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?

Flickr/EssjayNZ/CC

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:

[HTML1]

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

Flickr/BenKetaro/CC

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

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…]

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

Image via Flickr user johnmuk under CC

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

Image via Flickr user net_efekt under CC

Alarm over "pig MRSA" — but not in the US

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There’s some new news out — along with a fair amount of public reaction — regarding “pig MRSA” or, to use the technical term, MRSA ST398, the “third epidemic” strain that emerged in pigs in the Netherlands in 2004 and has since appeared, in animals, retail meat, and humans, across the European Union, in Canada, and in the United States. (My last post on it is here, and a long archive of my posts on it starts here.)

I wish I could say the attention to ST398 was being paid in the United States, where there is almost certainly more MRSA in livestock than has been recorded, given that the only published surveillance, from 2009, covered only Iowa and Illinois. Unfortunately, there is still no indication that federal agencies have any intention to test for the presence of the organism in animals or in meat. In fact, the major surveillance mechanism for drug-resistant organisms in meat animals, retail meat and meat-eaters in the US, the National Antimicrobial Resistance Monitoring System or NARMS, doesn’t test for MRSA at all; it handles only enteric or gut-borne bacteria such as Salmonella and Campylobacter. (NARMS IS shared among three agencies: the CDC handles drug-resistant foodborne bacteria in humans, the FDA looks for the same bacteria in food, and the USDA looks for those bacteria being carried by livestock.)

Instead, as so often seems to happen with antibiotic resistance, the country paying attention is in Scandinavia — in this case, Denmark. The annual report from Denmark’s surveillance scheme, DANMAP (Danish Integrated Antimicrobial Resistance Monitoring and Research Programme) is out. Denmark does surveil for MRSA, and here’s what they found: 13% of pigs, at slaughter, were positive for MRSA ST398.
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News break: FDA head promises "very serious scrutiny" of farm antibiotics

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Since July, the Food and Drug Administration has been moving — quietly and cautiously, but moving — to raise the stakes in its long and so-far unsuccessful battle to rein in overuse of antibiotics in agriculture. For those new to the topic, this is the use of antibiotics not in treatment-sized doses, to cure disease in farm animals, but in smaller doses to prevent disease or simply to make the animals gain weight faster so they can raised more efficiently and sold off more quickly than they would have otherwise.

There are decades of research by now, demonstrating that this contributes to the development of antibiotic-resistant organisms on farms that then move off harms and threaten human health. It’s not really a scientific question any longer; it’s a question of economics and politics.

(For a long discussion of what the FDA is proposing — and how much force it will, or won’t, have — see this post — at SUPERBUG’s earlier location, because we haven’t yet moved over all the archives.)

Yesterday, FDA Commissioner Dr. Margaret Hamburg gave a speech at the National Press Club at which she raised this issue and made some intriguing remarks. The overall point of the speech (see this AP article) was to promise increased investment and modernization — but she raised both the problem of antibiotic resistance generally and, in answer to a question, the problem of antibiotic use in farming.

First, here’s what she said generally about resistance (my transcription from CSPAN’s video above, starting at about 7:00):

There is increasing alarm about the problem of antibiotic resistance, and we worry with good cause. Today, antibiotic resistance mechanisms have been reported for virtually all known antibacterial drugs currently available for clinical use, which affects everything from global infectious diseases to ear infections in school children to staph infections in locker rooms. People actually talk today about a potential return to the, quote, pre-antibiotic era, unquote, where we no longer have effective tools to treat serious infectious disease. Clearly we must encourage more judicious use of these important drugs through improved infection control,  rational prescribing and better patient compliance.

But even if we improve these practices, resistant bacteria will continue to develop no matter what. We need new and better drugs and we need them now. Yet the research and development pipeline is distressingly low. The number of newly approved antibiotics, not just new formulations of previously existing drugs, has fallen steadily since the 1980s, and the range of new antibiotics in distribution is limited in terms of the types of classes of new antibiotics available and the diseases they can treat.

