Mapping Antibiotic Resistance: Know The Germs In Your Neighborhood

By Dr. David Scales

You may have heard about Daniel Fells, the tight end on the New York Giants who almost lost his foot due to a drug-resistant infection. You’ve heard about drug resistant infections like Fells’ because dire reports about “the end of antibiotics” are all over, but maybe you want to know if resistant germs are common near you.

Unfortunately, you’re out of luck. While your hospital probably collects that data, they probably won’t share it with you.

John Brownstein, an associate professor at Harvard Medical School, and his colleagues at Boston Children’s Hospital (the group responsible for, are working to make these data more available. They are tracking resistant bacteria through an online map called ResistanceOpen. The goal is to shed light on how much resistant bacteria is in your area and which antibiotics those bacteria are resistant to. (Full disclosure: I did my post-doc with HealthMap, leaving in 2013.)

Other groups track drug-resistant bacteria — like ResistanceMap put out by the Center for Disease Dynamics, Economics and Policy, based in Washington, D.C. — but it’s never been done at such a local level. ResistanceOpen provides data and information on four of the most dangerous types of resistant bacteria, including MRSA, the infection that Fells caught in his foot.

A screenshot from ResistanceOpen (Courtesy)

A screenshot from ResistanceOpen (Courtesy)

It’s not yet so detailed where you can get data on your local hospital, but currently you can search for information on which drug-resistant bugs are circulating in a 25-mile radius from your location, or any other location you choose. The hope is that if people know which resistant germs are in their area, it’ll help draw attention to the issue. One day, ResistanceOpen hopes to map data at the hospital level.

“I feel like antimicrobial resistance should be treated with the same urgency that other communicable diseases are met with and I believe it has to start with transparency and awareness,” Dr. Derek MacFadden, a Canadian infectious disease doctor who worked on the project, told HealthMap’s Disease Daily. “ResistanceOpen provides the public with both.”

While some of the data for the map comes from news reports about resistant bacteria, Dr. MacFadden, who is also a doctoral student at Harvard T.H. Chan School of Public Health, found much of the data for ResistanceOpen by scouring hospitals’ websites.

Hospitals routinely track antibiotic resistance on their wards and in their clinics. With that data they usually create a yearly “antibiogram” — a catalogue of bacteria found in patients treated at that hospital in the past year. Antibiograms help guide physicians at that hospital on how to treat patients by avoiding antibiotics that are unlikely to work. But antibiograms are not always public, so only the physicians (and patients) at that hospital benefit from the information. Continue reading

When A Burst Appendix Doesn’t Kill You: Big New Study Adds Data

An urgent laparoscopic appendectomy is performed aboard the nuclear-powered aircraft carrier USS Enterprise, in this undated photo. (U.S. Navy via Wikimedia Commons)

An urgent laparoscopic appendectomy is performed aboard the nuclear-powered aircraft carrier USS Enterprise, in this undated photo. (U.S. Navy via Wikimedia Commons)

If you’re a regular reader, you may have noticed that certain posts tend to dominate our most-popular list: on birth control and sex, on diet and exercise. Pretty predictable crowd-pleasers.

But one sleeper’s appearance on the list has repeatedly surprised us: “When A Burst Appendix Doesn’t Kill You.” Turns out, appendicitis is no lightning strike: It hits 300,000 Americans a year, one-tenth of adults over their lifetimes.

That 2012 post shared the story of Martha Little, who was then WBUR’s news director and who kept toiling away in the newsroom even though her appendix had burst — not because she was a hopeless workaholic, but because she was undergoing antibiotic treatment.

The post prompted dozens of edifying appendicitis stories in the comments section, and now a new study adds some helpful data. But first, the necessary background in the post, from Dr. Douglas Smink of Brigham and Women’s Hospital:

Twenty years ago, Dr. Smink said, surgeons would go in and operate on virtually all cases of appendicitis, whatever the level of inflammation. But research found that for a certain group of patients, it was better to wait. Now, even the “interval appendectomy” is becoming controversial; a newer school of thought holds that some patients may do best with antibiotics alone, no operation at all.

The problem right now, he said, is that there’s some data on the antibiotics-only strategy, but not enough to make clear which patients really need an appendectomy and which can get along without one. Patients who have a stone in the appendix, called an appendicolith, definitely need the organ removed, for example, but many other cases are not so clear cut. More research is needed, he said, to explore the effects of age, severity of illness and other factors on whether antibiotics-only treatment will work for a given patient.

