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How To Track And Attack A Superbug


This is TALK OF THE NATION. I'm Lynn Neary in Washington. The Centers for Disease Control is warning of another deadly superbug. This one, known as CRE, ultimately left seven patients dead after an outbreak in 2011 at the National Institutes of Health in Bethesda, Maryland. CDC director Tom Frieden has called the bug a nightmare bacteria. It can resist even the strongest antibiotics.

Patients in hospitals and nursing homes are most vulnerable to the bug, and Dr. Frieden is urging hospitals to take precautions to stop the spread of these infections. If you have any questions about superbugs, give us a call. Our number is 800-989-8255. The email address is Or join the conversation at our website by going to, and then you can click on TALK OF THE NATION.

Later in the program, Ken Rudin on filibusters, but first superbugs. Joining us to talk about this nightmare bacteria is Rob Stein, NPR correspondent and senior editor of the science desk, and he is here with me in Studio 3A. Good to have you with us.

ROB STEIN, BYLINE: Oh, nice to be here, Lynn.

NEARY: Also joining us, Carl Zimmer, a science writer and blogger specializing in the evolution of parasites, and he joins us from the Yale University studio. Good to have you also, Carl.

CARL ZIMMER: Thanks for having me.

NEARY: Rob, I wanted to start with you. First of all, what's unique about this particular superbug that we heard about earlier this week?

STEIN: Yeah, this is a family of bacteria that are highly resistant to antibiotics and as you mentioned are called CREs. That stands for carbapenem-resistant Enterobacteriaceae. It's a mouthful.

NEARY: Yeah.

STEIN: But what it means is that there's this last-ditch type of antibiotic called carbapenems that doctors use when nothing else works. You've tried everything else, nothing else works, and all they have left is just one group of antibiotics. And these bacteria don't even respond to that. They can't even cure people when they're sick. That's why people are so concerned about them.

NEARY: And that's why they're calling it a nightmare.

STEIN: Right, Dr. Frieden from the CDC, he called them nightmare bacteria for really three reasons. One is that they're so highly resistant, there's really very little of any antibiotics left that will work. Number two, they have a very high mortality rate. About half of people who get these end up dying. And the third reason is that the mechanism that these bacteria use to beat back the antibiotics can spread from one type of bacteria to another. So that raises the risk they could get out of hospitals and start to spread more widely.

NEARY: Yeah. Now scientists have been tracking this bug for a while, right, it's not a brand new bug.

STEIN: Oh that's right, this - it's a family of bacteria, and they've been around for a while, and they've been aware of them for a while. The reason they're concerned is when they took a look at what's happened over the past decade or so in this country, they found a very significant increase in how common these bacteria are now. It's - they're still very rare, and they're limited to hospitals, but they've quadrupled in terms of the proportion of bacteria that have this resistant capability and also quadrupled in terms of the proportion of hospitals that are reporting cases.

NEARY: Well, this is - so the people who are most obviously likely to get infected are patients in hospitals or nursing homes. How concerned should the general population be?

STEIN: We really don't have to be that concerned right now for the general population. As I said, these infections are really only occurring in hospitals, and they're still even in hospitals fairly rare and unusual. So they're not something that pose a threat to the general population. You don't have to really worry about picking this up by walking around right now.

This is something that they're trying to get the message out so that hospitals are much more aware of them and hospitals start taking more aggressive steps to prevent these infections from spreading.

NEARY: All right, well we're going to turn now to our other guest, Carl. Carl wrote the article how - Carl Zimmer wrote the article "How Scientists Stalked a Lethal Superbug With the Killer's Own DNA." And he wrote that for Wired last month about the superbug outbreak at NIH. And you can find a link to this article on our website at

So Carl, let's walk through this a little bit. As I understand it, scientists used genetic techniques to track this superbug at NIH. Can you explain how that works, or where did they start?

ZIMMER: Sure. So when these kinds of bacteria show up in a hospital, what usually happens is that microbiology use more traditional methods to figure out what's going on. So for example they might take a swab from someone's skin or from their mouth or so on and put it on a Petri dish or in a flask and just see what grows, and that can take a while. That can take, you know, up to a day or more even.

