug-resistant in the hospital, and therefore makes it more difficult to treat. (Source:

CAUSES: It’s hard to know exactly where an HAI came from, but some of the most likely culprits include:

• Use of indwelling devices like catheters

• Surgical procedures

• Injections

• Contamination of the environment

• Transmission of infection between patient and healthcare worker

• Overuse or misuse of antibiotics


NEW TECHNOLOGY: A team of researchers at the University of Chicago are currently studying the way in which humans change and interact with the community of bacteria living in a hospital. In the Hospital Microbiome Project, researchers are taking bacteria samples of various hospitals in order to understand how the microbiome changes. In a previous study, the same team found humans can change the microbiome in a home within 4 to 6 days. By gaining a better understanding of how the microbiome operates, researchers hope to be able to treat and avoid HAIs in the future. (Source:

Jack Gilbert, PhD, Environmental Microbiologist, Associate Professor, The University of Chicago, talks about the Hospital Microbe Project.

Can you explain a little bit about this project?

Dr. Gilbert: Human beings are mostly made of bacteria. We have about 100 trillion bacterial cells in our body and that outnumbers your human cells 10 to 1. There are only 10 trillion human cells, so you’re mostly bacterial. Those bacteria that are inside of you come from the places you live, work, and visit. And one of the places you are most likely to pick up a bacterial infection or maybe where you go to be cured of an infection is in a hospital. So what we’re trying to do in this project, the Hospital Microbiome Project, is to uncover the transmission routes between the building and its bacteria and the people and their bacteria to see how the bacteria from the building get into the people.

How did this project come about?

Dr. Gilbert: We were working in people’s homes. So we were going into their homes and looking at the bacteria that lived on their kitchen countertops, light switches, floors, and then on their hands, noses, and feet. Also, we looked at bacteria on the hands, noses, and feet of their dogs and cats. We found interesting transmission routes of how the bacteria moved between the people and the surfaces on their home and the surfaces on the people, which told us something about how the organisms in this house coexisted. When people move into a new house the bacteria from their skin leaves them and spreads out over the house. And you get this human microflora, these bacteria from the human skin just be distributed across surfaces in the home. So, we thought it would be fascinating if we could use the same techniques we had done in the home study in a hospital environment, but we needed to have a very unique setting. We wanted to get a setting where we had a hospital, which was just opening and was isolated from any other hospitals environment. So, we were very lucky in the fact that the hospital here at Chicago was just opening. We got in there before the hospital opened, sampled for two months, and then when it opened, when all these doctors and patients arrived with all of their microflora (their bacteria), we were able to continuously sample and see what effect they had upon the bacteria that lived in the building.

What has the effect had so far?

Dr. Gilbert: We’re still trying to figure that out. It’s a long and arduous process trying to work through these data streams, but immediately as soon as the patients and doctors moved in we saw a doubling, and in some case a tripling of the bacterial diversity. So the bacterial diversity is like the biodiversity of a rain forest. It’s incredibly diverse; there are lots of different types of bacteria there. When there were no doctors or patients in the hospital we saw very few bacteria living there day to day, it was quite sparse, like a desert. As soon as these doctors and patients moved in, we saw an incredible increase in the number of different types of bacteria that exist. This is remarkable because it suggests that the flora of the hospital or the microbial flora of the hospital comes from the patients, doctors, nurses, and the rest of the staff that utilize it day-to-day.

So why do you want to track individual people?

Dr. Gilbert: Because currently about 100,000 to 400,000 people die a year in the United States of bacterial infections potentially acquired while they’re in hospitals. It may be that the bacteria do not reside in the hospital, but come in via some other route which is highly likely, or maybe that the person brings the bacteria in with them and the treatment they get in the hospital to help cure them of whatever it is they are in there for actually triggers that bacteria to become a disease and that can end up in a fatality. So we’re trying to identify how the bacterial communities in this hospital look, who is there, how rapidly are they changing, and how they are moving between the surfaces and the people. That really gives us a good understanding of how people are bringing a disease into the hospital or if the disease spread within a hospital setting.

So if you can find that out, what are you hoping to achieve?

Dr. Gilbert: Stop people from dying, simple as that. We know that 400,000 people are dying a year, that’s not a good thing. It cost the US economy $40 billion every year. So, we’re dealing with an immense social, ecological, and economical problem. We need to find solutions to that problem.

How do you think you can find solutions? Do you just wipe out all of the bacteria and how does that differ from what’s being done now as far as sanitizing things?

Dr. Gilbert: That’s a difficult question. The answer is not to kill everything off. If we killed all the bacteria living inside your body, you would die. You need the bacteria that live inside your body, they help digest your food, and they produce vitamins and minerals for you. We can replace them with probiotics; you’ve had a yogurt? Well it has a bacterial community that lives inside it and you ingest it and it makes you feel better. When people’s bacterial flora is depleted or impacted in some way it makes them sick, and they are more likely to catch a disease. Similarly in a hospital setting, or any setting in the home, we’ve been able to uncover this quite simply. If you look at the bacterial flora on surfaces, if there’s a rich rain forest of bacteria on the surface, a pathogen landing won’t be able to set up shop. It can’t find a niche to live and so it dies off very rapidly. If there’s nothing there, there’s a higher probability that the bacterial pathogen, the disease-causing organism, will land on that surface and proliferate because there’s no competition. So we are trying to uncover whether cleaning strategies in hospitals are appropriate to help us determine whether the pathogens will be able to survive or will die off rapidly.

So are you also kind of thinking about adding bacteria?

Dr. Gilbert: Yeah, a building probiotic, just the same as we add probiotics to our food to make us healthy. There is insurmountable evidence now that this has significant impacts upon our health. There is no reason why we shouldn’t add probiotics to buildings to make them more healthy and this obviously is predicated on our assumption that diseases come from the hospital rather than can arrive into a hospital and proliferate. There is not substantial evidence that this is the case. Health care associated infections that kill people, such as MRSA, can come from environments but they may also be residing within you. We need to be able to rule out the hospital environment as a source of that infection so we can concentrate on other sources.

So MRSA that’s staph infection; it doesn’t come from surfaces necessarily. Does it?

Dr. Gilbert: It can be, but the patients probably brought it in with them. It probably already colonized in their body. And then when you go into surgery you get a big dose of antibiotics, you are generally stressed because your body is being cut open. You are under an immense amount of physiological pressure, which changes the relationship between you and that pathogen. So, you have MRSA in your body right now, right? You go into a surgical operation; your body is under stress. Your microbiome more importantly is under stress, probably depleted by a course of antibiotics, and this opens up the risk of that infection that MRSA can now take hold. Before, it might have just been hanging around in the background and now it can become predominant.

Is there a statistic on how many people have dormant MRSA in their body?

Dr. Gilbert: A couple of studies have been done. One in particularly, Denmark, has been really proactive in this and swabbing people as they come into hospitals and doing assays to determine if they are MRSA positive and it was somewhere in the region of 70 to 80% of the people coming into the hospital were MRSA positive, at least in their nose. This is quite common, Staph is found commonly on the outside of the body, it is when it enters the body through a cut that you can have a problem. Now, 70 to 80% of the people didn’t catch MRSA. So, there may be something else going on there that we don’t understand. Currently the tools we are using are helping us to elucidate some of these inconsistencies, but we’re still a long way before we can categorically stipulate what’s actually happening.