Maryn McKenna

Journalist and Author

Superbugs in Canadian chicken? Yes, and US too

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CBC News, the Canadian national TV network, has caused a stir in the food-blog world with the results of a nationwide investigation that found antibiotic-resistant bacteria contaminating supermarket chicken. In its words:

Chicken bought at major supermarkets across Canada is frequently contaminated with superbugs — bacteria that many antibiotics cannot kill — an investigation by CBC TV’s Marketplace has found.

Marketplace researchers — along with their colleagues at Radio-Canada’s food show L’Epicerie — bought 100 samples of chicken from major grocery chains in Vancouver, Toronto and Montreal… The 100 samples were sent to a lab for analysis. Two-thirds of the chicken samples had bacteria. That in itself is not unusual — E. coli, Salmonella and Campylobacter are often present in raw chicken.

What was surprising was that all of the bacteria uncovered during the Marketplace sampling were resistant to at least one antibiotic. Some of the bacteria found were resistant to six, seven or even eight different types of antibiotics.

“This is the most worrisome study I’ve seen of its kind,” said Rick Smith, the head of Environmental Defence, a consumer advocacy group.

I haven’t had time to watch the full program, but no question I think this kind of reporting is worth doing. Nothing brings the threat of agricultural antibiotic use home to people like showing them that resistant bacteria are living on the meat they might have brought home last night.

One important point, though: Don’t think for a moment this is just a Canadian problem.

Last month, a team from the University of Ioannina in Greece analyzed in Foodborne Pathogens and Disease 428 samples of various retail meats they bought in northwest Greece over three years:

E. coli from chicken exhibited high rates of resistance to ciprofloxacin (62.5%) followed by lamb/goat (10.9%), pork (15.7%), and beef (27.9%) meat. Resistance to nitrofurantoin dominated in the lamb/goat isolates (60%). Resistance to tetracycline predominated in pork (68.2%) and chicken (62.5%), and resistance to aminoglycosides dominated in lamb/goat meat isolates. S. aureus resistance to clindamycin predominated in lamb/goat isolates (50%), whereas resistance to ciprofloxacin predominated in the pork strains, but no resistance to methicillin was observed. Of the enterococci isolates 21.1% were resistant to vancomycin. High resistance to ampicillin (96%) was observed in Y. enterocolitica and all of the C. jejuni isolates were resistant to ampicillin, cephalothin, and cefuroxime. These results indicate that meat can be a source of resistant bacteria, which could potentially be spread to the community through the food chain.

Last year, a team from the University of Iceland found fluoroquinolone-resistant E. coli passing from chickens to humans there (the drug Cipro is a fluoroquinolone, and the human isolates were Cipro-resistant), a multi-institution team from Canada found resistance to third-generation cephalosporins in Salmonella enterica spreading from chicken meat to humans, and the Irish quasi-governmental group SafeFood released a long report (and hosted a conference) on “The Problem of Antimicrobial Resistance in the Food Chain.” And of course MRSA ST398, the strain of drug-resistant staph that arose in food animals, has now been found in retails meats across the EU.

Oh, but none of those countries are the United States, you say. Then take a look at these:

Those graphics come from a little-read report put out every year by the US Food and Drug Administration as part of its participation in NARMS, the National Antimicrobial Resistance Monitoring System that’s shared by the FDA, USDA and CDC. The FDA handles the part of NARMS that looks for resistant bacteria in meat (CDC does human illnesses, USDA does live animals), and the figures above show the percentages of Salmonella and enterococci that were found in retail chicken breasts between 2002 and 2008 (the most recent report) and were resistant to various drugs. The bar along the bottom of each figure shows the major drug classes. So in 2008: 45% of Salmonella on chicken were resistant to tetracycline and 30% to penicillins; among enterococci (common gut bacteria, and therefore common contaminants of meat during slaughtering), 65% resistant to tetracycline and more than 90% to lincosamides, which include the everyday drug clindamycin.

In the narrative portion of the report, the FDA said:

38.2% of chicken breast Salmonella isolates were resistant to ≥ 3 antimicrobial classes in 2008 compared to 51% in ground turkey, an increase in both from previous years. From 2002–2007, multidrug resistance to ≥ 3 antimicrobial classes ranged from 20–34.4% among chicken breast and 20.3–42.6% for ground turkey. More than 15% of chicken breast and ground turkey isolates showed resistance to ≥ 4 classes in 2008.

So, just to underline: Multi-drug resistant superbugs aren’t only on chicken in Canada; if you buy chicken in the United States, they are more than likely on your chicken too.

And whatever country they are occurring in, the solution is the same. Drug-resistant bacteria in food won’t diminish until we reduce the amount of drugs that food animals receive while they are raised.

Update: At Grist’s Meat Wagon, Tom Philpott very kindly points out that I actually broke the news of the latest NARMS report, which I didn’t realize (it was a busy day; see my next post for why). Apparently the report was posted to the FDA web site on Dec. 17, but neither of us can find any evidence that it was publicized, such as a press release on the FDA’s press site. His larger point is important:

We find out from the report that the FDA has been monitoring the situation since 2002 — and finding plenty of antibiotic-resistant strains on meat sold directly to consumers. And they’ve been sharing the information with other leading regulatory/public health agencies — but not so much to the people they’re supposed to be protecting and informing: i.e., us. … six weeks since the FDA report and a year since Sharfstein’s testimony [in 2010, promising scrutiny by the Obama adminsitration – m.], policy hasn’t moved at all. Where are the loud public statements from the FDA trumpeting the fact that our factory farms are cooking up superbugs that make their way to our meat? Where’s the USDA on this topic, which is supposed to protect the public from tainted meat? Where’s CDC?

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Brief promo: SUPERBUG is out in paperback!

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A brief pause for self-promotion:

My 2010 book SUPERBUG: The Fatal Menace of MRSA (Free Press/Simon & Schuster) has been released in paperback!

SUPERBUG tells, for the first time, the full 50-year history of the emergence of drug-resistant staph, MRSA, in overlapping epidemics in hospitals and health care, schools and families, and farm animals and agriculture. It’s based on 200 interviews with researchers, public health experts and MRSA victims and their families, and on about 1,100 journal articles dating back to the 1930s.

I’m open to doing a giveaway or a contest for free copies. If you have ideas for one, please leave them in the comments!

Meanwhile, here’s a sample of the praise for the hardback, published last March:

“Lays bare, often all too graphically, the ravages of a disease with the potential to do grievous international harm.” – Booklist

“A gripping account of one of the most devastating infectious agents on the planet… A meticulously researched, frightening report on a deadly pathogen.” – Kirkus

“Scalpel-sharp investigative skills … A scary and important book.” – Teresa Weaver, Atlanta Magazine

“Where will the next major epidemic come from? According to Superbug, that epidemic is already here. It grew out of our hospitals, our prisons and our high-school locker rooms. We fed it with our demand for antibiotic ointments, prescriptions we didn’t need and factory-farmed cows packed together and pumped full of their own antibiotics. We spread it with unwashed hands. The story of MRSA is more prosaic than tales of tracking Ebola through the African jungle, but that’s exactly what makes it terrifying, and fascinating.” – Maggie Koerth-Baker, BoingBoing.com

“During her years as a reporter covering the Centers for Disease Control and Prevention for the Atlanta Journal-Constitution, Maryn McKenna grew accustomed to being called ‘Scary Disease Girl,’ the bearer of titillating tales of exotic ailments unlikely to affect most people. McKenna’s new book, Superbug, is less deliciously frightening and more just plain scary.” – Alexia Elejalde-Ruiz, Chicago Tribune

“”If you want the short version, Superbug: The Fatal Menace of MRSA is a must read… McKenna makes it clear that this epidemic arose and persists because of human error.” – Mike The Mad Biologist, ScienceBlogs

“A readable, well-referenced, detailed and enjoyable book… Superbug: The Fatal Menace of MRSA is painstakingly researched and credit should go to Maryn McKenna for presenting some of the issues surrounding the emergence of community-associated MRSA in a way that is readily accessible to the general public.” – Jonathan Otter, Lancet Infectious Diseases