And here’s what she said about farm use, in response to a question (starting at about 31:00):

There historically has been a very considerable use of antibiotics as part of animal husbandry and also agriculture. I think that for many years individuals and organizations in public health and medicine have raised those very concerns, about what is the impact of the use of antibiotics in animal populations on human health and the availability of effective antibiotics to treat disease. We are in the midst of very serious scrutiny of these issues and we have made recommendations in support of judicious use of antibiotics. Nobody wants to deny antibiotics to animals that need medical treatment. But the use in certain preventive contexts, where it is not clearly medically indicated, is of growing concern,. And it is an area that, working with our partners in government, both the CDC and the USDA and others, that we are taking a very serious look at. (Emphasis mine.)

C. diff: Blame hospitals? Or food?

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People who are interested in infections that are transmitted in hospitals (umm, ghouls like me) have a special sick relish for Clostridium difficile, or in its short form, C. diff. C. diff lives in the intestines, part of a complex population of many bacteria — you did know there are more bacteria in your body than there are cells that belong to you, right? — but it roars out of control if those other bacteria are wiped out by a course of antibiotics, especially clindamycin. Removing the other bacteria clears out space for C. diff to reproduce in much greater numbers; the toxins it produces irritate the lining of the intestine, producing colitis, and triggering fever, cramps and diarrhea, and in the worst cases, sepsis. miscarriage and death.

C. diff colitis is one of the most common and serious hospital-acquired infections because — if you’re reading this over breakfast, you might want to stop eating now — severe diarrhea in a hospital patient who is confined to a bed and using a bedpan tends to get everywhere. Really, everywhere: bed linens and bedrails, floors and walls, stethoscopes, telephones, computer keyboards, and the hands of the healthcare personnel who operate those devices and then touch another patient.

C. diff persists so spectacularly because in the outside air, it forms a hard-shelled spore that protects its genetic material from assault — including from the alcohol in the hand gel that most healthcare workers use to clean their hands in between patients, and from the stomach acid of patients who swallow it. (See, I told you to stop eating.) Because of that, and because it’s such a devastating infection, hospitals toil incredibly hard at sanitizing to get rid of it.

C. diff colitis is a stubborn and ugly infection. Earlier this summer, an Illinois man named Ed Corboy Jr. described his mother Joan’s experience with it to the Infectious Diseases Society of America:

I watched helplessly as [she] grew weaker, more dehydrated, and nearly died. She was started on intravenous fluids and standard antibiotics while in the hospital two different times that December. Her blood pressure dipped dangerously low on many occasions. She had lost almost 55 pounds in the previous five months, and she was so profoundly exhausted, tired, and wasting away that it became apparent in early January she might die from this. She could hardly get to a bedside commode without two people helping her. Prior to this she was able to walk to her bathroom with her walker on her own for years.

Starting about 10 years ago, C. diff got dramatically more problematic: more virulent, more resistant to treatment, and more commonly occurring in people who would not have been expected to have it — often, healthy young people who had not been in hospitals, who seemed to be developing the illness in the outside world. Two CDC researchers said in 2008:

In the United States, the number of hospital discharges where (C. diff associated diarrhea, CDAD) was listed as any diagnosis doubled between 2000 and 2003, with a disproportionate increase for persons aged > 64 years. By 2003, regional reports of CDAD outbreaks from hospitals throughout the US and in Quebec, Canada emerged, describing severe disease associated with greater numbers of complications, including colectomies, treatment failures, and deaths. In 2004, the attributable mortality rate of nosocomial CDAD in Quebec hospitals was 6.9%, compared to 1.5% among Canadian hospitals in 1997. In the US, death certificate data suggest mortality rates due to CDAD increased from 5.7 per million population in 1999 to 23.7 per million in 2004. (Gould, Critical Care, 2008)

The reason for the surge has been understood to be the emergence of a new, hypervirulent strain of C. diff that produces up to 20 times more toxin than earlier ones. (C. diff nomenclature will make your brain hurt, but the strain is generally known as NAP1/027/BI, toxinotype III.) But increased virulence doesn’t explain the increased incidence, and the transmission patterns of the new strain have been murky.