And when you think about it, that's kind of an old-fashioned way of figuring out what's in your hospital and what's making people sick. So in July - I'm sorry in June 2011, there was a patient who was being brought to the National Institutes of Health Clinical Center, and they were told when this patient was arriving that this patient was carrying one of these bacteria, one of these nightmare bacteria; it's KPC for short.

NEARY: And how did they know that in the first place? Was there a test or something?

ZIMMER: Yeah, there's one of these more traditional tests. And so they knew what they were dealing with. And so they thought that they were - they could prepare for this patient, and they would prevent that patient from making other patients sick. This patient actually wasn't actually having an active infection with this disease. It was just sort of - the bacteria just sort of carried along.

And then the patient left, and they thought that they were out of the woods, this was in July, and then in August some - another patient got sick with KPC, a patient who had been there the whole time, and then another and then another, and then they started to realize they were dealing with an outbreak.

And rather than just using more traditional technology, they took advantage of the fact that the hospital is surrounded by the National Institutes of Health. And there are all these experts on sequencing genomes. So they did something that is almost never done: They actually started sequencing the whole genome of some of these bacteria to figure out how it was going from patient to patient, and so they could help them to actually fight this outbreak.

NEARY: And can I just back up and ask you something? In this case where they knew that this patient came in, had the bacteria, and then the patient left, and then a month later some other patient gets the bacteria, is that extremely unusual, an unusual way for something like that to spread?

ZIMMER: You know, we don't know enough about these outbreaks to say whether it's unusual or not. The thing is that, you know, scientists who track these outbreaks use very old-fashioned techniques that were really pioneered in the 19th century to figure out how diseases spread from one person to another, even within hospitals. So say OK, were these two patients in the same ward? And maybe that is - could be how it could have traveled from one to the other. They have all these sort of indirect clues.

So if you can actually look at the entire genome of the bacteria that were growing on one patient and then look at the entire genome of the bacteria on another patient, you can say wait a minute, these are exactly the same bacteria. They share the same mutations. And you can actually draw a much more accurate map of how that outbreak is spreading, and then you can take steps to stop it.

NEARY: Well, how - what did they discover? What did they find out?

ZIMMER: Well, one thing they discovered was that this bacteria, this KPC, was a lot tougher than people had really given it credit for. So it seems to have somehow colonized a lot of patients or maybe even surfaces in the hospital after this initial patient showed up, and then from there it made other people sick and infected other people.

So it seems to be a very durable, crafty, elusive kind of microbe, and so you can't just take kind of ordinary measures against this thing. You have to get really drastic, and that's what they did. And they did a whole lot of really draconian - they put a lot of draconian measures in place.

You know, they isolated all the patients, they call it cohorting. There was staff, nurses and doctors who could only treat them and nobody else, you know, hand washing, all these things that they were enforcing. And they even had sort of minders who would just go up to, you know, the chief of surgery and say you need to use two squirts of that hand gel if you're going to go in that room.

They were taking these sorts of measures, and they knew that they needed to because they could see from the genomes that this thing was still spreading, and it was going - it was jumping around different wards, even.

NEARY: Again they still had - but how was it spreading? I'm still not understanding exactly how it was spreading.

ZIMMER: Well...

NEARY: And I understand they tracked it genetically, but it had to spread somehow physically. Was it just spreading - I mean what was happening? What was making it...

ZIMMER: It is going from patients to - we don't know precisely how it's going, but there are some possibilities. One possibility is that it would go from one patient to a staff member to another patient. One possibility is that the patient contaminated the stuff in the room and it then contaminated a patient who used that room, those sorts of things.

They still don't know a lot, but what they do know is that even when they had all the patients as carefully quarantined as possible, the bacteria was still getting out and getting to different floors of the hospital.

NEARY: Wow. Rob Stein, this has great implications for hospitals and the precautions that they have to take against a superbug of this kind.