“Superbug provides a vivid and gripping account of the spread of MRSA and should be required reading at the US Food and Drug Administration.” – Yee Huang, Center for Progressive Reform

“Through powerful storytelling, Maryn McKenna has given voice to people who have suffered at the hands of a fast-changing health threat. Superbug reminds us all that, in an age of global epidemics, our vigilance must be global, too.” – Helene D. Gayle, M.D., president and CEO of CARE

“Maryn McKenna’s compelling history proves that antibiotic resistance is a global concern. The story of drug-resistant staph actually begins in the United Kingdom in the 1940s, with the introduction of penicillin. It continues  to this day, as staphylococcus continue to develop resistance to new antibiotics as soon as they are introduced, not only in the United States but everywhere where antibiotics are used – and misused – in today’s globalized world.” – David L. Heymann, M.D., Chair, the Health Protection Agency of the United Kingdom

“As compelling as a detective novel, Superbug tells the stories of the victims of MRSA to explain how this pathogen evolved into so serious a threat to human health and medical practice. The book reveals the inextricable links between human and animal health and the disastrous consequences for human health of using antibiotics to promote the growth of farm animals. McKenna has written a devastating critique of current systems of animal agriculture, health care, and drug development, as well as the politics of research. The solution to MRSA, she says, is a vaccine. But where is the political will to pay for it?” – Marion Nestle, Professor of nutrition, food studies, and public health at New York University, and author of Safe Food: The Politics of Food Safety

“Like a modern-day Rachel Carson, Maryn McKenna sounds a powerful alarm about the insurgency of a deadly infection lurking in our schools, our gyms and even our food.  Antibiotics are losing their life-saving powers because of our injudicious use that has helped spawn these increasingly invincible pathogens.  By connecting the dots, Superbug may give us the early warning we need to prevent an uncontrollable epidemic.” – Shelley A. Hearne, Dr. PH, Managing Director, Pew Health Group, The Pew Charitable Trusts

“Maryn McKenna tracks the harrowing biography of MRSA with all the skills of a first-rate investigative journalist. Superbug reads like a thriller and is presented in a nuanced and eloquent prose that is as infectious as the microbe it details.” – Howard Markel, M.D., Ph.D., George E. Wantz Distinguished Professor of the History of Medicine, The University of Michigan; author of When Germs Travel

“Superbug is essential for anyone going to the hospital or working in healthcare. Too often even top doctors dismiss the threat, saying ‘the germs are everywhere.’ Patients and medical professionals should read this book and take its lessons seriously.”
– Betsy McCaughey, Ph.D., Founder, Committee to Reduce Infection Deaths

New antibiotics: Not many and fewer all the time

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The New England Journal of Medicine last week published the results of a Phase 3 trial of a new antibiotic called fidaxomicin, made by a company called Optimer Pharmacuticals. Fidaxomicin is the first of a new class of antibiotics called macrocycles; it’s a narrow-spectrum drug aimed specifically at Clostridium difficile, the bacterial, toxin-producing, potentially fatal infection of the gut that occurs when broad-spectrum antibiotics have killed off the other populations of bacteria that normally live in the intestines.

Fidaxomicin’s existing competition is vancomycin, the 50-year-old broad-spectrum big gun used for MRSA and many other serious bacterial infections. As compared against vancomycin, fidaxomicin was “noninferior,” in industry jargon; its selling point was a lower rate of recurrence of C. diff among patients who received it compared to those getting the older drug. From the paper:

A total of 629 patients were enrolled, of whom 548 (87.1%) could be evaluated for the per-protocol analysis. The rates of clinical cure with fidaxomicin were noninferior to those with vancomycin in both the modified intention-to-treat analysis (88.2% with fidaxomicin and 85.8% with vancomycin) and the per-protocol analysis (92.1% and 89.8%, respectively). Significantly fewer patients in the fidaxomicin group than in the vancomycin group had a recurrence of the infection, in both the modified intention-to-treat analysis (15.4% vs. 25.3%, P = 0.005) and the per-protocol analysis (13.3% vs. 24.0%, P=0.004). The lower rate of recurrence was seen in patients with non–North American Pulsed Field type 1 strains. The adverse-event profile was similar for the two therapies. (NEJM Louie et al.)

Fidaxomicin has been in the works for a while — it was given Fast Track status by the Food and Drug Administration back in 2003 — and it has faced some criticism for not being different enough from vanco to justify the price that a new drug can charge. Nevertheless, on the basis of this and other trials, Optimer has completed its New Drug Application, and the FDA’s Anti-Infective Drugs Advisory Committee will review it at a meeting in April.

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Opposing industrial-scale pig farming — in Europe

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Well, wow. National legislators stand up to oppose the use of tax revenues to subsidize large-scale confinement pig farms out of concern for food safety and antibiotic resistance, declaring that they are “going to war in defense of pigs.”

In Europe, though.

At the European Parliament today, three national representatives — Janusz Wojciechowski of Poland, José Bové of France and Dan Jørgensen of Denmark — declared their opposition to industrial-scale swine agriculture, positioning themselves for a fight over the European Union’s Common Agriculture Policy, which is up for revision this summer.

Jørgensen represents the country that has done the most to place controls on agricultural antibiotic use; Bové is a farmer and political organizer who famously destroyed a McDonald’s by driving a tractor through it; and Wojciechowski is the son of pig farmers who wrote on his blog today:

Chcemy poruszyć sumienia posłów i doprowadzic do likwidacji tego typu “fabryk miesa” w Unii Europejskiej, no czywiscie takze w Polsce, gdzie takich fabryk jest juz ponad sto.
Chcemy doprorowadzic do tego, aby wielkie fermy nie były wspierane środkami europejskimi, aby wstrzymać lokalizacje nowych obiektów, po czym stopniowo likwidować te, które już istnieją.
Chcemy, żeby na miejsce fabryk miesa powróciła normalna hodowla świń.
We want to move the conscience of members and lead to the liquidation of this type of “meat factories” in the European Union, also in Poland, where such plants are already over a hundred.
We want to ensure that large farms are not supported by the European funds to stop the locations of new facilities, then gradually eliminate those that already exist.
We want “meat factories” returned to normal breeding of pigs. (via GoogleTranslate)

As I’ve written before (long archive here and here),the MRSA strain ST398 arose on Dutch pig farms in 2004, among pigs that had been given prophylactic doses of antibiotics, especially tetracycline. It has since spread through the EU, Canada and the United States, affecting not only farm workers and veterinarians, but also hospital patients with no connection to agriculture.

(Self-promotion alert: This may be a good time to tell you that my book SUPERBUG: The Fatal Menace of MRSA, which tells the full story of the emergence and spread of ST398, has just been released in paperback.)

In advance, this morning the trade paper Farming UK wrote this about the planned European Parliament announcements:

(Members of the European Parliament) will hear evidence that European taxpayers’ money is being used by the European Bank for Reconstruction and Development, together with Common Agriculture Policy payments, to subsidise industrial pig farming even though there is increasing concern over the impact on human health. With a vote this summer over reforms to the Common Agricultural Policy, MEPs will come together to take a stance against the crisis in agriculture with critically low prices for pork, poor labelling, and widespread disregard for animal welfare laws.

MEPs and NGOs will condemn the overuse of antibiotics in factory farms which has led to the emergence of antibiotic-resistant bacteria such as MRSA and ESBL E. coli. A recent report by the Dutch Food Standards Agency estimated that one third to one half of all antibiotic resistance in human diseases in the Netherlands derives from farm antibiotic use. American scientists recently found that flies and cockroaches from intensive pig farms carry bacteria resistant to the same antibiotics routinely used in pig farming, and warned that the insects were likely to be able to spread the disease from the farms to local people.

The event was co-organized by Tracy Worcester, who is both a British aristocrat and director of a documentary, Pig Business, that has not yet been shown in the US. Here’s its trailer:

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In both medicine and agriculture, Europe has been ahead of the US in addressing concerns about antibiotic resistance. This morning’s announcements are yet more evidence of just how far ahead they are.

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Disease v. culture: Botulism in the Arctic

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What if there were a food whose consumption carried a predictable risk of contracting a  fatal illness?