An emerging line of inquiry suggests that the transmission patterns become much more clear if you look in a different place for the bacterium’s origin: not in hospitals, but in food.

C. diff has been identified in live pigs, cows and chickens. The bacterium has been found in retail meat in the United States and in Canada (in three separate studies), and in salad greens in Scotland. And in a paper published this month, the main authors from those Canada studies establish that minimum recommended cooking temperatures for ground beef don’t kill C. diff spores.

(You’re really not eating now, right?)

So, OK: But are the C. diff strains found in animals the same ones that are causing human disease? The answer turns out to be Yes. Several researchers have found overlaps, in 2007, 2009 and earlier this year, in a study with the perfect title: “Innocent bystander or serious threat?”.

And in what looks certain to be a provocative presentation, a team of researchers from Houston is going to present a paper at the annual meeting of the Infectious Diseases Society of America in a few weeks, titled: “Potential Foodborne Transmission of Clostridium Difficile Infection In a Hospital Setting.” (Uh-oh.)

The case for C. diff as a foodborne illness still isn’t made. In an excellent paper published last month, L. Hannah Gould and Brandi Limbago of the CDC go over the findings so far, and detail what evidence and further research are still needed.

It is reasonable to assume that the general public is and has been often exposed to low numbers of potentially infectious C. difficile spores. There is currently limited epidemiologic evidence to support or refute the hypothesis that C. difficile is transmitted by the foodborne route; the presence of C. difficile on retail foods suggests but does not prove that some proportion of infections is acquired this way. The food supply may thus serve as a source of new strains causing human infections; alternatively, food could be another constant and normally innocuous exposure. (Gould, Emerging Infectious Diseases, 2010)

What’s really interesting, though, is that microbiologists aren’t the only ones noticing this accumulation of evidence. C. diff as a possible foodborne pathogen caught the attention of foodborne-illness attorney Bill Marler early last year.  If Marler — the most aggressive and, I suspect, successful foodborne-injury lawyer on the planet, dating back to the 1993 Jack-in-the-Box outbreak — is starting to notice the evidence tying C. diff outbreaks to food, there might be a lot more attention paid to this connection fairly soon.

Image of C. diff by Janice Carr, courtesy of Public Health Image Library, CDC.

Pigs, antibiotics, and staph where it shouldn't be

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The “third epidemic” of MRSA (drug-resistant staph) — the one that started in farm animals given antibiotics, and subsequently spread to humans — has been contentious since its emergence. This week there are several pieces of new news about it. They’re not likely to solve any of the disagreements, but they’re certainly interesting.

Very quick recap for those coming in late: MRSA, short for methicillin-resistant Staphylococcus aureus, describes strains of staph that have become resistant to most common antibiotics. It’s been gaining ground on us for about 50 years, first in hospitals, then in the everyday world and now in farm animals and farm-workers. Surveillance for it is not excellent, but in various studies, it kills 19,000 Americans, puts about 370,000 in the hospital, and sends possibly 7 million to a primary care visit or ER, and causes billions of additional dollars in health care spending — all in a year. For the most serious infections, there are only a few drugs that still work. It’s the leading organism in the under-appreciated international epidemic of antibiotic resistance. (If you’d like to know more, I wrote a book about it.)

