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Long-Dreaded Superbug Found in Human and Animal in U.S.

A gene conferring resistance to the last-ditch drug colistin has been found in E. coli in the United States.
A gene conferring resistance to the last-ditch drug colistin has been found in E. coli in the United States.
Photograph by Ian Cuming, Alamy

The antibiotic resistance factor MCR, which protects bacteria against the final remaining drugs of last resort, has been found in the United States for the first time—in a person, and separately, in a stored sample taken from a slaughtered pig.

Department of Defense researchers disclosed Thursday in a report placed online by the journal Antimicrobial Agents and Chemotherapy that a 49-year-old woman who sought medical care at a military-associated clinic in Pennsylvania last month, with what seemed to be a urinary tract infection, was carrying a strain of E. coli resistant to a wide range of drugs. That turned out to be because the organism carried 15 different genes conferring antibiotic resistance, clustered on two “mobile elements” that can move easily among bacteria. One element included the new, dreaded gene mcr-1.

The discovery “heralds the emergence of truly pan-drug resistant bacteria,” the DOD personnel, Patrick McGann of the Walter Reed Army Institute of Research and Kurt Schaecher of the Walter Reed National Military Medical Center, along with eight colleagues, write in the journal report.

Beth Bell, director of the National Center for Emerging and Zoonotic Infectious Diseases at the Centers for Disease Control and Prevention, said the CDC has begun working with the researchers and the Pennsylvania Department of Health to understand how the woman came to be carrying the highly resistant bacterium. (Later Thursday, Pennsylvania Governor Tom Wolf confirmed the case, and the CDC joint investigation, in a statement.)

The DOD researchers who described her case, who did not immediately respond to a request for comment, provided no other information on her case, except to say that she had not traveled in the previous five months, suggesting she did not pick up the bacterium outside the U.S.

“It is extremely concerning; this is potentially a sentinel event,” Bell said in a phone interview. “There is a lot that needs to be done in terms of contact tracing and field investigation, to have a sense of who else might have been exposed or might be carrying this resistant bacterium.”

Bell disclosed that the U.S. Department of Agriculture will shortly announce the first identification of MCR in the United States in an animal. It was found in a stored sample of pig intestine that was collected as part of the National Antimicrobial Resistance Monitoring System, a shared project of the CDC, USDA and Food and Drug Administration that looks for resistant foodborne bacteria in people, animals, and meat.

“We have been intentionally looking for this since MCR was first announced,” she said.

The Department of Health and Human Services subsequently confirmed the pig finding in a blog post Thursday afternoon.

The existence of MCR was reported for the first time just last November, in a report by British and Chinese researchers who said they had found the gene in people, animals, and meat in several areas of China. Subsequently it has been found in people, animals, or meat in at least 20 countries across the world.

MCR is so troubling because it confers protection against colistin, the last remaining antibiotic that works against a broad family of bacteria that have already acquired resistance to all the other antibiotics used against them. Colistin has worked up to this point because it is a toxic drug from the early days of the antibiotic era, seldom prescribed because of its side effects; because it was used so infrequently, bacteria had not adapted to it.

But because it is effective, agriculture adopted it instead, using it widely and legally for prevention of diseases in food animals. By the time the medical community discovered that it needed the drug back, resistance to colistin was already moving from agriculture into the human world.

Colistin is not actually used in animals in the United States, though it has been approved for use by the FDA. That makes the arrival of colistin resistance a mystery that will have to be plumbed through genetic sequencing.

Advocates who track antibiotic resistance, especially in agriculture, reacted to the news of U.S. colistin resistance by emphasizing the gravity this finding deserves.

“This shows that we are right on the verge of getting into the territory of routine bacterial infections being untreatable,” Steven Roach, the food safety program director at the Food Animal Concerns Trust, said by phone. “It underscores the failure of both the federal government and Congress, and the industry, to get a grasp of the problem. We can’t continue to drag our feet on taking needed action.”

The Pennsylvania woman’s diagnosis occurred thanks to a system set up within the DOD after MCR was discovered. Since last fall, any E. coli that was already resistant to a family of drugs known as ESBLs (extended-spectrum beta-lactams), as hers was, has been sent up the chain to Walter Reed, to be scrutinized for colistin resistance. That kind of systematic checking for antibiotic resistance, known as active surveillance, is rare in the United States. Most civilian surveillance systems are patchy; they focus only on foodborne illnesses, or rely on physicians or labs to report diagnoses, or draw from a few state health departments with already well-funded labs.