What if consumption of that food were so deeply embedded in a culture that there was no chance of stopping people from eating it?

That’s not a hypothetical. It’s the dilemma facing Arctic indigenous communities and health authorities over the risk of botulism from traditional foods — raw fish, whale, seal, walrus or beaver — that are “cured” by being wrapped, buried and left to rot. Alaskan Natives and Canadian First Nations members have eaten them since some lost time in their history: They’re full of minerals, vitamins and beneficial fatty acids, fresh-food nutrients that are in short supply when the world is frozen over and dark.

(I hear you gagging. So: Who eats country ham? Fish sauce? Roquefort? Products of rot, all of them. We’ll move on, shall we?)

The traditional foods aren’t fermented, strictly speaking; they’re decayed in an airless environment. That makes them friendly breeding grounds for Clostridium botulinum, the organism that produces botulism toxin. Since 1947, according to two new papers in Clinical Infectious Diseases, there have been 317 cases (159 small outbreaks) of foodborne botulism just in Alaska, as tracked by the Indian Health Service and the Alaska Division of Public Health. Out of the 317 individual cases in those records, 8.2 percent died of the paralysis of botulism poisoning.

Measured against the population, the rate of botulism in Alaska is 836 times what it is in the Lower 48. It’s such a persistent problem that the Alaska division spends scarce funds to maintain a 24-hour botulism emergency line.

There’s something interesting hidden in those numbers: Since the 1970s, the incidence of foodborne botulism has been increasing. That’s roughly coincident with the point at which Native communities began a transition that must have looked like a good idea, from

placing meat and fat tissues into skin bags … which are sewn shut and aged for weeks or months under rocks or buried under gravel

to

us(ing) either plastic bags or buckets, metal barrels, or glass containers in place of the skin pouch. (Austin and Leclair)

It turns out that something in the modern materials may have increased the possibility of C. botulinum growth: maybe the temperature differential, since they are more likely to be kept above ground; maybe the lack of contact with soil microorganisms. (A hypothesis-generating experiment showed that salmon heads kept for 17 days in a plastic container produced botulinum toxin, but salmon heads buried in a moss-lined pit did not.) One of the papers notes:

Among outbreaks for which a preservation process was described, 67% (56 of 84) were associated with storage of food in sealed plastic or glass containers, 23% (19 of 84) with storage in wood or cardboard containers, 6% (5/84) with storage in sealed metal containers, 4% (3/84) with storage in moss- or tundra-covered holes, and 1% (1/84) with storage in a sealskin bag. (Fagan et al.)

The cured foods are so intricately tied to family, tribe and place that repeated rounds of public health education haven’t dislodged them from Inuit culture. One paper notes, rather wistfully:

…an educational botulism video was distributed to all rural schools and medical facilities in Alaska, but 1 year after distribution, only 38% of Alaska Native adults had seen the video, and no behavior changes were noted that might reduce risk for botulism. (Fagan et al.)

But modernity might yet prove the cure, in two dimensions. First, the mortality rate from botulism is going down, to less than 4 percent in recent years, probably because cases are recognized and antitoxin distributed faster than in decades past. Second, and probably more important in the long run, the taste for traditional foods may be passing from Native culture. Of those 317 cases,

Overall median age was 45.0 years (range, 5–93 years). Incidence was associated with age group; age group–specific incidence was greatest among Alaska Natives aged ≥60 years. … Patient age increased from 1970–1979 (median age, 39.0 years) to 2000–2007 (median age, 49.5 years). (Fagan et al.)

If younger generations of Inuit no longer care for traditional foods, the risk of botulism will naturally diminish: no anaerobically rotted salmon heads, no Clostridium, no deaths. It ought to be something to rejoice in. I wonder though. There’s something especially compelling about foods tinged with risk; think of foraged mushrooms, or puffer fish. Inuit foods — which, I confess, I can’t quite imagine eating — must have offered deliciousness and danger, and comfort, and memory. It would have been a potent, and poignant, combination; for all its harms, a sad thing to lose.

Cites:

Austin JW and Leclair D. Botulism in the North: A Disease Without Borders. Clin Infect Dis. (2011) 52 (5): 593-594. doi: 10.1093/cid/ciq256

Fagan RP et al. Endemic Foodborne Botulism among Alaska Native Persons—Alaska, 1947–2007. Clin Infect Dis. (2011) 52 (5): 585-592. doi: 10.1093/cid/ciq240

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Farm antibiotics, human illness and what connects them. (It has legs.)

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When it comes to the impact of farm antibiotics on human health, there’s a data gap.

That the use of antibiotics on conventional/confinement farms provokes the emergence of drug-resistant bacteria really isn’t in dispute; it’s been proven, over and over again, for about 30 years now. (Here’s a long bibliography from the Pew Charitable Trusts that lists the major pieces of research.) And there’s good research as well that those bacteria move off farms via animals, farm workers, groundwater and air currents. (Another long bibliography here, from the Center for a Livable Future.)

But proving the links between resistant farm bacteria and human illness is trickier. Among the reasons: When an individual person who is sick with a foodborne illness goes to the doctor, that doctor does only enough testing to figure out how to treat them. The kind of subtyping you would need to do on a foodborne organism to prove its farm-drug link isn’t useful to a primary-care physician, and the equipment isn’t accessible either; it’s found in academic medical centers and state public health labs. But the public health system isn’t filling the data gap either. The CDC’s main foodborne outbreak-tracking program, FoodNet, monitors the prevalence of 10 illness-causing organisms, but doesn’t test for antibiotic resistance. And the joint federal program that does monitor resistance, NARMS (for National Antimicrobial Resistance Monitoring System, shared by the CDC here, USDA here and FDA here) uses randomized anonymized samples from humans, animals and retail meat, so it can’t illuminate whether resistant bacteria are causing outbreaks.

So are resistant bacteria from farms causing outbreaks of human illness? The Center for Science in the Public Interest says yes. In a white paper published this week, the group documents 35 outbreaks between 1973 and 2009 for which epidemiologic and microbiological links are clear. Quoting from the report:

  • Reporting of outbreaks due to antibiotic-resistant bacteria has increased in each decade since the 1970s, with 40% (14 out of 35) occurring in the last decade … Outbreaks were most common in dairy products (34%) and ground beef (26%). Two outbreaks each were linked to poultry, pork, produce, and seafood, and one outbreak each was linked to eggs and multi-ingredient foods. The food vehicle was unknown in four of the outbreaks.
  • A total of 19,897 people were sickened from these 35 outbreaks, resulting in 3,061 hospitalizations and 26 deaths.
  • For the 31 outbreaks for which antibiotic-resistance patterns were determined, the responsible bacteria displayed resistance to a total of 14 different antibiotics … Of those antibiotics, seven are classified by the World Health Organization (WHO) as ‘critically important’ to human medicine and eight as ‘highly important’ to human medicine. Bacteria showed resistance to tetracycline in 30 outbreaks. Resistances to streptomycin and ampicillin, both classified as critically important antibiotics, were the next most common. Bacteria associated with 19 outbreaks were resistant to at least five antibiotics. Fifteen of those occurred between 1990 and 2009.

There’s still a data gap, of course: Exactly how are the organisms getting from the animals or their manure into the guts of humans? Via meat, or milk, is the logical assumption. But an article also published this week suggested the organisms might have help — from cockroaches and flies.

Researchers from Kansas State University and North Carolina State University scooped up house flies and German (common) cockroaches on conventional confinement farms in both states, and also scooped up poop from the pigs being grown on the farms. They tested all three for the presence of resistant forms of the common gut bacteria Enterococci. Almost all — 89 percent of the pig-manure samples, 94 percent of the cockroach guts and 98 percent of the flies’ guts — contained Enterococci. Of the Enterococci, at least 90  percent of those found in each species were resistant to tetracycline; from 50 percent to 70 percent were resistant to erythromycin; and from 10 percent to 40 percent were resistant to ciprofloxacin and streptomycin — NB, all drugs used in essentially identical forms in humans as well as livestock. PFGE analysis of the Enterococci from the pigs and the insects showed they were carrying the same bacterial clones.