Meanwhile, some studies also suggest that for many patients with uncomplicated appendicitis — the appendix still intact — antibiotic treatment alone may be enough as well.

Continue reading

From McDonald’s To Obama To Prizes, Efforts Ramp Up To Save Antibiotics


You know the antibiotics issue is really getting serious when even the biggest fast food chain in the world gets on the bandwagon — joining the president of the United States, among a great many others.

Last week, McDonald’s announced that it would phase out serving chicken raised with medically important antibiotics. Slate argues that we can surely thank Chipotle, which has long offered antibiotic-free meat, for this move. But whatever the motive, Slate writer Alison Griswold says that when the fast-food behemoth that buys up to 4 percent of the nation’s chicken “decides it’s done with certain antibiotics, you can bet that the agriculture industry is going to listen.”

Meanwhile, President Obama recently proposed doubling the federal funding for research on how to fight antibiotic-resistant bacteria, to $1.2 billion. The CDC estimates that 23,000 Americans die each year from antibiotic-resistant infections. And a headline last week in the journal Science asks if we’re headed back to the bad old pre-penicillin days: A Return to the Pre-Antimicrobial Era?

Got your attention yet? If so, now is the moment to read “Preventing An Antibiotic Apocalypse,” an interview with Boston University health law professor Kevin Outterson. He co-authored a recent Health Affairs piece on economic reforms needed to spur development of more new antibiotics, a theme also explored in a recent New York Times op-ed. Two of Outterson’s most striking excerpts:

If superbug bacteria become endemic in US hospitals, it will shake our health care system at its foundations. Why would you get a hip replacement, or a cardiac stent, or do anything else in a hospital that wasn’t a life-saving emergency, if you knew these infections could kill you?

We have MDR (multidrug-resistant) gonorrhea in the US and around the world. Only one drug remains against the nastiest strains. On the CDC’s threat assessment list in 2014, gonorrhea made the list of the three most dangerous resistant pathogens. We’re close to having no effective treatment for gonorrhea.

We’re almost back to the 1930s. The same is true with XDR (extensively drug-resistant) tuberculosis. Our best treatments for malaria are showing signs of resistance, too. For a number of serious hospital infections, we are down to the last-ditch treatment. Continue reading

Appreciating The Nature In Your Medicine Cabinet

By James Morris
Guest contributor

One of the the most exciting aspects of the recent discovery of the new antibiotic teixobactic was the way scientists discovered it — and where.

The antibiotic comes from a bacterium that was found in a sample of soil from Maine. To uncover it, scientists used a new technique that allowed them to screen bacteria for antibiotics without growing them in culture, opening the door to finding newer, more potent and less resistant antibiotics in the future.

It’s worth noting that teixobactic is not the only antibiotic that comes from a bacterium. In fact, many of our antibiotics come from bacteria and other microbes, and many of our medicines come from nature. It’s one of the benefits of biodiversity.

Recently, I was teaching a class on biodiversity to college students. To get them thinking about how we benefit from species richness, I asked the class to name a couple of medicines that derive from nature.

I thought this would be an easy question. To my surprise, the class (of 250 students) was silent. This was unusual — I usually have more trouble keeping them quiet. Finally, after maybe 20 seconds (a long time in a large lecture hall), a hand shot up. “Marijuana!” one student proudly exclaimed.

I was taken aback. Not because weed was mentioned in a college classroom. And not because the student was incorrect — she was of course correct. Marijuana comes from the plant Cannabis and it has some useful medicinal properties, for example to treat nausea caused by cancer chemotherapy, and fatigue, appetite loss and pain associated with AIDS. There is continued debate over its use, but that’s not the point.

The point is that while the class was hard-pressed to come up with more than one medicine derived from nature, the reality is just the opposite: It’s difficult to think of a medicine that doesn’t ultimately come from nature.

If apples and carrots are nature’s toothbrush, grapes are nature’s jellybeans, and raisins are nature’s candy, then certainly plants, animals, fungi, and microbes are nature’s medicine cabinet.