“This shows how much we need comprehensive surveillance, so that things are not discovered by accident,” Bell said. The CDC recently received additional funding under the Obama Administration’s national strategy for antibiotic resistance that will allow it to begin to set up regional lab networks. “We’ll be able to identify things systematically, identify clusters and begin contact investigations quickly,” she said.

“The first known case of MCR-1 in a U.S. patient underscores the urgent need for better surveillance and stewardship programs to combat antibiotic resistance,” agreed Dr. David Hyun, an infectious-disease specialist who is a senior officer in a long-running antibiotic resistance project at the Pew Charitable Trusts.

If there is any good news in the announcements of MCR’s appearance in the United States, it is that it has not, as yet, combined with other resistance genes into a completely untreatable organism. Bacteria acquire resistance genes like gamblers amassing a hand of cards, but the way the “cards” arrive is not step-wise—bad resistance, and then worse resistance, and then the worst—but randomly. What that means, in this case, is that the Pennsylvania E. coli possesses ESBL resistance (bad) and colistin resistance (worst)—but it remains susceptible to other intervening categories of drugs. (The stored pig sample has a yet different resistance pattern, colistin plus what is known as ASSuT, for the drug families represented by ampicillin, streptomycin, sulfas and tetracycline.)

But the random roulette of bacterial genetic recombination makes it more likely that an untreatable combination—of, for instance, colistin resistance plus carbapenem resistance, which the CDC has previously called “nightmare bacteria”—might occur. In fact, it already has occurred in patients in China, where MCR was first identified.

“We’re one step closer to carbapenem-resistant and colistin-resistant E. coli  bumping into each other in someone’s gut,” Lance Price, a molecular biologist and the director of the Antibiotic Resistance Action Center at George Washington University, said by phone. “It doesn’t matter in which direction the transfer takes place—if the carbapenem-resistant strain picks up colistin resistance, or if the colistin-resistant strain picks up carbapenem resistance. It’s double jeopardy.”

Once bacteria begin to collect resistance to multiple families of antibiotics, the speed and direction of their spread becomes hard to predict, because using any of the antibiotics to which they are resistant allows them to increase in number. (Not because the drugs affect the resistant bugs—they don’t—but because they kill susceptible organisms nearby, freeing up additional living space and food.) That makes it crucial to create surveillance systems that can identify them early.

The Department of Defense system that detected the Pennsylvania organism is a model for how surveillance ought to be carried out, Price said: “We need active surveillance for multi-drug resistant or high-priority resistant organisms, in animals and people, throughout the U.S.”

Previous coverage on Phenomena:

37 thoughts on “Long-Dreaded Superbug Found in Human and Animal in U.S.

  1. It was bound to happen, but still scary as can be. Colisitin isn’t used on pigs in the US, so maybe the mcr-1 gene got here the same way the recent PEDv in pigs made it to the U.S.
    Finding this gene in animals means it may be more widespread here than we think, since we don’t sample very much meat or very many animals, compared to the number of animals slaughtered every year.

    1. Considering that the USA sold Smithfields (the US largest pork supplier and food processor) to China the end of 2013 (despite consumer protest) THIS bit of news does NOT surprise me since China is now in control of OUR pork supply.

      When will America wake up and pay attention to what is happening in this corrupt country?

    2. You’re beginning to touch on the foundation of this problem, which is a culture that stresses the over use of antibiotics. Political lobbying from the meat and dairy industry has basically seen them able to abuse these drugs until they eventually lose almost all effectiveness. It’s a shame though that no one seems interested in doing anything about it, such as passing legislation banning the rampant abuse of antibiotics in cattle stocks. God forbid, that would cost us money.

  2. What the hell is CRISPR for if we can’t use it to genetically modify bacteria to infect other bacteria? We can make puppies glow in the dark – how about getting something going to attack the antibiotic resistant germs?? Lots of potential here. I just don’t believe we can’t use our knowledge for something that will actually save lives, now that we’ve played around with it for a while.

    1. Because gene-editing, or synthetic biology in general is a very nascent science that has a long way to go before it’s even remotely effective in such a specific and targeted manner. There are also complications that can arise from this approach, such as bacteria simply evolving (something they’re very good at) to have different gene sequences which do the same thing. Bacteria are very good at responding to selective pressure(s) and quickly find ways around the obstacles we throw at them. Prokaryotic organisms were here long before we were and they’ll be here likely long after we’re gone.

  3. I have noticed over time that whenever new anti-bs came out, they became the go-to meds for bacterial infection; but what about penicillin?
    I have long held the belief that since the new meds are not working, then they should try the old (barring allergies, of course), unless it has already been done.