The researchers write:

Organic wastes in and around animal production
facilities including swine farms provide excellent habitats for house flies and German cockroaches. Several features of house flies and cockroaches, including their dependence on live microbial communities, active dispersal ability and human-mediated transport, attraction to places where food is prepared and stored, developmental sites, and mode of feeding/digestion make these insects an important “delivery vehicle” for transport of bacteria including antibiotic resistant enterococci from reservoirs (animal manure), where they pose minimal hazard to people, to places where they pose substantial risk (food)…

High frequency of resistance to tetracycline, erythromycin, streptomycin, kanamycin, and
ciprofloxacin in our study likely reflects use of tetracyclines, macrolides, aminoglycosides and
fluoroquinolones as feed additives for swine in the USA… The source of antibiotic resistant
enterococci in house flies and cockroaches in this study was the swine manure due to very high
prevalence of antibiotic resistant enterococci in all three sources.

Cite: Ahmad, A et al. Insects in confined swine operations carry a large antibiotic resistant and potentially virulent enterococcal community. BMC Microbiology, 26 January 2011, 11:23doi:10.1186/1471-2180-11-23

Food bin Flickr/j_bongio/CC; Fly face Flickr/e_monk/CC

Spreading cholera, maybe polio: Now will we care about Haiti?

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It’s been two weeks since the one-year anniversary of the devastating Haitian earthquake, and the ongoing crisis in that desperately poor island has once again sunk below the news-radar horizon. Which is of course outrageous: Most of the infrastructure has still not been rebuilt, and 800,000 people are still living in tent cities parked precariously in the rubble. The non-profit Oxfam has pinned some of the responsibility on Haiti’s long-standing political chaos: “It doesn’t matter how much money you pour in unless you build up a government that is strong enough to take decisions.” Simultaneously, the United Nation’s special envoy, former Canadian Governor-General Michaelle Jean, has scolded the  industrialized world in an open letter published on the anniversary: “What began as a natural disaster is becoming a disgraceful reflection on the international community.”

Well, maybe this will get their attention.

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Dangerous makeup: Eyebrow tattoo infections

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Girly confession: I love makeup. I cannot get through an airport in Asia without hitting the cosmetics kiosks. I spent a half-day in Paris last summer tracking down a cult eyeshadow shade. I once lured every woman in my newsroom into testing long-wearing lipsticks against caffeine, pizza and a workout in the building’s gym.

But for all my obsession, I’ve never been interested in permanent makeup. Partly that’s because I love the process — the brushes, the textures, the ritual — as much as the results. Probably also I feared poor technique: I know how hard it is to draw a perfect cat’s-eye, but if I make a mistake, I can wipe it off and try again. And I imagined there were infection risks, though the few papers in the medical literature focus on mistakes and dissatisfaction more than they do on bad bugs.

Turns out that last was a reasonable fear. A new paper in Clinical Infectious Diseases describes a cluster of infections in Switzerland among women who had their eyebrows improved with tattooing: 12 developed infections with Mycobacterium haemophilum, 10 required surgery, and 9 required excision not only of an eyebrow but also all or part of a parotid gland — the big salivary gland in front of the ear through which a major facial nerve travels.

The women came into the infectious-disease practice of the Centre Hospitalier Universitaire Vaudois in Lausanne over 8 months, starting in April 2009. They all had the same symptoms: From two to seven weeks after getting their tattoos, they developed rashes and pustules at the site where they had been inked, followed by pain and swelling in the parotid nearest the infected eyebrow. (Weirdly, the paper says each woman had only one eyebrow infection, as though they were not tattooed on both sides of the face at the same time.) The glands in eight of the 12 abscessed, and 7 developed a fistula, meaning the infected gland started draining through their skin. (That looks like this.)

M. haemophilum is a tough bug; like its distant relative M. tuberculosis, it requires a multi-drug cocktail that can last for weeks. The women took antibiotics for two months without much success before the doctors decided surgery was necessary, and at least three months afterward. Seven of them had to stop or switch drugs during their treatment, for side effects that ranged from white blood cell suppression to elevations in liver enzymes to rashes and nausea.

When the physicians looked for what connected the women, they discovered that they had gotten their tattoos in different studios, but all from the same artist, who freelanced around the area. When they tracked her down, they found that she was following all the correct infection-prevention procedures, though she no longer had the equipment she had used when the women’s infections developed. When they tested her inks, though, they found DNA from M. haemophilum in some of them. Because that bacterium tends to live in water, they hypothesized she had diluted her inks with tap water that was locally contaminated.

The tattoo artist told them that, during the time the 12 women developed infections, she had done permanent makeup on about 400 women. She hhad no way, though, of tracking those clients down.

I think I’ll stick to Lancome.

Cite: Giulieri S, Morisod B, Edney T et al. Outbreak of Mycobacterium haemophilum Infections after Permanent Makeup of the Eyebrows. Clin Infect Dis. (2011) 52 (4): 488-491. doi: 10.1093/cid/ciq191

Flickr/Jeff_Werner/CC

ScienceOnline 2011: Do old ethics apply to new media?

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It’s been so long since ScienceOnline 2011 (started a week ago, ended Sunday) that I am almost embarrassed to post on it. (It was a long drive. I came back to monster deadlines. I’m moving. OK, enough sniveling.)

But as I mentioned last week, I was involved at the conference in a discussion about how — and whether — to bring the standards of journalism to blogging, in a session that veteran journalist Paul Raeburn kindly asked me to join. As a long-time journalist myself, I think this is an important question, so I’m tossing my thoughts and our materials up here to see if anyone reacts.

Here’s the program description of our session:

The web in many cases has undermined the wall that traditionally separated reporters from advertisers in 20th century offline journalism. One example is placing pop-up ads in blogs without the bloggers’ permission. With new models of web advertising and funding appearing daily, it seems, can we keep reporters independent? And what does it mean to be independent when a website is supported by a foundation, or a single advertiser or patron? Bloggers share responsibility for the credibility of their sites with their employers, advertisers, or other supporters. How do we make sure that the new financing models do not destroy our credibility?

Background: There’s an active ongoing debate over whether blogging is journalism and whether bloggers are journalists; both those links go to posts by Bora Zivkovic (editor of Scientific American’s blog network and co-founder of Science Online with Anton Zuiker).

So: Constant readers will remember that I spent most of my career to date within the mainstream media as a newspaper reporter, exiting 4 years ago to blog and write for magazines. Legacy journalism did many things badly, but one thing I’ve always felt it did well was to establish a shared ethical understanding. Whether or not your organization’s code was actually written down — most were by sometime in the 1990s, and many are collected here by the American Society of News Editors — everyone in newspapers, from their earliest days on the night cops beat, understood what the shared principles were.

If you asked a reporter about their ethics, you might have gotten something offhand like “Don’t have sex with someone you are writing about,” or “Don’t take money from an organization on your beat,” or “Always be sure the person you are interviewing understands you are a journalist and not just someone chatting them up while on line in the bank.” But laying flippancy aside, those rules would all have aspired to the same result, of attempting to ensure that what appeared under the institution’s banner was as fair and complete as possible given time and production constraints, and that the people producing it had no undeclared biases or hidden allegiances.

Well: Here we are on the web, in a world where journalism is done by legacy media organizations who’ve made the online transition (e.g. the New York Times), new journalism organizations who operate only online (e.g. Pro Publica), and solo practitioners who come at writing from an array of backgrounds and experiences that they may or may not have declared. As the Pew State of the News Media report put it in 2009:

Power is shifting to the individual journalist and away, by degrees, from journalistic institutions… Through search, e-mail, blogs, social media and more, consumers are gravitating to the work of individual writers and voices, and away somewhat from institutional brand.

When I worked for an institutional brand, it conferred several things upon me: a regular paycheck, access to tech support people who were not me, and coverage by an ethics code that someone else had written and that I only had to agree to. Replacing the paycheck and the tech support were straightforward tasks, though difficult. Replacing the ethics code took more thought. Did I need to state my own best practices up front?