Perhaps the most famous example is penicillin. Continue reading

Rare Good News On Antibiotic Resistance: Promise Of Tougher New Drug

Northeastern researchers use an "iChip," a miniature device that can isolate and help grow single cells in their natural environment, and was instrumental in the discovery of teixobactin. (Slava Epstein/Northeastern U.)

Northeastern researchers use an “iChip,” a miniature device that can isolate and help grow single cells in their natural environment, and was instrumental in the discovery of teixobactin. (Slava Epstein/Northeastern U.)

Here’s a rare treat: potential good news about antibiotic resistance.

For years, the drumbeat of warnings has grown increasingly dire: The bugs are evolving more and more resistance to our biggest antibiotic guns. Some bacteria — strains of tuberculosis and gonorrhea among them — have even become resistant to all antibiotics. Remember the bad old days before these wonder drugs, when bacterial infections were so often death sentences? No one wants to go back there.

So today’s report in the journal Nature offers a nicely contrasting ray of antimicrobial hope: It reports the discovery in soil of a potentially powerful new antibiotic, dubbed teixobactin (pronounced takes-o-bactin), that appears to be less vulnerable to evolving resistance than other antibiotics.

“Early on, we saw that there was no resistance developed to teixobactin, and this is of course an unusual and intriguing feature of the compound,” says Northeastern professor Kim Lewis, senior author on the Nature paper. The methods used to discover and develop the compound have “a good chance of helping revive the field of antibiotic discovery,” he says.

Northeastern Prof. Kim Lewis, director of the Antimicrobial Discovery Center in the College of Science, researches novel antibiotic treatments. (Brooks Canaday/Northeastern Univ.)

Northeastern Prof. Kim Lewis, director of the Antimicrobial Discovery Center in the College of Science, researches novel antibiotic treatments. (Brooks Canaday/Northeastern Univ.)

Teixobactin worked “exceptionally well” to kill resistant bacteria in mice, Lewis says, but it will take several years and probably over $100 million to develop it into a drug that could be prescribed to human patients. It’s among two dozen other compounds that he and colleagues have turned up using a novel method to develop substances found in soil that could be useful as antibiotics.

Teixobactin works by attacking the biological building blocks of the bacteria’s cell walls, says co-author Tanja Schneider of the University of Bonn. That basic target, which is hard for the cell to modify, may help explain why the bacteria seem unable to develop resistance, she says. Continue reading

If You Find A Tick: Why I Resorted To Mooching Pills To Fight Lyme Disease

A March 2002 file photo of a deer tick under a microscope in the entomology lab at the University of Rhode Island in South Kingstown, R.I. (Victoria Arocho/AP)

A March 2002 file photo of a deer tick under a microscope in the entomology lab at the University of Rhode Island in South Kingstown, R.I. (Victoria Arocho/AP)

I’ve never done anything like this before. I’m a good little medical doobie. I’m wary of pills, take them only with prescriptions, and follow the instructions to the letter. But last month, I “borrowed” a friend’s extra 200 milligrams of doxycycline — the onetime antibiotic dose shown to help prevent Lyme disease soon after a prolonged tick bite.

What brought me to that desperate point? A doctor declined to prescribe the pills, even though this is prime Lyme disease season and the patient, my family member, fulfilled every one of mainstream medicine’s requirements for the single dose aimed at preventing Lyme. To wit:

• The tick was a fully engorged deer tick that had been attached for more than 36 hours.

• We sought treatment within three days of removing it.

• The tick came from a Lyme-endemic area.

• And the patient had no medical reason to avoid antibiotics.

The antibiotics I “borrowed” from a generous friend (Carey Goldberg/WBUR)

The antibiotics I “borrowed” from a generous friend (Carey Goldberg/WBUR)

But still. The doctor argued that the chances of contracting Lyme from the tick were very small, perhaps 1 in 50, and that overuse of antibiotics contributes to the growing problem of drug-resistant bacteria. This is what he would do for his own family member, he said: skip the doxycycline, wait to see if Lyme develops, and treat it with a full 10-day course of antibiotics if it does.

I was frustrated and frankly a bit appalled. WBUR ran a series on Lyme disease in 2012, and I knew that controversy raged around many aspects of the disease, particularly the use of long-term antibiotics to treat long-term symptoms. But I was just trying to follow the widely accepted guidelines written by the Infectious Disease Society of America, to be found in reputable medical venues like UpToDate. And I knew from that same series that Lyme is rife in New England, and so are personal stories of health and lives ruined or seriously harmed.