    1. People are avoiding using Penicillin because the number of bacterial species that are resistant to Penicillin, or β-lactam antibiotics in general, is rapidly increasing. The rapid-fire changing of antibiotics in modern medicine is a direct result of the kind of Hell and breakfast mentality you’re espousing. Physicians are having to resort to second and third line antibiotics because the number of species with multi (and recently emerging pan) antibiotic resistance is so high.

      If anything, there needs to be a moratorium on superscribing antibiotics for anyone that’s not in real danger of suffering life-threatening complications from infection. That means people in the United States are going to have to come to terms with actually being sick for a week while your highly derived immune system does what it’s good at.

      1. tell that to someone in the federal government who will listen. to meet arbitrary and poorly conceived federal sepsis metrics we are required to use aggressive broad spectrum antibiotics from the get go. when we figure out the agent we then stop some drugs, and with the occasional short exposure are likely promotion resistance. but that doesn’t matter to Washington – only bad science matters.

      2. You know the problem isn’t from the US doctors handing out antibiotics like candy. The real problem is that in third world countries like India you have people so poor that they can’t afford to buy all the antibiotics they need when they are prescribed them so they rarely take the full course, only take them till they start feeling better that increases the probability of creating drug resistant strains.

    2. Bacteria are already widely resistant to penicillins, with the exception of streptococcus. Colistin, the antibiotic in this article, is in fact one of the oldest antibiotics and not used. The problem here is mostly agriculture: industrial farms have been filling feed with antibiotics…they use tons and tons of it annually. This wide exposure gives the bacteria a chance to gain resistance. We then pick up the resistant bacteria. It’s a well-known problem, but congress hasn’t acted on limiting this because of lobbying pressure. Please, if you or anyone has any influence, start demanding that we set serious limits on the agricultural use of antibiotics. It’s going to be the cause of many deaths in the future if we don’t make changes.

    3. Many bacteria are resistant to penicillin due to its widespread use back in the past. For instance, the infamous MRSA strain is resistant to beta lactams (the family to which penicillin belongs) and to cephalosporins. Often nowadays, treatment involves the combination of two different types of antibiotics of different classes, so that bacteria which are resistant to one drug will be killed by the other.

  4. MCR has generally been media hype. I would wait for the details to emerge before freaking out. Basically, MCR has been limited to hospital environments, in which there is extreme antibiotic pressure on bacteria, and it is functional for them to acquire such biologically costly immunity to them. For bacteria in more real world environments is not realistic. Why would such bacteria carry “15 different genes conferring antibiotic resistance” when they are not generally challenged by such drugs and there peer bacteria without such costly baggage will out grow them.
    I would like to know if this woman has been in a hospital environment recently. As for pig intestines there are many bacteria in that location. Your feces are largely made up of bacteria. They are not necessarily a risk for infection. And again what was the environmental exposure of the pig? Were they fed antibiotics routinely to reduce piglet mortality? Without such a challenge MCR should not be a problem until proven otherwise

  5. Maybe just maybe every time some boob runs to the doctor because they have the sniffles for antibiotics they might think twice, but I doubt it. Frankly I think the medical community should be reprimanded for their abuse of antibiotics along with the drug companies that push them!

  6. Pigs and Bats and Lions and Tigers oh my…I think I’ll be spending my evening watching the movies “12 Monkeys” and “Outbreak”…

  7. Should have listened to Alexander Fleming, and his warning that misuse of antibiotics would lead too this very problem. We need to outlaw immediately the cattle industry’s practice of administering prophylactic antibiotics on their herds.

  8. And now, with nation of origin labeling unlawful, for the first time on meat products. The consumer will have less opportunity to avoid food products from nations where these problems are developing. Thanks to the World Trade Organization and our Congress.

  9. I was poisoned by an antibiotic called cipro, and now they are using these drugs in our food, and when you mix chemicals and certain animal flesh or blood (as specific animals have specific and sometimes chemical filled diet), there may be a chemical or even microbial byproduct. Same as using any antibiotics in our food. Corporations THINK they have it so hard because there are “regulations”, but I PROMISE you, our regulations are not as sound as we all think them to be. The FDA allows drugs to be passed through without 3rd party testing (to ensure quality control without a chance for corruption), so in turn pass products (food AND drugs) that are dangerous and sometimes deadly to ppl and the environment. Our “regulatory bodies are ABSOLUTELY CRAP!