Livestock-associated MRSA — many researchers just call it “pig MRSA,” which makes swine agriculture very unhappy, but the more technical term is MRSA ST398 — was first noted in 2004 in a Dutch toddler being prepped for surgery; then identified in her family and their social circle, all of whom were pig farmers; and then was found in their pigs. Along with the standard suite of MRSA resistance factors — all the beta-lactam antibiotics, which means anything ending in “-illin,” most cephalosporins, the monobactams and carbepenems, and also erythromycin — this new strain was resistant to tetracycline. That was odd, because the Netherlands’ rate of MRSA was so low that they were not bothering to give humans tetracycline for MRSA; but tetracycline was the most common drug given to pigs in large-scale agriculture there. It was proof the organism had been resident in pigs, become resistant as a result of ag antibiotic use, and then crossed to humans. (Yeah, this is all told in the book. OK, no more shilling.)

Since that first finding, ST398 has spread throughout the European Union, into Canada, and in one state in the US, Iowa. (Veterinarians assume it has spread more widely than that, but Iowa happens to be the only state where researchers have looked for it.) It is less common than other strains of MRSA, but it has been identified as the cause of mild skin infections among farm workers, serious hospital infections such as ventilator-associated pneumonia, and life-threatening community infections such as flesh-eating disease. It’s also been found in retail meat in several different countries. (We haven’t yet managed to move my archives over, but there’s a 2-year history of ST398 coverage at my old blog.)

Despite the low number of known cases, MRSA ST398 is important, for several reasons: First, because as those death and illness numbers demonstrate, any additional MRSA is bad news. Second, because MRSA ST398 bridges the human and animal worlds, demonstrating how easily an organism that is resident in animals can cause illness to humans, and also can move across the world with agricultural trade. And third, because its occurrence underlines the consequences of antibiotic overuse in agriculture: If they hadn’t been giving tetracycline to pigs in the Netherlands — a country that, within about a decade, went from small family farms to the largest user of ag antibiotics in the EU — “pig MRSA” might not exist.

So, this week’s update, courtesy again of the Interscience Conference on Antimicrobial Agents and Chemotherapy, or ICAAC: two findings that are somewhat contradictory.

First, a team in the Netherlands wanted to know how much of an infection risk ST398 truly poses. That’s an especially important question in the country where the strain got going. In the Netherlands, which exerts very close control over MRSA overall, certain categories of hospital patients are checked to see whether they are carrying the resistant bug, and if so, put into isolation and treated until they are clear. But some people are considered to be such high infection risks that they are put into isolation presumptively — and since 2007, those categories have included farm workers and veterinarians.

That’s a lot of tests, which means a lot of expense. So the team who presented this week tried to assess whether that isolation and testing are necessary, by measuring how often carriage of MRSA ST398 converts to an active infection. They looked at every MRSA isolate identified in 2009 at two hospitals in the southeast, where pig-raising is most dense, and identified a huge reservoir of carriage of ST398: 61% of the MRSA-positive patients, or 298 out of 486. But of those 298, only 7 developed an infection, and none of them passed the infection to a second patient. The 188 patients carrying hospital MRSA, on the other hand, caused 83 secondary cases — enough to force closure of a department in one of the hospitals. (van de Sande et al., ICAAC 2010)

So while pig MRSA’s easy to acquire, given the right exposure, it may not often cause illness. Problem is, according to a second piece of research discussed this week, when it does, it can be unexpected and devastating.

A coalition of 21 hospitals in Spain wanted to know how many of the MRSA bloodstream infections occurring in their institutions were caused by the community strain of MRSA instead of the hospital strain — something that would signal a change in the epidemiology of what can be a devastating illness. They checked every MRSA bacteremia case from June 2008 through December 2009. They found 324, overall, with 10 of them caused by community strains. But they also found something they didn’t expect: Almost as many, eight of 324, were caused by ST398. (Camoez et al., ICAAC 2010)

This isn’t the first time that MRSA ST398 — an organism linked to agriculture and to spread through farm workers and veterinarians — has been found to cause hospital infections or serious infection. It has caused ventilator-associated pneumonia in Germany and post-surgical infections in Canada.

One of the ways that epidemiology measures the seriousness of an outbreak is to compare it to the expected background occurrence of a disease. In the case of MRSA ST398, that background rate is zero. The strain’s an artifact of the overuse of antibiotics in agriculture. It’s really worth thinking about how many more such organisms we want to produce.