Still, maybe I was overreacting? I’ve since sought a reality check from three experts, including the lead author of the guidelines. And here’s what I come away with: No, I was not unreasonable in seeking the preventive doxycycline. Arguably, though I hate to admit it, the doctor was not being totally unreasonable in declining it. The guidelines say a doctor “may” prescribe the antibiotic; it’s not a “must.”

In the end, I think, the crux of the question may lie in how you see the doctor’s role: Is it to lay out the risks and benefits and then let the patient choose? Or to impose his or her own best medical judgment on the patient? (You can guess where I come down on that one.) Also, “better safe than sorry” tends to rule when it comes to my loved ones. But what if the risk is small and the benefit uncertain? Continue reading

‘Missing Microbes’: How Hard Should You Resist Antibiotics? And Why

(Photo: R. Zimmerman)

(Photo: R. Zimmerman)

The new book “Missing Microbes” posits that our rampant overuse of antibiotics is not just creating antibiotic-resistant “superbugs”; it is contributing to many of our modern maladies, particularly those affecting children: asthma, allergies, diabetes, obesity.

It’s an idea that has lately been gaining attention and adherents. But you’re especially likely to pay attention and be persuaded when you’re hearing about it from a leading authority on the microbial “ecologies” in our bodies that are damaged by antibiotics: Dr. Martin Blaser, director of the Human Microbiome Program at New York University. Dr. Blaser, who wrote “Missing Microbes,” is in town for a microbiology conference and will be on Radio Boston this afternoon. Our conversation, lightly edited:

As you write, antibiotics are prescribed at incredibly high rates in this country. That’s the big picture, and it’s clear that it’s a problem, but what’s the pragmatic translation? The small picture is something more like a baby who’s been screaming for days and a scared parent who needs to know, just how hard should we resist antibiotics, and in what situations?

We’re starting with perhaps the most difficult question. But you see, in the United States, in order to get antibiotics, you need a prescription. And that means it’s really up to the doctor. And because everyone has thought that antibiotics are ‘free,’ there has been a tendency by both doctors and parents to over-prescribe them and to over-want them. But once you start assigning a cost to them, then the situation changes. And so for parents, I advise them that when their child is sufficiently sick, that they should seek medical attention, and they should try to ensure that the doctor — and that’s shorthand for doctor, nurse, nurse practitioner, physician’s assistant — that the doctor do a careful exam. And then if the doctor says your child does not need an antibiotic, that parent should be relieved. Not thinking, ‘Why is my child deprived?’

But isn’t it so often unclear whether antibiotics are actually needed?

It is unclear, and in fact we know that most of the upper respiratory and ear infections that children have are caused by viruses that don’t even respond to antibiotics. As I write in my book, in the U.S. in 2010, there were 258 million courses of antibiotics prescribed. That’s five courses for every six people. So point number one is that that’s a lot. Point number two is that there’s enormous regional variation — variation that cannot be explained based on variation in the prevalence of different bacterial infections. So that means that it’s a function of how medicine is practiced. And the practice of medicine involves both the doctors and the patients. Both are parties. And what I point out is that in Sweden, where the people are at least as healthy as we are, at every age they’re using 40 percent of the antibiotics that we’re using. And that means, across the board, that 60 percent of the antibiotics are unnecessary. And that’s at every age, not just in childhood –though it’s especially important in childhood at every age. Continue reading

Are Antibiotics Partly To Blame For Obesity Epidemic?



This morning’s On Point with Tom Ashbrook raised a critical question: might antibiotics be “a scale-tipping X-factor” driving the American obesity epidemic?

Featuring reporter Pagan Kennedy, who just wrote a piece on this topic, “The Fat Drug,” for the New York Times Magazine, and researcher, Dr. Illseung Cho, with the New York University School of Medicine, author of a recent Nature article on antibiotics’ impact on the microbiome, the radio segment explored the possibility that missing microbes in our gut might be party responsible for our growing weight.

Who knew, for instance, that a single course of antibiotics can potentially alter your gut bacteria forever?

Here’s more from Kennedy’s report:

American kids are prescribed on average about one course of antibiotics every year, often for ear and chest infections. Could these intermittent high doses affect our metabolism?