    1. Kyah,
      May I ask what you mean when you say that you were poisoned by Cipro? I took it once and it make me very ill, I wouldn’t say poisoned just sick to my stomach. Never took again.

  10. I’m not surprised that she could have been exposed to the bacteria, even if she didn’t travel outside the US. She could have been exposed to contamination from people or animals or products brought to the US from an MCR endemic country such as China.

  11. Is there another micro organism or bacteria which is not resistant to antibiotics and could be inoculated into the person so it can kill the E-coli and then doctors can get rid of it with antibiotics? Is this possible?

    1. phage bacillus therapy–you drink a cocktail of a hundred bacteria killing viruses and hope that one is a close match to your bacteria. The therapy originated in Eastern Europe where peasants were successfully treating badly infected wounds with swamp mud. A little research showed the effective agent in the mud was the viral culture.

  12. I almost thought I was the woman in this article when I first read it because I had the exact same ongoing health issue for 5 or 6 years that appeared to be resistant to multiple antibiotics I was prescribed during that time. At first, I thought I just kept getting infections, but then became convinced that the original infection was never completely cured, as symptoms would subside temporarily, and then reappear. E. Coli ended up being the cause of the infection I had. I came to the conclusion that consuming meat treated with heavy doses of antibiotics was the cause of my body’s resistance to treatment even before I read this article. This is not a new health crisis! I think this is far more pervasive than people realize.

  13. The fact that we are hearing this now, means they can no longer hide the fact we have out-run of arrows in our medical quiver. This is just the tip of the iceberg. How many times have you heard the term antibiotic resistant “X”? My sister and cousin died of an anti-biotic resistant Staff infection. I got a lung infection last fall that my doctor tried for months to squash, the last anti-biotic they gave me came with the warning “if this doesn’t work, you’re in big trouble”. Fortunately it did work, but it was quite a scare. The problem is two-fold; first anti-bionics are handed out too freely, in most countries no prescription is required. Second, people don’t finish the dosing schedule, as soon as they feel better, they stop taking it. The bugs that survive are now resistant to that anti-biotic. The bugs are going to win, it’s just a mater of when.

  14. To all the religious people reading this, please tell us what role in “god’s perfect plan” deadly bacteria play. Nothing rings more hollow than the tortured excuses of a person trying to shore up his belief in an invisible man in the sky. Bacteria would kill the entire human race and think nothing of it. And yet, frightened, credulous fools will frantically attempt to make everything always work out in a way that supports their superstitions (aka, religion). Thanks to all the men/women of science who did the hard work of developing antibiotics. Those are the gods we should be thanking, not the man-made god of the bible.

    1. As far as scientists deserving some credit for what they accomplish, sure. But, my friend, your ignorant opinion that there is no God or that God is a man made belief is why this world is in its sick state & continuing to decline in its ability to function in a positive direction. Sure,many irreprehensable events have happened through the ages “in the name of god” but that is not god at work but the darker side of mankind at work.

  15. Many posting here are far more knowledgeable than me regarding the antibiotics and maladies. Please bear with my prejudice and ignorance.

    As a layman, I get a sense of yet another “crisis” that is urgently in need of “funding”. I am quite aware of the $500 million already diverted from the monies allowed “Zika”. I am weary of allowing yet more public monies to be taken.

    When a medical catastrophe as is suggested (as a potential) here does emerge, I hope we are not so jaded with “manufactured and hyped issues” to deny it due resources.

    At least bacteria is not partisan.

  16. To say that because she had not traveled outside the US in the past five months that she must have caught this strain here seems illogical. E. coli are part of our normal gut flora and urinary tract infections with it are opportunistic infections, when the normal flora of one body site gets into where it doesn’t belong. As such, she could have been carrying this strain as a part of her normal flora for quite some time!

  17. Isn’t that grand and it is found in meat. Coincidentally congress passed a law that doesn’t require the country of origin of meat products to be labeled anymore. Yaaay congress another good job you have done for the people of this country!

    1. A little context goes a long way….

      “On Friday, Congress repealed the country-of-origin-labeling rule (COOL) on beef and pork after the World Trade Organization (WTO) imposed $1 billion in retaliatory import tariffs against United States if the rule was not overturned. The repeal was part of the omnibus spending bill signed by President Obama on Friday.”

      “Canada and Mexico had argued that the mandatory U.S. labeling program discriminated against meat imports and violated WTO limits on what sorts of product-related “technical regulations” WTO signatory countries are permitted to enact. … The United States has lost two rulings and two appeals with the WTO regarding COOL since 2011. The import tariffs were authorized by the WTO on December 7th.”