I decided I did. On the index page of Superbug’s original incarnation at Blogger, I ran the text block in the screenshot at right. It followed me to Scienceblogs, and then back again to Blogger after I left Scienceblogs in the wake of Pepsigate. In fact, having put up that declaration played a large part in why I left; having put my marker on the table, I had to live up to it.

(Alert readers may have noticed that I have no such block here at Wired. It’s ready and waiting for as soon as we get customizable back pages, which are promised soon; until that happens there is nowhere in the page template to put it.)

So, this is my own answer to the question of how to maintain journalism standards on the web, which is for someone operating independently, as I do now, to find (or write ) and declare one’s own ethical code. For me, it hasn’t been necessary to write one, because there are existing ones with which I entirely agree: the code of the Society of Professional Journalists, and the additional statement of principles of the Association of Health Care Journalists, where I am a board member. I subscribe to both because, while SPJ’s code is excellent overall (its subheds, each with much text under them, are Seek truth and report it; Minimize harm; Act independently; and Be accountable), the AHCJ’s code speaks specifically to what I do as a science/medical writer. Among its provisions:

  • Understand the process of medical research in order to report accurately… It is misleading to report bold or conclusive statements about efficacy in Phase I trials since the primary goal of Phase I trials is to evaluate safety, not efficacy.
  • Be cautious in reporting results of preliminary studies, in vitro or animal studies. Give accurate portrayals of the status of investigational drugs, devices and procedures, including significant caveats and explanations of hurdles, unknowns and potential problems.
  • Preserve journalistic independence by avoiding the use of video news releases or the use of quotes from printed news releases. Label and credit the source whenever a portion of a video or printed news release is used.
  • Refuse gifts, favors, and special treatment. Refuse meals from drug companies and device manufacturers and refuse to accept unsolicited product samples sent in the mail.
  • Weigh the potential benefits involved in accepting fees, honoraria, free travel, paid expenses from organizers of conferences or events against the desire to preserve our credibility with the audience and the need to avoid even the appearance of a conflict of interest.

These codes speak to my work as a solo practitioner. What about the actions of a publisher or blog platform? There are existing principles that cover their actions as well, which could be declared and/or linked to. In the case of Pepsigate, for instance (which, for those who weren’t reading last summer, involved Seed Media, publisher of Scienceblogs, running a corporate-written advertorial blog without labeling it as such), the American Society of Magazine Editors has standards for advertorial in print, and also a codicil that addresses advertorial and other promotional content on the web. Another option is the more than a decade old HON Code, developed by the Health on the Net Foundation, which asserts that any health-information site carrying its badge ascribes to certain ethical principles.

During our session (which was streamed and taped; I’ll embed the video when it gets posted), Paul read a statement from Mary Knudson, who had planned to moderate but was unable to attend. The full post, which guested on Deb Blum’s blog last October, describes Mary’s experience starting a blog for US News & World Report and discovering her text had been adorned with hover ads that she had not been consulted about. Unable to square the implicit endorsements with her own desires for transparency and autonomy, she turned the blogging contract down.

Mary’s experience suggests the next ethical battleground. New media pioneer and chronicler Scott Rosenberg, who was kind enough to come be part of our engaged audience, pointed out that the principles I’ve linked/excerpted above barely apply to the kind of web writing being produced by firms such as Demand Media in response to (or anticipation of) Google search results. (Here’s a 2009 Wired story on Demand.)

The reactions we’ve had so far, that I know of:

In a really great (and not because he praises us) post, Dave Mosher, staff reporter at Wired Science, backs Paul’s-Mary’s-my comments, points out how cumbersome handling disclosures and transparency can nevertheless be, and proposes a tech solution (I’m in.):

There’s got to be a way we can quickly and cleanly allow readers to see writers’ baggage without marring a design or taxing the flow of writing. Editors are impatient, writers don’t have extra time and designers sure as hell don’t want to add yet another unstable widget to a teetering mountain of code…
Let’s create an easy-to-use, icon-based platform that clearly communicates disclosures and the context of content. Imagine the magical association of  Twitter and Facebook buttons with a set of expected behaviors, merged with the pervasiveness and diversity of traffic signs. Now hover over those icons and read statements about disclosures.

On the other hand, Bora, and also Christina Pikas, point out that not everyone who blogs wants to function as a journalist. I acknowledge that. (And I think there was a tweetstream about it during our session, but we were short a back-channel  moderator so I don’t know who was speaking.) Once we get the video, I hope to transcribe Ed Yong’s comment in our SciO session, which said (reconstructing freely from memory) that whether or not people intend to act as journalists in their blogging, they may nevertheless be construed as such by their readers.

This has turned out to be my longest post yet. Any comments, anyone who has stuck with me thus far?

Flickr/Laineys Repertoire/CC

ScienceOnline 2011 — and you can watch too

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Along with a majority of my Wired Science colleagues, I’ll be in North Carolina this weekend attending and speaking at Science Online 2011, a crazy-intense weekend that some smart person called the Bonnaroo of science blogging. SciO11 draws “scientists, students, educators, physicians, journalists, librarians, bloggers, programmers and others interested in the way the World Wide Web is changing the way science is communicated, taught and done,” in the words of the organizers — and registration this year sold out in 45 minutes. I’m privileged to be going.

Out of the packed program, here’s what I’ll be panelizing about (SciO is an unconference, so being a panelist means being a discussion leader for an engaged audience, not an academic-style PresenterGod):

Blogs as a book-writing tool, along with Sheril Kirschenbaum, author of The Science of Kissing; Seth Mnookin, author of The Panic Virus; and Brian Switek, aka Laelaps here at WiSci, and author of Written in Stone.

How to explain science in blog posts, along with nine awesome bloggers from journalism and academia.

And, as a last-minute substitution, How can we maintain high journalism standards on the web?, with veteran journalism Paul Raeburn, currently with the Knight Science Journalism Tracker.

You can follow the chatter from SciO11 at the Twitter hashtag #scio11 or via livestream here thanks to a generous grant from the National Association of Science Writers, of which I’m proud to be a member. If you have questions or thoughts, I’d love to hear them below.

Cartoon courtesy xkcd.com

Farm worker infections with MRSA — the first numbers

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Since the first identification in 2004 of MRSA ST398, also known as “pig MRSA” or livestock-associated MRSA (archives of posts here and here), that drug-resistant organism has been found being carried asymptomatically by farm workers and veterinarians, and causing illness in health care workers, hospital patients, and people with no known ties to agriculture. One of the persistent data gaps, though, has been whether farm workers themselves have been made sick by it.

It’s a difficult question to answer for a nested set of reasons: First, in most of the states, MRSA (methicillin-resistant Staphylococcus aureus, or drug-resistant staph) is not a reportable disease; that is, a doctor who diagnoses it in a patient is under no obligation to tell any public health authority about that patient’s case. And second, the testing required to distinguish livestock-associated MRSA from community-acquired or hospital-acquired is not something that primary-care medical personnel have access to; you have to go to a state laboratory or an academic medical center to do the appropriate molecular typing. Those tests are expensive to perform, and their results primarily are useful to public health, not to individual medical practitioners. So finding out where that nascent epidemic is going has been unusually challenging.

Comes now a team from the University of Iowa — the same team that first identified ST398 in pigs and pig-farm personnel in the United States — to start to fill the gap. [Read more…]

Disease detectives and the 12th blue man

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Pretty much every disease-detection geek — which includes me, since I wrote a book about disease detectives — has read, at some point, the story “Eleven Blue Men” by Berton Roueche. Roueche was a journalist who worked for the New Yorker for almost 50 years, and for most of that time, he was responsible for the column “The Annals of Medicine,” which was created for him. “Eleven Blue Men” was the first installment. It ran June 5, 1948. It begins like this:

At about eight o’clock on Monday morning, September 25, 1944, a ragged, aimless old man of eighty-two collapsed on the sidewalk of Dey Street, near the Hudson Terminal. Innumerable people must have noticed him, but he lay there alone for several minutes, dazed, doubled up with abdominal cramps, and in an agony of retching. Then a policeman came along. Until the policeman bent over the old man, he may have supposed that he had just a sick drunk on his hands; wanderers dropped by drink are common in that part of town in the early morning. It was not an opinion that he could have held for long. The old man’s nose, lips, ears, and fingers were sky-blue.