Image: photographer unknown.

News break: "Pig MRSA" ST398 involved in the death of a child?

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The latest postings to the website of the CDC journal Emerging Infectious Diseases include a sad and very troubling letter from physicians in Lyon and Paris, reporting the death from necrotizing pneumonia of a previously healthy 14-year-old girl. That would be sad under any conditions, but here’s what makes the death so troubling: It appears to have been caused by MRSA — but not by the community strain, USA300, that has been implicated in a number of deaths from necrotizing pneumonia. (Several such stories are told in SUPERBUG the book.)

Instead, her death appears to have been caused by infection with MRSA ST398 — the livestock-associated strain that was first noted in pigs raised with antibiotics, and the pig-farm workers caring for them, in the Netherlands 6 years ago, and that has since spread across the European Union, Canada and into the United States. (My 3-year archive of ST398 posts is here.)

This may be the first death associated with ST398, though I can’t say that for sure as I am away from my big computer and working without my database. I’ll update later today and confirm or knock that down.

The physicians say that the girl came in with flu-like symptoms and abdominal pain, was put on IV antibiotics (cefotaxime and amikacin), underwent an exploratory laparotomy that showed nothing, and shortly afterward developed acute respiratory distress and was put on a vent. A chest X-ray was shadowy on both sides. She went rapidly downhill and died 6 days later.

On analysis, the staph strain infecting her was ST398; there was no indication where she had picked it up. The strain had an unusual characteristic: It possessed the ability to make the cell-destroying toxin Panton-Valentine leukocidin, PVL for short, a genetic trick that until now has been a property only of community MRSA strains such as USA300. Though its role is disputed, PVL has been linked to community MRSA’s ability to start infections on intact skin, and to the cellular damage that destroys children’s lungs in cases of pneumonia caused by USA300. Until now, ST398 has been PVL-negative.

The physicians’ letter is short and there’s much more to find out about this case. But if the report and analysis are correct, this is bad news. One of the repeated themes in the 50-year evolution of MRSA has been its ability — all staph’s ability — to promiscuously swap and share the bits of DNA that confer resistance and enhance virulence. Another, since the emergence of ST398, has been the potential peril of a staph strain adapting and mutating in the millions of farm animals around the world that are routinely given antibiotics — and that for the most part are not checked to see whether they harbor resistant organisms. If this report (and my interpretation) are correct, then those two trends are converging in a way that cannot bode well.

Hospitals want patients to eat antibiotic-free meat

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Huge news, and hat tip to excellent food-policy writer Monica Eng at the Chicago Tribune: In a piece published Tuesday, she details that 300 hospitals in the Chicago area and nationwide have begun preferentially buying and serving meat that is raised without the use of antibiotics.

Using the ingredients is primarily a response to patient demand, said (Carolyn Lammersfeld, national director of nutrition at Cancer Treatment Centers of America) but the centers are also “watching the controversy over the nontherapeutic use of antibiotics and their potential to cause resistant strains of bacteria.”

The issue is of particular concern for cancer patients, who have compromised immune systems, she noted. “Many also might already being taking antibiotics, so they don’t want additional ones in food if they can avoid it,” Lammersfeld said.

The drug-free meat is more expensive, but the cost balances out within the budget:

(Diane Imrie, director of nutrition services at Fletcher Allen Health Care in Vermont) estimated that her food costs rose about $67,000 last year when she switched to antibiotic-free chicken from conventional. “But that’s also about the same cost as treating a single MRSA infection,” she said.

It’s interesting to see this story land just as a new paper in Foodborne Pathogens and Disease is making the rounds. The paper (Jiayi Zhang, Samantha K. Wall, Li Xu, Paul D. Ebner. “Contamination Rates and Antimicrobial Resistance in Bacteria Isolated from “Grass-Fed” Labeled Beef Products,” doi:10.1089/fpd.2010.0562) compares the bacterial burden in grass-fed and conventionally raised beef and finds no significant  differences: equivalent amounts of both drug-sensitive and drug-resistant bacteria in both types of beef.