STEIN: Absolutely, absolutely. This - that's - the case that Carl's describing is a very dramatic example of the sort of thing that happens in hospitals, you know, to some degree fairly routinely with this infection and with other types of infections. And that's the key, really, at this point for these CRE superbugs, to try to keep it in check is to get hospitals to be much more aware of the problem and much more aggressive in terms of identifying patients who might be infected, taking steps to isolate them, sterilizing everything they come in contact with, making sure that staff, nurses and doctors, do commonsense things like wash their hands and sterilize themselves before they go from one patient to another.

NEARY: You know, I have to say I've spent some time in hospitals over the last couple years, in emergency rooms, and, you know, no criticism of the hospitals I've been in, but, you know, they're not always as careful as they could be, I don't think. I mean, what is a patient supposed to do, stop everyone and say did you wash your hands for, you know, the length of the song "Happy Birthday"?


STEIN: Yeah, yeah, well, you know, increasingly people are giving advice like that to patients to say don't be shy. You know, if a doctor walks into the room, you'd say hey, doc, did you wash your hands today? You can do it with a smile in a way to sort of disarm them, but, you know, this is nothing to be messed around with. You have to take it very seriously.

NEARY: Yeah, so implications here for hospitals, implications here for patients and their caregivers, the people who are taking care of them.

STEIN: Right, right, of course, if anybody comes in contact with somebody who is carrying one of these infections, they have to be very careful themselves that they don't become infected and then spread it to somebody else and onward and onward like that.

NEARY: Yeah, and that would be how it would get outside the hospital or nursing home environment.

STEIN: Yeah, and again that's the big concern with these CRE bugs is that right now it's limited to hospitals, but there's no reason to think that it might not start to spread if we're not careful.

NEARY: Yeah, and if you have any questions about superbugs for Rob Stein and Carl Zimmer, give us a call. The number is 800-989-8255. And you can send us an email at This is TALK OF THE NATION from NPR News. I'm Lynn Neary.


NEARY: This is TALK OF THE NATION from NPR News. I'm Lynn Neary. Superbugs like CRE are clearly a problem. The head of the CDC made that point on Tuesday when he held a press conference meant to, quote, "sound an alarm." Health care institutions in at least 42 states have reported at least one infection. But there may be more to it than that, something the CDC acknowledges.

So far only six states mandate reporting cases, and there are several separate systems for keeping an eye out for outbreaks. Dr. Frieden did sound a hopeful note, though, saying that there's a narrow window of opportunity now to fight these bugs and stop their spread. What questions do you have about superbugs? Now is your chance to get them answered.

Give us a call, our number is 800-989-8255. You can also email us or join the conversation on our website. Go to, and click on TALK OF THE NATION. Science writer Carl Zimmer and NPR's Rob Stein are my guests. And we're going to take a call now. Let's go to Rodney(ph) in Framingham, Massachusetts. Hi Rodney.

RODNEY: Hi, how are you all doing?

NEARY: I'm good, go ahead.

RODNEY: Listen, I am a seventh grade science teacher, and for the last seven years while teaching evolution, we've explored the evolutionary arms race that we're losing with drug-resistant bacteria. And particularly we've done an experiment where we test antibacterial soaps versus non-antibacterial hand-washing methods.

And over the last seven years of this launched a little study. We've come up with hot water does generally better than all the other hand-washing methods, and in no year have the triclosan-based soaps worked any better than anything else, which raises a lot of questions for our students about how we are affecting the evolution of bacteria with the overuse of the (unintelligible) antibacterial products in our society.

And I wanted to know what the guests had to say about the role that humans are playing in some of these sort of choices of hand washing and antibiotics in livestock feed and so forth in the speeding up of the selection for drug-resistant bacteria like this (unintelligible).

NEARY: Thanks, Rodney, thanks for that. Rob Stein?

STEIN: Yeah, he raised a very important point, which is that we certainly are playing a big role in this, and the overuse of antibiotics certainly is fueling the development of superbugs, and one of the things that the CDC and others are urging is that doctors be much more cautious and judicious in the way they prescribe antibiotics because we know that it is often prescribed in cases where it's not necessary, and the overuse of these drugs causes these bacteria and other microbes to mutate and become resistant, and that's really part of what's fueling the problem here.