[Read more…]

News break: First guidelines for treating MRSA

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For my book SUPERBUG: The Fatal Menace of MRSA (came out last March; paperback will be out in February), I spent several years talking to about 100 victims of antibiotic-resistant staph, and family members of victims who did not survive their infections. There were some striking things about their stories.

One was the variability of the bug, which can cause anything from mild one-time skin infections to lethal necrotizing pneumonia, adding up to almost 19,000 deaths, 369,000 hospitalizations and possibly 7 million medical office visits a year. The other was the variability of the patients’ treatment. Some had the good luck to find physicians who knew about the bug, understood the layers of testing needed to determine the best antibiotics to use, and were sensitive to the possibilities of over- and under-treatment. Others were not so lucky: They went to doctors who didn’t recognize the infection, didn’t prescribe drugs that worked, didn’t have anything to offer when the infection recurred — a whole panoply of errors.

It was a lesson for me in how long it can take news of a new medical development to percolate through the clinical community, especially to primary-care practitioners — people who don’t have a channel for new news because they don’t work for an academic medical center or belong to a specialty society that puts out a journal or at least a substantial newsletter. But it was also a lesson on how few agreed-upon standards of practice there were for treating MRSA. For many presentations, there was no evidence refer to; clinicians were thrown back onto poring through the literature, or on making educated guesses based on their past experience.

As of this week, that should change. The Infectious Diseases Society of America has publshed the first-ever clinical practice guidelines for treating MRSA in adults and children. It’s a substantial document, 38 pages (in the advance access section of Clinical Infectious Diseases) and should be a tremendous resource for patients and their physicians. (I know of one patient who printed it out yesterday and took it to an office visit — only to find the physician had just downloaded a copy himself.) [Read more…]

The Wakefield fraud and the return of whooping cough

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By, now, 24 hours later, I imagine that everyone who cares about the subject has read or heard about the BMJ’s masterful assessment and rejection of the original paper that linked childhood vaccines and autism, calling it an “elaborate fraud” perpetrated by a researcher who had entered into a relationship with class-action attorneys. (Here are the BMJ’s editorial, the first part of the investigation, and the concurrent blog by the journalist who pursued the story for almost a decade.) That original paper, by a British physician named Andrew Wakefield whose license to practice has since been revoked by the UK’s General Medical Council, did untold damage to public health: It sparked a distrust of vaccines that has led to the return of almost-beaten diseases around the world.

The BMJ’s pronouncement and its larger significance for distrust of vaccines have been thoroughly covered by major media (CNN, Associated Press) and by a number of good bloggers, including Orac,  PZ Myers and Seth Mnookin (author of a forthcoming book on vaccine refusal). I’ve been wondering what I could add to the discussion. In the end, I thought I’d re-run this, a post from last summer when Superbug was still at Blogger. It’s a look at the return of those potentially deadly diseases from the perspective of a patient, who happened to be me.

A few years ago, I went to India on a reporting trip. When I came back, I had a troublesome cough. I figured I’d picked up a bronchitis aggravated by New Delhi’s smog-laden air, or by the dung smoke from the fires in the villages where I’d spent most of my time. The cough got worse instead of better. It was especially bad at night: I’d lie down to sleep and that would trigger a paroxysm. Sometimes I’d cough until I couldn’t breathe. A few times, I vomited. Eventually my side began to hurt. (Months later, I discovered I’d cracked a rib.)

As a medical reporter, I spent most of my time around doctors and nurses, but I had a rule about never bothering them — first because I was pretty healthy, and second because no one wants to be the guy at the cocktail party who finds out someone’s a doc and backs them into the corner of the buffet table. But one day, worn out by the spasms, I mentioned my symptoms to a friend. His eyes got big. He went and got a textbook.

I didn’t have bronchitis. I had pertussis — whooping cough.

This made no sense, of course. Between a day job as Scary Disease Girl and a childhood spent moving between continents, I am pretty much the most vaccinated person on the planet.  I’d had my full series of pertussis vaccinations as a child. Surely I was protected?

Actually, no — and unless you’ve had a booster, neither are you. The immunity created by the 5-dose childhood series wanes over time; by the age of 12, even fully vaccinated people are vulnerable to pertussis again. Since 2006, the Advisory Committee on Immunization Practices has been recommending a single additional pertussis (Tdap) booster for anyone between the ages of 11 and 64. That may seem like overkill — adult cases of pertussis in previously vaccinated people are often milder than the child version; after all, I survived my bout. But as with so many vaccines, the beneficiary here isn’t just the adult taking the booster. Even more, it’s the more vulnerable person to whom that adult might pass the disease: an elderly person with age-related immune decay; someone with a chronic disease; an infant too young to be vaccinated. In those people, the disease can and does kill — as it did an 18-day-old infant, Nelyn Baker, whom I wrote about in 2004.

Because vaccine immunity fades, pertussis is always with us: in good years, about 1,000 cases across the United States. Lately, though, we’re in bad years. Pertussis cases are rising dramatically, in Alabama, Georgia, Arkansas, Texas, South Carolina, Michigan, Oregon and Ohio. The worst by far is California, where so far this year almost 1,500 cases of pertussis have been reported and another 700 are suspected — compared to 258 for the same time period in 2009. (Jan. 2011 update: The California count is now 7,800 cases, and 10 children have died.)

“We are facing what could be the worst year for pertussis that this state has seen in more than 50 years,” Dr. Gilberto Chávez of the California Department of Public Health said last week in a statement put out by the agency’s Center for Infectious Disease.

The worst news in this upsetting trend is this: We’re doing it to ourselves. As far as anyone can tell, the rise in pertussis is not due to any change in the organism, or to any mysterious error among the manufacturers who make pertussis vaccines. It’s due to vaccine refusal, to parents turning away from vaccines because they think the vaccines are more harmful than the diseases they prevent — or, more selfishly, because they think the wall of immunity created by other vaccinated children will protect their unimmunized ones.

That’s an incorrect assumption, by the way. Work published last year by several scientists at Kaiser Permanente of Colorado found that unvaccinated children were 23 times more likely to contract pertussis than vaccinated ones. And yet, as numerous stories (LA Times, MedPage Today) have pointed out, California’s epidemic has blossomed in a state that gives some of the most generous “personal belief exemptions” from vaccination — and the epidemic’s worst hot spots neatly correlate with the most concentrated areas of vaccine refusal.

Pertussis is an awful disease. A child in the throes of a paroxysm sounds like nothing else on earth. Children turn blue, give themselves black eyes, die. We kept it down to manageable levels with the help of a vaccine. That we would willingly bring it back it is beyond belief.

(For a physician’s take on pertussis, see this post by my fellow former Scibling Pal MD. The CDC’s information page on pertussis is here and the National Network on Immunization Information explains the vaccination schedule here.)

Flickr/NizNoz/CC

NDM-1: More Evidence It Started in India

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So it looks like the researchers who named NDM-1 — New Delhi metallo-beta-lactamase, the “Indian super-enzyme” that renders common gut bacteria impervious to all but one or two antibiotics — were right all along.

According to a study just published in Antimicrobial Agents and Chemotherapy, the problematic gene that produces it has been circulating in Indian hospitals since at least 2006.

Kinda undermines the claims by Indian politicians and the country’s health ministry that the resistance factor did not originate in India, but was given its name in an act of “malicious propaganda” aimed at undermining the subcontinent’s multimillion-dollar medical-tourism industry.

A brief recap: [Read more…]

Flu: Still a problem, just not here

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What a difference a year makes: At about this time in 2009, the world was still in the midst of the H1N1 “swine flu” pandemic, though cases had already trended down from their fall peak. Here at the end of 2010, flu has made barely a ripple.