It concludes, “There are no clear food safety advantages to grass-fed beef products over conventional beef products” — an assertion that’s likely to be seized on by those who see no need to change current antibiotic use in agriculture. (For an example of that POV, here’s the testimony from last week’s House of Representatives hearing by Richard Carnevale, DVM of the Animal Health Institute.)

I suspect though that the paper’s analysis doesn’t look far enough. Here’s one example: the authors found that Enterococcus species in both conventional and grass-fed meat were resistant to chloramphenicol, erythromycin, flavomycin, penicillin, and tetracyline — drugs that are used in agriculture (and that could have been given to the grass-fed animals, which were not guaranteed to have been raised drug-free). But  Enterococcus spp. isolates from conventional beef were more frequently resistant to daptomycin and linezolid — which are new-to-market drugs of last resort in human medicine that are not given to animals

That finding, right there — the migration of resistance to a human-only drug into an organism carried by an animal — signals one of the insoluble problems of overuse of antibiotics. Once created, resistance factors move horizontally among bacteria, from the farm to humans, and apparently in this case, from humans to the farm as well. We have almost no control over their movement, and on the agricultural side, almost no surveillance to detect it, either. That argues for reducing the overuse of antibiotics in human medicine and on the farm.

If this health care coalition’s refusal to purchase meat raised using antibiotics helps to enlarge the market for drug-free meat, then it may reduce ag antibiotic use, and therefore the selective pressure that encourages resistant organisms to emerge. That can only be a good thing.

(The paper in Foodborne Pathogens has also been covered by my former colleagues at CIDRAP; here’s their link.)

Antibiotic use in animals: The feds move, a little

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(You leave the country for a few days — I spoke at a conference in Brussels, which was was lovely, thanks for asking — and all kinds of news breaks out. So, sorry to be late on this, but it’s an important issue.)

Last week, the Food and Drug Adminstration took the first (baby, mincing, tentative) steps to address the problem of antibiotics being used in animal agriculture, not to treat disease, but to make animals grow up to market weight faster. This practice — variously called subtherapeutic dosing, growth promotion, and “for production purposes” in the FDA’s exceedingly careful language — has been fully banned in the European Union for 4 years, and some aspects of the practice have been banned longer.

The simple reason for the ban: There’s decades of good science and real-world experience showing that it contributes to the development of drug-resistant organisms in farm animals and the farm environment, organisms that leave farms in the animals and in their manure, and also contaminate the environment beyond farm borders via leakage into groundwater and dust blowing off manure lagoons.That movement off the farm is critical because many of the drugs used in agriculture are the same, or close analogs, of drugs used in human medicine; so resistance that develops on the farm endangers human health as well. (MRSA ST398, livestock-associated MRSA, is the latest example of this. Find a long archive of posts on ST398 here.)

Just to be clear, growth-promoters don’t treat disease; they’re given to healthy animals solely for the purpose of getting them up to sale weight and to market faster. The ways in which antibiotics are given to livestock to treat or prevent disease have their own issues, but those are not part of the FDA effort. (Historical note: The growth-promoting effect of trace amounts of antibiotics was first recognized in 1947, when scientists at Lederle were looking for something to do with the leftover fermentation mash from the manufacture of chlortetracycline, fed it to chickens, and discovered they thrived on it. Stuart Levy’s The Antibiotic Paradox tells this story in detail.)

In human medicine, when we give antibiotics to people who are not sick with a bacterial illness, we call it inappropriate use — and aim massive education campaigns at the practice in an attempt to dial it down. In contract, the animal side has had a free pass for a long time, to the extent that it remains unclear how many antibiotics are used in farming in the US (best estimate: about 70% of all antibiotic use in the US per year), and there is no organized surveillance that would look at what organisms are emerging in animals from that use.

