Maryn McKenna

Journalist and Author

For a moment, a different pathogen: swine flu

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Constant readers, some of you know that I have a long history of covering pandemic flu (I wrote the first story in the US media about avian flu back in 1997, and covered pandemic preparations for years). I’ve had that somewhat on the back burner while I worked on this MRSA project and handled some personal family matters, but with the book manuscript almost completed and the family stuff ending, looks like I will be covering flu again.

For now, let me direct you to some resources:

  • My colleagues at the news site of the Center for Infectious Disease Research and Policy are doing yeoman work with very few resources. Some of you many know CIDRAP as home base of Michael Osterholm, PhD, advisor to several administrations on pandemics and disasters and pandemic-flu interviewee on Oprah. The CIDRAP site includes a series I wrote about 18 months ago now that explains why it will be so hard to achieve a flu vaccine in time for the start of a pandemic.
  • Helen Branswell of the Canadian Press is the most connected flu reporter on the planet; because she is at a wire service, there is no one page to send you to, but Google her name, or follow her on Twitter @diseasegeek.
  • My fellow global-health reporter Christine Gorman, formerly of TIME Magazine, has put up a thoughtful post with many links on her blog Global Health Report.
  • There are seriously good flu blogs (also in the blogroll) at Effect Measure, H5N1, Avian Flu Diary, Scott McPherson’s Journal, A Pandemic Chronicle and the indefatigable preparation-conscious groups bloggers at ZoneGrippeAviare (in French and English).
  • University of Iowa epidemiologist and zoonotic-disease expert Tara Smith, PhD., is blogging thoughtfully at Aetiology.
  • Several years ago I helped conduct a conference at Nieman House at Harvard, the home base of the Nieman Foundation and fellowships, on understanding and getting ready to cover pandemic flu. The materials are here.

That’s all for now. More soon, I expect on both MRSA and flu.

ST398 found again — in Italy

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There’s a letter in the upcoming issue of Emerging Infectious Diseases (hat tip Pat Gardiner) alerting the medical community that “pig MRSA” ST398 has been found in Italy, adding t the steadily enlarging list of countries where this strain has been identified.

(NB: Because most of these surveys are one-offs, we don’t yet know whether ST398 is truly expanding its range, or has always been there, but no one looked until now.)

Angelo Pan and colleagues of the Cremona Hospital and other institutions report that a pig-farm worker was discovered to have a severe pyomyositis (abscess buried in muscle):

The case-patient was a 58-year-old man admitted to a surgical department in Cremona, Italy, on July 30, 2007, because of a 1-week history of fever and intense pain in his right buttock. He worked on a pig farm, was obese, consumed high volumes of wine (1.5 L/day), was taking medication for hypertension, and had not had recent (<5 years) contact with the healthcare system. At the time of hospital admission, he was moderately ill, oriented, and cooperative. His right buttock was extremely painful. He reported neither recent trauma nor anything that would explain infection. ...
Based on clinical and magnetic resonance imaging data, the diagnosis was cellulitis, pyomyositis, and pelvic multiloculated abscess of the buttock. A needle aspiration of the abscess, guided by computed tomography, was performed. Because of persistent fever (38.5°C), oral ciprofloxacin was added to the patient’s treatment regimen on day 3. Blood and abscess cultures yielded MRSA that was sensitive to glycopeptides, rifampin, linezolid, gentamicin, and mupirocin and resistant to co-trimoxazole, macrolides, clindamycin, and fluoroquinolones. After treatment was switched to vancomycin plus rifampin, the patient’s general condition improved; he was discharged from the hospital after 24 days.

An investigation was launched, and the results were intriguing:

Two fellow workers were colonized with S. aureus, 1 with methicillin-sensitive S. aureus (MSSA) and the other with MRSA. The pig farm, a farrow-to-finish production farm with 3,500 pigs, was screened for MRSA … Dust swabs were taken from 5 areas of the farm; 7 MRSA isolates were detected.
The isolate from the patient belonged to spa type t899, was ST398, carried an SCCmec type IVa cassette, and was PVL negative. The isolate from the MRSA-colonized worker was a t108 strain carrying SCCmec type V. The isolate from the MSSA-colonized worker was identified as t899. The dust swabs yielded 7 isolates: 2 belonged to t899 and carried SCCmec IVa; 5 belonged to t108 and carryied SCCmec V. The isolates obtained from the patient, farrowing area 7, and gestation area 1 were indistinguishable (i.e., same spa type, SCCmec type, and ST profile; Table), thus confirming the animal origin of transmission.

So, we have:

  • A high rate of carriage on the farm (3 of 4 workers with ST398, either MR or MS)
  • A strain-type that is both MRSA and MSSA, suggesting that in its drug-sensitive state it can acquire resistance factors rather easily
  • A PVL-negative strain that nevertheless causes invasive disease requiring more than 3 weeks hospitalization

None of these are good news.

The authors very sensibly call for more public-health attention to this strain, which — we have contended before — is long overdue:

…attention should be given to the emergence of MRSA strains among animals, and continuous surveillance in humans should monitor the extent of disease from MRSA ST398, especially in areas of intensive animal farming. Collaboration between infectious disease specialists, microbiologists, and epidemiologists, on both the human and the veterinary sides, should be strengthened and readied for appropriate action whenever complex, zoonotic, public health issues occur.

The cite is: Pan A, Battisti A, Zoncada A, Bernieri F, Boldini M, Franco A, et al. Community-acquired methicillin-resistant Staphylococcus aureus ST398 infection, Italy [letter]. Emerg Infect Dis [serial on the Internet]. 2009 May. DOI: 10.3201/eid1505.081417

Does ethanol production produce resistant bacteria too?