In the United States, seasonal flu has been a non-story: The Centers for Disease Control and Prevention reported last week that flu activity is low by almost every metric: from the number of states where flu is widespread, to proportion of outpatient visits for flu-like illness, to adult deaths from pneumonia and influenza, to flu-related deaths among children.*

Here’s the map of flu activity in the US: By Dec. 18, only one state, Mississippi, was experiencing what is called “widespread” flu, the highest category:

And here’s the trend line for doctor visits for “influenza-like illness” — something that felt to the patient like flu. That black line is what the CDC considers the “epidemic threshold” for a flu season; this year’s case reports, the red line, fall below it:

But if there’s one thing that’s predictable about influenza, it is that it is going to behave in a not-predictable manner. That turns out to be true this year as well — because while the US is having a very mild season, the United Kingdom is getting punched. Look at this, from the BBC’s Health Desk, charting flu cases among adults — and note how close the current peak is to the peak cases during their swine flu epidemic:
The BBC is reporting that flu cases in the UK have risen by 50 percent in a week. Last weekend, the Telegraph reported that cases of flu serious enough to need intensive care had doubled in a week. And today, the Daily Mail is saying that Arrowe Park, a hospital in Wirral near Liverpool, has banned visitors in an attempt to slow down the spread of flu to vulnerable patients from the outside world.

Right now the UK seems to be alone in the intensity of its epidemic. Google’s Flu Trends (which doesn’t seem to sample the UK) is showing high search activity for flu-related terms only in Ukraine and Norway. (“High” is 4th on a scale of 1-5.) HealthMap, which does include the UK in its searches, shows hot spots only in England, Germany, and the east coast of Australia.

All of which makes it sound as though — for the US at least — flu is just not that much of a concern. That assumption would be a mistake, as two new articles underline. In Clinical Infectious Diseases, Jeffery Taubenberger (who recovered the virus of the 1918 pandemic) and co-authors remind us that 2010 marked the 500th anniversary of the first verifiable flu pandemic, suggesting that there are many more to come. And in the latest Scientific American, notable flu reporter Helen Branswell explores how little surveillance for flu there is at crucial chokepoints, such as pig farms, where new flus are likely to emerge. (Story is behind a paywall, but here’s the free podcast.) Branswell warns:

The 2009 influenza pandemic appeared to come out of nowhere. It started as what seemed like a lethal outbreak in Mexico, then spread north of the border. By the time health officials learned that the virus responsible for the alarming explosion of cases was new and an infection threat to most of humankind, they had no way to keep it from spreading around the world. By a stroke of luck, symptoms were mild in the vast majority of cases. What if next time we are not so lucky?

That question weighs heavily on the minds of influenza scientists and public health planners as they prepare for the next big outbreak. And there will be a next time.

*Frustratingly, the CDC doesn’t assign static links to its weekly FluView reports, so if you read this post after Dec. 31, that link may take you to a different report than the one this post references. I’m using data that was on the site Dec. 30 for week 50 of 2010, ending Dec. 18.

Update: Well, that was quick. The link above now goes to the FluView for the week ending Dec. 25. The number of states with “widespread” flu has risen to five: Alabama, Georgia, Mississippi, New York and Virginia. Things are picking up.

Update 2: But they’re picking up much more in the UK, and the spillover from flu cases is affecting hospital operations overall. The Guardian reported Dec. 31:

NHS pressure group Health Emergency today claimed a number of hospitals in East Anglia were on black and red alert, saying the NHS was already struggling as a result of the flu outbreak.

Chairman Geoff Martin said the James Paget University hospital in Great Yarmouth, Norfolk, yesterday declared a black alert – the most severe status level – and that the Norfolk and Norwich University Hospital was on red alert – one step lower.

He said: “We warned that hospitals would be forced on to black alert as the flu cases fill the available beds. Now it’s happening and we do not believe that the chaos is restricted to East Anglia. The NHS is now on the brink of the worst winter crisis in over a decade as the harsh reality of cuts to beds and staffing numbers is exposed with lethal consequences.”

Image: Mine, Brussels, July 2010

Update: Farm Animals Get 80 Percent of Antibiotics Sold in U.S.

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Two weeks ago, I broke the news of a new FDA report that estimated for the first time the amount of antibiotics sold in the United States every year for use in agriculture: 28.8 million pounds.

That long-awaited report didn’t answer a crucial question: What volume of antibiotics are sold in the United States each year for human use. It’s a crucial question because, in answer to concerns about antibiotic resistance arising on farms, the answer has always been that human medicine is equally culpable because it uses similar volumes of antibiotics.

The only research that has attempted to answer that question is contained in a decade-old report by the Union of Concerned Scientists that put the proportion of antibiotics going to animals at 70 percent of the U.S. total.

That UCS report and estimate are a decade old not because no one has cared about the topic, but because accurate updated figures have been so hard to get. So we owe a special holiday thank-you to the researchers at the Center for a Livable Future, who decided the release of the FDA report justified another attempt to get the numbers straight. They succeeded.

The proportion of antibiotics sold in the United States each year that go to animals turns out to be not 70 percent, but rather 80 percent. Here’s CLF’s Ralph Loglisci, who got the confirmatory numbers from the FDA:

In accordance with a 2008 amendment to the Animal Drug User Fee Act, for the first time the FDA released last week an annual amount of antimicrobial drugs sold and distributed for use in food animals. The grand total for 2009 is 13.1 million kilograms or 28.8 million pounds. I … contacted the FDA for an estimate of the volume of antibiotics sold for human use in 2009. This is what a spokesperson told me:

“Our Office of Surveillance and Epidemiology just finished an analysis based on IMS Health data. Sales data in kilograms sold for selected antibacterial drugs were obtained as a surrogate of human antibacterial drug use in the U.S. market. Approximately 3.3 million kilograms of antibacterial drugs were sold in year 2009. OSE states that all data in this analysis have been cleared for public use by IMS Health, IMS National Sales Perspectives™.”

3.3 million kilograms is a little over 7 million pounds. As far as I can determine, this is the first time the FDA has made data on estimates of human usage public.

At its blog, CLF lays out the math for each major drug class as sold for animal use and human use, with a long discussion of the significance of the different drug classes. Here’s the CLF table summing up the math, but please go over to CLF’s blog for its discussion.

Most important to note: Most of the drugs used in animal agriculture and in human medicine are functionally identical. That’s one reason why the overuse of antibiotics in animals is such a concern: When organisms become resistant on the farm to drugs used on livestock, they are becoming resistant to the exact same drugs used in humans. (One major drug category used in animals, ionophores, do not have a direct human analog. But use of them on farms is still a concern, because resistance factors can move freely between species of bacteria. That’s a discussion for another day.)

Loglisci’s conclusion is also worth underlining:

The next battle, which industry has already begun, is defining what non-therapeutic use will constitute. Producers are already claiming that the use of antibiotics for growth promotion has decreased, maintaining current low-dose usage is aimed at disease prevention. Regardless, all low-dose usage of antibiotics can lead to a significant increase in antibiotic resistance.

Image: Flickr/Epsos

The food safety bill and the long cost of foodborne illness

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In a nailbiter ending tonight, the US House of Representatives passed the long-stalled, almost-lost, back-from-the-dead FDA Food Safety Modernization Act, a decades-overdue piece of legislation that will equip the US Food and Drug Administration with enforcement tools to help it prevent and track foodborne illness outbreaks.

For people who don’t know the regulatory landscape of food in the United States, it comes as a shock that FDA (which regulates both drugs used in food production and much of the food produced in the US, except for meat and poultry which are under USDA) has so little power. Until now, the FDA could not compel a food recall; it could only ask for a problematic or dangerous food to be recalled, and the food producer could demur. That was, if the FDA even associated a particular food with a foodborne outbreak, which was unlikely given its lack of surveillance resources or inspectors. (A remarkable number of foodborne outbreaks are solved not by the feds but by the Minnesota Department of Public Health, which is well-funded by the state it represents.) The last time food-safety legislation was updated in the US was 1938. [Read more…]

"Pig MRSA": New human infections in France

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It’s one of the touchiest topics under the broad category of antibiotic resistance: Whether the drug-resistant organisms that emerge on farms as a result of antibiotic use stay on farms, or pose a risk to humans who have no connection to agriculture.

That drug resistance emerges under any selective pressure is basic biology: Resistance is an inevitable process. That they emerge on farms when antibiotics are used broadly — that is, in growth-promoting or prophylactic ways, not to treat disease in individual animals — really isn’t in dispute any more. It’s now a question of economics and politics, not science. (See this bibliography, stretching back to 1969; and the news I broke yesterday of FDA’s estimate of US farms using almost 29 million pounds of antibiotics last year.)