The FDA has been trying to put curbs on growth promoters since the 1970s, always without success; the lobbying against it, by agriculture and also by pharmaceutical interests, is reliably intense. There’s been a parallel effort in Congress to limit the use in animals of drugs that have close analogs in human medicine, via the Preservation of Antibiotics for Medical Treatment Act, or PAMTA, authored by Rep. Louise Slaughter (D-NY), Congress’s only microbiologist. PAMTA has been introduced in several Congresses but this year finally gained some traction. Last year, the Obama administration signaled, in testimony by then-new assistant FDA commissioner Joshua Sharfstein, that it might be friendly to the idea of dialing back on growth-promoter antibiotic use, and it looked as though the long logjam might finally be broken.

Well, OK: Not broken, exactly. Just shifted a little, and maybe showing a tiny bit of light.

On Tuesday, the FDA released a “draft guidance” that proposes animal ag do two things: stop using growth-promoting subtherapeutic dosing, and administer antibiotics to animals under the supervision of a veterinarian. That’s the good news.

The bad news: It’s only a guidance, not a regulation. In other words, it has no force in law. It’s more like a request — though in a press conference last week, Sharfstein suggested it might also be a shot across agriculture’s collective bow:

We have the regulatory mechanisms and the industry knows that. But we are also interested in what things can be done just voluntarily that they would do them. And I think it’ll be interesting to see how the industry responds to this and how – what direction their comments take. …We’re not handcuffed to the steering wheel of a particular strategy at this point. We really want to understand what people think. And but we’re also – I’m not ruling out anything that we could do to accomplish these important public health goals. (Transcript)

Reactions to the FDA announcement were predictable — effectively “No science, more research needed”: Here’s the National Cattlemen’s Beef Association, the National Pork Producers Council, and a standing statement by the Animal Health Institute. (Supporting the FDA move: the Pew Charitable Trusts, the New York Times.)

The draft guidance stays open for public comment for 60 days, until Aug. 30. The required Federal Register posting is here, with the mailing address. Electronic comments can be left at Regulations.gov; the docket number for the guidance is FDA-2010-D-0094; 33 comments have been posted already.

Antibiotic resistance in food — some governments pay attention

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Folks, I told you Tuesday about a Congressional hearing on antibiotic resistance, featuring NIAID Director Dr. Anthony Fauci and CDC Director Dr. Thomas Frieden. Not much new was said, but it’s encouraging that the hearing was held at all. (Fauci testimony here, Frieden here.)

Coincidentally, constant reader Pat Gardiner of the UK alerted me to a gathering being held on the same day in Ireland, by the quasi-government agency SafeFood—which reports to the North-South Ministerial Council of Ireland, which deals with whole-island issues under the Good Friday agreement, which is more about the Irish political structure than you probably ever wanted to know.

The conference was titled Antimicrobial resistance and food safety and featured government officials and academic researchers from across Ireland. Here’s the agenda, and here’s the press release with the names of key speakers. Even more important, here are links to a report on antibiotic resistance in food that Safefood released in advance of this conference: executive summary and whole thing.  I especially recommend from p.25 in the big report for an accessible discussion of the connections between ag antibiotic use and human health. Key quote among many:

The majority of the evidence acquired through outbreak and epidemiological investigations of sporadic infections, field studies, case reports, ecological and temporal associations and molecular sub-typing studies support the causal link between the use of antimicrobial agents in food animals and human illness. A few papers have questioned this but these have not survived detailed scrutiny.

It’s refreshing to see a government body engage seriously with this emerging issue, which we’ve been talking about for, well, years now, on this blog (sometime this month we passed our 3-year anniversary). I wish, wistfully, that the government doing the discussing was ours.

A blog reaction so perfect I want to print the whole thing…

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(…but I won’t, because it’s not fair use or good blogger behavior. But I want to!)