To find out, Dr. Blaser and his colleagues have spent years studying the effects of antibiotics on the growth of baby mice. In one experiment, his lab raised mice on both high-calorie food and antibiotics. “As we all know, our children’s diets have gotten a lot richer in recent decades,” he writes in a book, “Missing Microbes,” due out in April. At the same time, American children often are prescribed antibiotics. What happens when chocolate doughnuts mix with penicillin?

The results of the study were dramatic, particularly in female mice: They gained about twice as much body fat as the control-group mice who ate the same food. “For the female mice, the antibiotic exposure was the switch that converted more of those extra calories in the diet to fat, while the males grew more in terms of both muscle and fat,” Dr. Blaser writes. “The observations are consistent with the idea that the modern high-calorie diet alone is insufficient to explain the obesity epidemic and that antibiotics could be contributing.”

MIT Lab Hosts Nation’s First Stool Bank, But Will It Survive?

Bottles of frozen human stool for fecal transplants at the nation's first stool bank, OpenBiome. (Photo: Gabrielle Emanuel/WBUR)

Bottles of frozen human stool for fecal transplants at the nation’s first stool bank, OpenBiome. (Photo: Gabrielle Emanuel/WBUR)

You walk through a labyrinth of MIT buildings and into what looks like a typical laboratory: white walls and clean counters, the constant buzz of machines, the clutter of pipettes. In the corner, you open the door to a hulking freezer.

When the puff of frosty air clears, you see stacks of plastic bottles filled with what looks a little like smoothies — in tawny, rusty colors Odwalla would never market. That’s your first hint of this lab’s unique purpose. Then there’s the giveaway: on the sterile countertop, you see a trophy of a squatting muscleman, labeled “Most Generous Donation.”

Welcome to the first national stool bank. It’s like a blood bank, but for fecal matter. And that brown smoothie is actually very healthy stool, parasite-free and loaded with happy bacteria.

In early October, the stool bank — called OpenBiome — started shipping these bottles around the country. Once that FedEx box of dry ice and stool arrives at the hospital, the doctor can do a fecal transplant — which is exactly what it sounds like. You take a healthy person’s feces and put them into a very sick person’s gut. And if all goes well, a few hours later that sick person is much better.

America is just beginning to develop a stomach for this procedure — it’s gaining popularity among patients and doctors. And by all accounts the stool bank has made things much easier. But there is a chance those stool shipments will come to an abrupt halt.

Late last week, the FDA released a draft of its new fecal transplant guidelines. As they are worded, things don’t look good for the OpenBiome stool bank.

The FDA is thinking about requiring the patient or the doctor to personally know the donor. But that doesn’t work so well for the stool bank, where the donations come from “Donor One” and “Donor Two.” They are anonymous gifts and soon that might not be allowed.

The Ecosystem In Our Gut

But, first things first, why are we even talking about poop transplants? Continue reading

Study Suggests Cell Damage As Potential Danger Of Antibiotic Use

Cipro (Wikimedia Commons)

Cipro (Wikimedia Commons)

By Karen Weintraub
Guest Contributor

Might antibiotics be causing harm at a cellular level? That’s one possible conclusion from a new study by researchers at Boston University.

We’ve long known about the dangers of antibiotic resistance – that one day, the drugs will stop working – and scientists have learned in recent years that antibiotics also kill off “good” bacteria with the “bad.” But now, James J. Collins, a B.U. biomedical engineer, says his research in mice suggests that certain antibiotics, taken long-term, could be damaging our own cells.

In a study published today in Science Translational Medicine, Collins’ team showed that widely used antibiotics like ciprofloxacin and ampicillin can damage the cells’ fuel supply and cause oxidative stress, which has been linked to cancer, heart disease, Alzheimer’s and other ailments.

The research is still early and far from conclusive, but Collins says he thinks it’s convincing enough to at least merit more study.

When he and his colleagues exposed cells in a dish and then mice to these antibiotics over several weeks, they saw signs of serious cellular damage. The doses were similar to those given patients taking long-term therapy. The damage may explain why antibiotics have long been associated with side effects such as tendon, kidney and liver problems, says Collins, also a founding faculty member of the Wyss Institute for Biologically Inspired Engineering at Harvard. Continue reading