So the argument over farm antibiotic use now tends to focus on whether the resistant organisms that emerge on farms are only an issue within a farm’s confines, or rather pose a broader human health threat — and that’s where the continuing story of the “third epidemic” of MRSA becomes so important. Recapping, this is a strain known as MRSA ST398 that emerged in pigs and passed to pig farmers in the Netherlands in 2004, subsequently spread across the European Union, and crossed to Canada and then to the United States. (Key posts on ST398: here, here, here and this archive at my old site. Yes, it will be moved soon, promise.)

Most of the identifications of MRSA ST398 in humans, including those first identifications above, were colonizations, the term for symptomless carriage of staph in the nostrils and on the skin; in other words, it wasn’t making people sick. News of actual illnesses has been rare — especially illnesses among people who have no contact with farming, such as the post-surgical infections found in Canada earlier this year.

But they’re getting a little less rare, as demonstrated by a letter just posted ahead-of-print to the journal Clinical Infectious Diseases. It recounts the finding, via annual surveys of bloodstream infections, of four cases of ST398 in four different hospitals in France. One may have been due to animal exposure. Three were hospital-acquired.

Examination of patient histories revealed exposure to animals in 1 case, a fatal idiopathic community-acquired bloodstream infection in an 84-year-old man who lived on a farm at which 1 pig was being raised. The remaining cases were hospital-acquired and included 1 case of catheter-associated infection observed in a 58-year-old man with advanced multiple myeloma, 1 case following elective digestive tract surgery in a 69-year-old woman, and 1 case following cardiac surgery in a 68-year-old man.

There’s an especially interesting thing about these cases. In Europe and the US, ST398 has particular characteristics: It is resistant to tetracycline (the drug most commonly given to pigs) and does not manufacture the toxin Panton-Valentine leukocidin or PVL, which is suspected to be a cause of community-strain MRSA’s uncommon virulence. (See this story, from the book SUPERBUG, of how PVL-positive pneumonia almost killed a toddler.) The strain in the French cases, though, does manufacture PVL, and shares some virulence characteristics with the dominant community strain, USA300. It is less like the European strain of livestock-associated MRSA and more like a livestock-associated strain that appears to be emerging in China, ST9 (more on that here).

The argument against the significance of these cases is likely to be that they are, again, just one data-point, and may be just rare and random. That is worth considering. But it is also worth considering that they continue to be found.

And, also, that the community epidemic of MRSA was first flagged in a discovery of 25 cases in children in Chicago back in 1998, a finding that was also dismissed at the time as rare and random — and that grew into an epidemic of millions of cases a year.

(H/t to constant reader Pat Gardiner for flagging this paper for me.)

Cite: van der Mee-Marquet N et al. Emergence of Unusual Bloodstream Infections Associated with Pig-Borne–Like Staphylococcus aureus ST398 in France. Clin Infect Dis. (2011) 52 (1): 152-153. doi: 10.1093/cid/ciq053

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News break: FDA estimates US livestock get 29 million pounds of antibiotics per year

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This afternoon, the Food and Drug Administration posted without fanfare a report that many people have been waiting a long time for: Its first-ever estimate of the amount of antibiotics sold for use in food animals in the United States.

And the number is: almost 29 million pounds in 2009.

That’s a lot.

Is it more or less than was expected? It’s almost impossible to say. Estimates of the amount of antibiotics given to food animals in the United States are ferociously contested and plagued by squishy definitions and category creep. In 2000, the Animal Health Institute, which represents veterinary drug manufacturers, put total use at 17.8 million pounds. In 2001, the Union of Concerned Scientists, which campaigns (among other issues) to dial back use of agricultural antibiotics, estimated that 24.6 million pounds per year are used only for “non-therapeutic purposes” — that is, to make animals grow to market weight faster and to prevent them catching diseases in the close quarters of confinement agriculture.

The reason why antibiotic use on farms is a concern, of course, is because such use stimulates the emergence of drug-resistant organisms that move off the farm in animals, in groundwater, in dust, on the wind and in the systems and on the clothes of those who work there, and makes new resistance factors available to be swapped among bacteria. (For much more about that, see these three posts and this long archive at my former blog.)

The FDA’s estimate comes as the agency has been moving to curb agricultural antibiotic use after years of non-action. Today’s report, which is very short — basically a table and a bunch of footnotes — is the direct result of a 2008 amendment to the Animal Drug User Fee Act of 2003, which required manufacturers to report yearly on sales of agricultural antimicrobials. (Here’s an FDA Q&A on the report background.)

More important, though, today’s report dovetails with the FDA’s new effort to curb antibiotic use in agriculture, which Commissioner Dr. Margaret Hamburg said in October would involve “very serious scrutiny.” (Video here.) The main instrument of that effort is a “draft guidance” that the FDA opened for public comment over the summer, “The Judicious Use of Medically Important Antimicrobial Drugs in Food-Producing Animals” (pdf here). The point of that guidance is to ask agriculture to voluntarily withdraw from use the ag drugs that are functionally identical to drugs that are important in human medicine — because if bacteria become resistant to those drugs when they are used in animals, that newly derived resistance will also affect humans, making common diseases difficult or impossible to treat.

In addition to the volume figure, the real value of today’s brief report may be simply to make clear just what antibiotics are used in agriculture. Take a look at the report table at right, which lists the animal drugs used by amount sold within drug classes. (Note that the amounts are given in kilograms.) It lists:

Aminoglycosides: Human versions include streptomycin and amikacin.

Cephalosporins:  Human versions include Keflex and Rocephin.

Lincosamides: Human versions include clindamycin.

Macrolides: Human versions include erythromycin.

Sulfas: Human versions include half of the very common drug combos Bactrim and Septra.

Penicillins and tetracyclines: Yup, just what they sound like.

“NIR”: That’s FDA shorthand for “not independently reported” because they have few manufacturers or make up a small portion of the market. Among them are fluoroquinolones. Human versions: Cipro and Levaquin.

There’s much more to be said about the issue of antibiotic use in agriculture, especially because the lone piece of legislation addressing it, the Preservation of Antibiotics for Medical Treatment Act, is currently in lame-duck limbo. This report is an important piece of data for the ongoing debate.

Update: I asked some experts in the field to comment on the release of this data. Dr. David Wallinga, director of the Food and Health program at the Institute for Agriculture and Trade Policy in Minneapolis (also William T. Grant Foundation Distinguished Fellow in Food Systems and Public Health at the University of Minnesota School of Public Health) replied:

Clearly, antibiotic use in animal agriculture is huge, and as the FDA and CDC and WHO all agree, much of it is unnecessary. Data collection is important. But, because resistant bugs quickly adapt, we can’t afford to wait for data to take action to reduce antibiotic use wherever possible. That includes routine uses of antibiotics for cattle developing liver abscesses because they’re force-fed grain rather than grass, as well as antibiotics used to make animals get fatter faster.

Update 2: A day after the release of this report, Rep. Louise Slaughter (D-NY), author of PAMTA and a public-health microbiologist, commented on the data — and also said she’ll be reintroducing the legislation again in the next Congress in January.

This report illustrates the overuse of antibiotics in food animal production and makes a strong case for some common-sense limits on antibiotic use. We are putting millions of pounds of antibiotics into the food supply unnecessarily every year. This cannot continue and it’s my hope that these new data from the FDA will encourage even more members of Congress to join me next year when I reintroduce this legislation.  Moreover, the FDA must move fast to issue strong regulations on antibiotic usage in agriculture.

Update 3: Tom Philpott, senior food and agriculture writer at Grist — and a farmer, so he knows the territory — covered the FDA report and this post in a very kind and typically forthright post of his own.

Update 4: Helena Botttemiller, ace food-policy reporter for Food Safety News, covers this as well, noting how little mainstream media interest there has been. Any opinions why?

Cite: 2009 Summary Report on Antimicrobials Sold or Distributed for Use in Food-Producing Animals, FDA, Dec. 9, 2010

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