Melissa Graham of Chicago had a great corporate life — and then she re-evaluated, became a chef and caterer, and began organizing in Chicago for sustainable local food, farmers’ markets, and a family-friendly food system. She blogs at the food and food-policy blog The Local Beet. And she’s written a reaction to SUPERBUG that not only completely gets the book, but is emotional and thoughtful and moving besides.

She says, in part:

Before reading Superbug, the question of confinement raised animals was an ethical one for me – whether the misery inflicted upon animals and, for that matter, the humans working in those facilities by the putrid conditions outweighed the need to eat cheap meat. Even the environmental degradation resulting from the inevitable careless management of CAFOs seemed a distant and intangible casualty. For me, Superbug has changed the argument from one of ethics to a moral imperative. In every hamburger of unknown origin, I see Tony Love’s face or even worse that of Carlos Don IV.

Carlos was another healthy kid who left on a school trip to the mountain and returned with a 104°F fever. The first doctor diagnosed Carlos with walking pneumonia so his mother kept him home bundled and hydrated until she realized that he was beginning to hallucinate. She rushed Carlos to the hospital and the doctor’s ultimately diagnosed his condition as MRSA. A long slow death march ensued during which Carlos’s lungs dissolved and clotting choked off the blood to his lower intestines, legs and arms. In two weeks, he was dead.

After reading Carlos’s story late in the evening, I woke a bewildered little locavore from a dead sleep to scrub his hands clean. I hugged him as tightly as I could.

…[recently] I had the pleasure to hear Ruth Reichl speak and she implored the audience to stop eating confinement raised animals. As she put it, if everyone stopped buying them and eating them, the practice would be history. Knowing what I now know, I think it’s our moral duty.

To give the post the traffic it deserves, please go here.

Antibiotics in chickens, and links to human infections

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From the January issue of Emerging Infectious Diseases, published by the CDC (and therefore free. Must I keep urging you to read it? Go, already), here’s a roundup of bad news about bad bugs.

In Canada, researchers from that country’s Public Health Agency have found a “strong correlation” between the use of ceftiofur, a third-generation cephalosporin, in chickens; the rates of a resistant strain of Salmonella in chickens; and the appearance of that same strain in humans. The strain is Salmonella enterica serovar Heidelberg, one of the most common salmonella strains in North America, and one which can be nasty: It may cause mild illness, but also causes septicemia and myocarditis and can kill. Quebec created an unplanned natural experiment: Hatcheries there were broadly using ceftiofur until 2004, backed off from its use in 2005 and 2006, and then began using it again in 2007 in response to a growing problem with a particular infection. When the drug was withdrawn, resistant infections in birds and humans plunged; when it was reintroduced, they rose again. (Look at the black and red lines in the graph above left.)

Meanwhile, broiler chickens in Iceland are passing fluoroquinolone-resistant E. coli to humans there. Researchers at the University of Iceland were puzzled by an earlier finding that bacteria resistant to fluoroquinolones (a family that includes the human drug Cipro) were increasing among chickens raised in Iceland, despite strict controls on antibiotic use in food animals and stringent disinfection in chicken batteries after cohorts of birds were sold for slaughter and removed. They have two findings: The source of the resistant bacteria in the birds appears to be feed contaminated with resistant E. coli; and resistant bacteria in Iceland residents are microbiologically indistinguishable from those in the birds. Because E. coli is a very diverse organism, the very close resemblance between the isolates from chickens and the isolates from humans pins chickens as the likely source.

And just to make clear we’re not blaming every microbiological evil on farming: Seagulls in Portugal have been found carrying multi-drug resistant E. coli in their feces. The public health concern here is obvious: Just think back to the last time you were at a beach, or anywhere else seagulls frequent, and envision a seagull perch — and the masses of seagull droppings streaking it. Now imagine those droppings transmitting antibiotic-resistant E. coli into the surrounding environment: the boardwalk, the beach, the towels… Additional problem: Seagulls are migratory birds, so the resistant bacteria easily cross borders and oceans.