And the same goes with the use of - there's a lot of concern about the use of antibiotics in livestock, that's another issue that people are concerned about, that that may also be playing a role.

NEARY: And what about antibacterial soap? We have a question here from an email from Virginia(ph) asking about that: Does the use of antibacterial soap increase the likelihood that my body won't respond properly to standard antibiotics?

STEIN: Yeah. I have not seen any evidence of that sort, that by using those soaps that you're going to be somehow making yourself more vulnerable. But as the caller said, you know, washing your hands with good hot water, regular soap, is probably really all you need to do to protect yourself in terms of personal hygiene.

NEARY: Carl, do you have anything to add to that?

ZIMMER: Well, by doing anything that exposes bacteria, even good bacteria, to antibiotics, you're creating the opportunity for the evolution of resistance. Any genes that provide resistance are going to become more common, and mutations to those genes are going to be favored by natural selection. And the real tricky thing about bacteria is that once they've got these highly evolved resistance genes to different drugs, they trade them. They swap them around. And actually you'll have some bacteria like the bacteria we're talking about today, which have accumulated lots and lots of genes for lots of different antibiotics.

And so you are - sometimes you're facing bacteria that are resistant to just about every known antibiotic. So in my article in Wired where I was talking about this outbreak of these bacteria called KPC, there are really just a handful of antibiotics that were left that could be used because they had become resistant. They evolved resistance to so many other kinds.

And these are nasty things. These are drugs like there's one called Colistin, which scientists, which doctors had abandoned in the 1970s because it does things like cause kidney failure. But they were faced with a situation where their patient was either going to have to die because they didn't give them antibiotics or be given a drug that was going to cause them some serious harm.

And the really amazing thing was that over the course of this outbreak, they could watch mutations arise which made these bacteria become resistant to Colistin, as well. So there were patients where these bacteria were evolving to become resistant to everything we have.

NEARY: Well, so Rob Stein, does that mean we're going back to a time - I mean, there was a time when there were no antibiotics, which was not a good situation, either. Are we going back in some way? Is this a - is that where this is leading, to a time when we can't use antibiotics?

STEIN: That's the fear. I was talking to somebody about this the other day, and that was the image that they raised, that we might be returning to the pre-antibiotic era, when we couldn't treat commonplace infections. We've all grown up with antibiotics, so we're used to, you know, if you get sick, you go to a doctor, you get an antibiotic, and you get better.

You know, as time goes by, and more and more of these superbugs evolve that we may get closer and closer to a time when they're not working. I mean we're certainly not there yet, and there's - most infections can be treated. Most people get better.

NEARY: How far away are we? I mean, is there any way of knowing?

STEIN: We don't know, we don't know, but , you know, the concern certainly is intensifying, and there's starting to be some efforts now to try to get at this in lots of different ways, including trying to develop new antibiotics, trying to develop new ways to treat infections that don't fuel the evolution of resistant microbes, that sort of thing.

NEARY: I have a question here from Kate(ph), and it's a good one. A question: What are you talking about? What does this sick look like? You keep saying bug, sick, it. What does it look like?

STEIN: The bacteria themselves?

NEARY: The illness. I mean, what are we talking about? I think that's what she means by that.

STEIN: Yeah, well, these infections can manifest themselves in lots of different ways. In fact Carl mentions, you know, sometimes people who are infected with these microbes don't have any symptoms at all, which is part of what makes it so...

NEARY: Really?

STEIN: Yeah, they might just be carrying it. It might not be causing any illness. But then they - like that patient showed up at the NIH Clinical Center, ended up spreading it to other people who did develop symptoms and did get sick. And, you know, the symptoms can range, you know, range widely to being very serious. If these infections get into the bloodstream, that's when they can become life-threatening.

NEARY: But what kind of illness might a person experience?

STEIN: Well, it could be anything like a gastrointestinal, you know, symptoms that - a lot of these bugs, these CRE bugs, that's where they live normally is in our gut, and they're there, and they're not causing any illness. It's when they spread outside of - to other parts of our body when they cause more serious symptoms.