      It’s easy to blame “congress” but reality is much more complicated. President Obama also signed the legislation into law.

      Where did WTO come from? It was part of a trade agreement that was pushed by President Bill Clinton in 1995.

      As reported on SNOPES:
      “As Vilsack’s statement explains, the previous country of origin labeling regulations were of debatable value to consumers. Regardless of a meat’s country of origin, all meat sold inside the United States is subject to the same USDA regulations and standards as before.

      In short, it is true that mandatory COOL labeling was officially repealed in the U.S. late December 2015, but those revised labeling requirements applied only to some meats and had no effect on the required certifications that apply to meat sold in the U.S. (whatever its source). Attachment of the bill to omnibus spending legislation wasn’t sneaky, as USDA provisions are generally passed as part of budget bills for upcoming fiscal years. Finally, nothing about the COOL repeal prevents manufacturers from labeling meat: those vendors who wish to do so are free to label their meats without penalty.”

  18. Meanwhile, what happened to the woman?

    Dead, alive, sick? Prognosis?

    MM: There’s no indication that she died or even was seriously ill. (People can carry these bugs without being made ill by them.) Beyond that, to respect medical privacy, no one has said, yet. Given the amount of reaction, it’s an understandable move.

  19. Last month I was hospitalized in Pa.With flu like symptoms and severe pain in joints and abdomen.I received a Kidney transplant last July and am on the necessary anti rejection meds.in order to stop rejection of new kidney,so this leaves me with no immune system.I had IV anti biotic in hosp.and 14 days IV antibiotics at home.Afterwards I developed a UTI and am now on Cipro.I am frightened because while in hospital many Drs.including Infec.disease Drs. And Gastro.Drs came to examine me.I feel ok but this uti.doesnt seem to be going away.I have to do urine test again Monday once I’m done with the cipro.
    I’M afraid I may be in trouble here,and not know it.They said the infection in my blood was from my intestines,and ND no one knows how it got there.
    I had a kidney biopsy several months ago by a dr.who was training at this hospital and had a physical disability and had trouble shaking while inserting needle into my abdomen to perform biopsy.It hurt terribly,and it should not have.My previous biopsy I didn’t even feel.
    Since I have had pain since then I’m wondering if he pierced my intestine slightly and this has been brewing all this time.I told my Drs how I felt but no one seemed concerned until I was hospitalized with this blood infection.
    I’m frightened but I don’t think they are going to let me know if I’m still in danger.I think there may be concern because I complained since my biopsy.I knew something felt wrong.
    I guess I will see after this next urine culture.I pray everyone else reading this stays safe and healthy.Keep a check with blood work.Check Ur white count because mine is still low despite treatment and injection to boost it.I am immune system compromised so my concern is great.Gid Bless us all.

    1. Christine,
      Demand to know your condition, if they do not tell you everything to your satisfaction request to see the Administrator of the hospital. You will suddenly see people moving at a different pace and you will see the administrator. Get well and God Bless.

  20. A year ago my 58 year old husband, sick and in the hospital for 60 days, was getting better until he tested positive for one type of carbapenem resistent enterobacteriacae (CRE). Three horrible weeks later he had three types of CRE including e-coli. Despite being treated with the newest drug tigecycline, the much older drug colistin and host of others he died a horrible, painful death. Hospital acquired infections are a big deal, they are most certainly deadly and they are spread by personnel, procedures and equipment in hospitals throughout the US. Read “Horizontal Transfer of Antibiotic Resistance Genes on Abiotic Touch Surfaces: Implications for Public Health” if you want to understand that these bacteria can survive a LONG time in the healthcare environment. I was appalled by the lack of knowledge the staff had about CRE or how serious the transmission risks were at a very large and “good” hospital. Unfortunately, CRE is NOT a reportable event in many states, like mine, so you won’t know if your hospital has a problem ….until its too late.

    MM: I’m so very sorry. Thank you for sharing your story.

  21. OH MY THIS IS EXACTLY WHAT’S WRONG WITH ME! !!! DRs keep changing my antibiotics every time I’m diagnosed with the UTI and is ALWAYS POSITIVE FOR ECOLI!!!!!



    CAN’T GET MY DRs To hear me

    1. Hello Dear,
      So sorry to hear what your going through. The one thing that struck me, you said was the pain. I know this is probably a useless reply but I must make sure, have you’re Doctor’s prescribed Uribel. I have Kidney failure with frequent UTI’s and the Uribel immediately takes care of the pain. God Bless.

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