NEARY: All right, let's take a call from Lisa(ph) in California, in Truckee, California, Lisa?

LISA: Hi, how are you?

NEARY: I'm good, thank you.

LISA: I had a quick question. OK, back in 2004, I got a community-acquired methicillin-resistant Staph, the MRSA. I was a runner. I had no experience going in the hospital, but I managed to get this bug in the community. I was not a drug user, IV drug user like some people can get it out in the community. So basically I went in with flu-like symptoms and ended up with pneumonia. And I went onto a respirator and was in a coma for a month and a half.

And luckily there were the two drugs, the Vancomycin and the Zyvox, that I was able to take. However, at that time in 2004, this seemed to be a hospital-acquired bug, as well. So I was wondering how you can see this progression of the current bug that is now in the hospitals either getting into the community or how it basically - if it did transform from MRSA or some relative of MRSA how you can see how it could still get out into the community. Thank you.

STEIN: Absolutely. The MRSA experience is exactly the scenario that people are worried about. MRSA first came to attention as a hospital infection, it was limited to hospitals. There was a lot of attention given to it to try to keep it from spreading outside hospitals. Nevertheless, it did. And as the caller said, now it's pretty commonplace outside in communities around hospitals. And the concern is that the CRE infections will follow that same pattern.

NEARY: All right, thanks for your call, Lisa. Here's an email from Kay(ph) in San Jose: Is there a way I can find out if a hospital has antibiotic-resistant cases? I don't think asking them will result in anything definitely, more likely a vague reassurance. In my great-grandmother's day, infection was the reason people felt a trip to the hospital was a death sentence.

ZIMMER: Yeah. There are more - I think, as we mentioned earlier in the program, there are - more and more states are requiring hospitals to report hospital-acquired infections, and some of those databases are available publicly. And you can go online and, sort of, see what the infections rate are at your local hospitals.

NEARY: OK. Let's take a call from Minneapolis. Hello. Go ahead.


NEARY: Hi. Go ahead.

UNIDENTIFIED WOMAN: I'm calling regarding MRSA, the methicillin-resistant Staphylococcus aureus. That is what was just discussed and previous caller regarding community acquired - it's community acquired and hospital acquired. And if the hospital does not report it, tell you, it generally goes on your - in your file, in your chart as complications of surgery. So it's very important. I had a heart attack. It's really important that when you go into the hospital you tell them or give in a written request that you've been tested before or during the process of the admittance.

NEARY: OK. Let me ask our experts here about that. Thanks for calling very much. Rob, as I understand it, that's one of the things I think the CDC wants hospitals to start doing is testing patients, I guess, who are at risk of this - or would be all patients - as they come in to see if they have these bacteria in their system. But I gather that either not all hospitals are equipped to do it or don't have the resources. I mean what's the situation there with - how would that help, and why aren't hospitals doing it?

STEIN: Right. That is absolutely the first step in trying to control something like this is to identify patients who are carrying these infections. And so, as you mentioned, that's one of the things the CDC is urging hospitals to do, more routinely, is to test patients as they come in to see if they're infected with this. And if they are, take some steps to prevent it from spreading, immediately isolate them from other patients and also for hospitals that are transferring patients from one to another, from one facility to another to alert the next facility that they have a patient coming in who's carrying this infection, because the places that are hit hardest by this are long-term care facilities.

Those sort of hospitals, the infection rate is closer to 17 percent. And what happens often is you have a patient transferred from a hospital to a nursing home, and the nursing home doesn't know that - or from a nursing hospital to a hospital and, one, the hospital doesn't know that they're getting a patient who's carrying this infection. So they don't know to take these steps to prevent it from spreading.

NEARY: Yeah. But a hospital - can a hospital test every patient who's coming into their emergency room?

STEIN: You know, they can test patients who they have some reason to believe may be infected. And if they can do that, that would go a long way toward preventing this from spreading even further.

NEARY: So is - the burden for preventing the spread of this, is it really on the hospitals?

STEIN: At this point, yes, absolutely. The burden is on the hospitals, because that's where these infections are occurring. They're not occurring in the communities yet. So it's not your regular doctor's office or your mini-clinics where this is a real problem. It's in community hospitals and nursing homes and places like that. Those are the places where we have a window of opportunity, here, to prevent these from spreading further.

NEARY: We're talking with NPR's Rob Stein and science writer Carl Zimmer about super bugs and how to prevent them from spreading. And you are listening to TALK OF THE NATION from NPR News. Carl, I just want to follow up with you on this idea of testing patients as they come in, because at the NIH they knew that a patient - the patient had this bacteria, and yet, they still weren't able to prevent it from spreading, right?

ZIMMER: Well, yes, that's true. I mean - but they learned a lot along the way after the out - during the outbreak. And afterwards, they took a big risk by actually going quite public with this. They published a detailed paper in a scientific journal explaining their experiences. They went to other hospitals and said this is what happened to us, don't let this happen to you. And so there are lessons that they have learned, and that they hope will become a part of the regular practice of stopping these bugs.

And, you know, the fact is that now they do actually test a lot of the patients that come into their hospital. And if they have any suspicion, they run a test. And it's actually a test that they themselves designed, because the earlier tests just weren't sensitive enough. They were missing people. They - people would basically just test negative who actually had the bacteria on them. So now, they're using much more sensitive tests. And so obviously, this kind of test should not be limited to this one hospital.

I mean the fact NIH took a big hit for going public about this, but the fact is that this is happening all over the place, as Rob was saying. I mean the fact is there are two million hospital-acquired infections in the United States every year. There are over 90,000 deaths from hospital-acquired infections every year in the United States. And this is not limited to the United States. This is a problem that is being faced all over the world. We actually exported this particular strain of bacteria, I wrote about, called KPC.

We exported it all over the world to places like Israel and Greece and so on who have been dealing with huge outbreaks. It's the same bacteria. And so we're all grappling with this together. So we all need to be much more careful about stopping this thing.

NEARY: Let's see if we can get one more caller in here. Christine in Sacramento, California. Hi, Christine.

CHRISTINE: Hi. How are you doing?

NEARY: Good.

CHRISTINE: I am both a registered nurse, I'm also a health care attorney, and I advise health care providers on how to treat patients appropriate way and how to follow the law and regulations. But in September, I was hospitalized at a major university medical center. And it was - I was very diligent. Every time someone came into the room, no matter who it was, I asked them to make sure they had cleaned their hands. And I watched them as they used the canisters that were mounted on the wall, and I contracted Clostridium difficile, and - which is a very severe infection and very difficult to treat.

And the - I later found out and was advised by my physician was that the alcohol-based solutions that are in those canisters are not effective in killing off the Clostridium difficile bacteria.

NEARY: Interesting.

CHRISTINE: It has to be soap and water so...

NEARY: All right. I'm going to let - we'll going to run out of time, so I'm going to ask Rob Stein to respond to the point that you're making, Christine. Thanks very much for calling in.

STEIN: Yeah. It really does - it illustrates really how tough a problem this is. I mean we sort of say, oh, hospitals ought to do a better job of controlling these infections, and they do, but it's tough. And so really, no one step is going to prevent these infections from emerging or spreading. But it is clear that if you combine all of these steps, you combine testing people, with isolating people, with sterilizing equipment that they come in contact with, making sure that staff are taking steps, that does seem to be effective and can halt the infections from - outbreaks from spreading even further.

NEARY: That was NPR's Rob Stein, correspondent and senior editor on our science desk. Thanks for being with us.

STEIN: Oh, thanks for having me.

NEARY: And we were also joined by Carl Zimmer, a science writer and blogger, especially regarding the study of evolution and parasites. Thanks to you, Carl.

ZIMMER: Thank you.

NEARY: Up next, Wiz Khalifa and Jay-Z on the Senate floor, sort of. Ken Rudin joins us to talk about filibusters. I'm Lynn Neary. It's TALK OF THE NATION from NPR News. Transcript provided by NPR, Copyright NPR.