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One of the challenges of disappearing down the rabbit hole of a gnarly chapter — gee, it’s dark down here — is that I get behind on my RSS feeds, and suddenly every entry in my Google Reader is at 1000+ and it’s all just too daunting.

So, trying to catch up a bit, I found two related, interesting and troubling stories from the Associated Press (4 April) and the online magazine Grist (7 April — yes, I said I was behind…).

Synopsis/synthesis: Corn-based ethanol, former darling of the energy and large-scale agriculture industries, suddenly doesn’t look like such a good idea – and not just because the market for it is crashing. Turns out that ethanol is made by adding yeast and sugar to corn mash; the yeast convert the carbohydrates to the alcohol that is the basis of the fuel. (Yes, just like making beer.) However, the mash is particularly attractive to Lactobacillus and other bacteria that produce lactic acid as a waste product rather than alcohol, and a tank full of lactic acid doesn’t make very good fuel. So, to keep the bacteria under control, ethanol producers add antibiotics. Specifically, penicillin and erythromycin — you’ll recognize those — and tylosin and virginiamycin, two macrolides, related to erythromycin, that are approved in the US for veterinary use.

Now, the problem with this practice, as you might predict, is that if the mash is not appropriately dosed, the presence of antibiotics within it can prompt some of the bacteria to develop resistance. (Here’s an article from the trade magazine Ethanol Producer discussing just that possibility.)

And the further complication of this is that the leftover mash, now called “distillers’ grains,” is sold as animal feed. Ask yourself: Where in animal production are animals most likely to eat grains? Answer: At finishing, in feedlots. In other words, fermented grains that may contain antibiotic residue, and may contain resistant bacteria, are being sold as feed to animals that are already being raised in conditions that have been shown to foster the development of resistant bacteria through subtherapeutic and prophylactic antibiotic use. In fact, some research has drawn an explicit link: Kansas State University scientists have found higher levels of E. coli O157 in the guts of cattle that were fed distillers’ grains.

All of this was new to me, but there’s an additional facet to the story that the AP and Grist pieces don’t highlight, and that just makes my head hurt: the use of virginiamycin. For those new to the story, virginiamycin is an allowed, widely used veterinary antibiotic in the US. However, it is not used in the European Union: It was banned there in 1998 because the EU’s ag authorities believed that it promoted resistance to the drug Synercid (quinupristin+dalfopristin), which is a drug of last resort against vancomycin-resistant bacteria such as VRE. (Here’s a Lancet paper that talks about that resistance mechanism.) Synercid was approved by the FDA in 1999 — two years after Synercid resistance had already been found in the US. (For a long but cogent explanation of the complex story of virginiamycin, see the book The Killers Within.)

So, just to recap: We have an industry whose long-term earnings are shaky, whose economic survival is partially secured by the sale of its waste product, and which via that waste product is putting antibiotic residues and antibiotic-resistant bacteria into the environment, and is conveying them into food animals, and is making particular use of an antibiotic that other countries have banned because they believe that, via its use in animals, it exerts an adverse impact on human health.

Something to remember the next time ethanol subsidies come up.

Appearing today on The Ethicurean

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Constant readers, I want to let you know that the terrific food policy blog The Ethicurean (motto: “Chew the right thing“) very kindly had me over to do a Q&A on MRSA in meat. Please take a look and let them have some clicks: They are smart people thoughtfully elucidating a difficult subject, and worth following.

(And I would say that even if they hadn’t called me the “Superbug supersource,” honest.)

More MRSA in pigs, in Portugal

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A brand-new report, in a letter to the International Journal of Antimicrobial Agents, indicates that ST398 “pig MRSA” has been found in Portugal for the first time.

Constanca Pomba and colleagues from the Technical University of Lisbon swabbed and cultured the noses of pigs and veterinarians on two pig farms in different regions of Portugal, and also checked the air at both farms.

What they found:

  • On Farm A: All pigs and the veterinarian positive for ST398, the pig-origin strain that has been found so far in Iowa, Ontario, the Netherlands, France, Denmark, Germany and Austria and has, depending on the country, caused human disease and/been found on retail meat. The veterinarian was transiently colonized, which is to say that he was not carrying the bug long-term.
  • On Farm B: All pigs — but neither of two veterinarians — positive for a different MRSA strain, CC (or ST) 30. This is very interesting, because CC30 is usually a drug-sensitive strain (MSSA, methicillin-sensitive S. aureus), and has been found in pigs primarily in Denmark and France. In Portugal, it is a human MSSA hospital-infection strain.

Strains from both farms were resistant to tetracycline; this is turning out to be a great marker for these strains having emerged due to antibiotic pressure in animals, because tetracycline is very commonly used in pigs. but not much used for MRSA in humans. The strains have the genes tetK and tetM, so they are resistant not just to tetracycline itself, but to the whole class of tetracyclines including doxycycline and minocycline. The Farm B strains also carried the gene ermC, which encodes resistance to erythromycin.

So what does this tell us?

  • First, that (once again), every time people look for ST398, they find it; it is now a very widely distributed colonizing bug in pigs, and is repeatedly spreading to humans. What we don’t know, because all these studies are so new, is whether ST398 is actively expanding its range, or has been present in all these countries for a while. We have been anticipating its presence or spread (take your pick at this point) through the European Union because of open cross-border movement of food animals, meat, and agriculture and health care workers.
  • And second, it should tell us that it is really past time to start looking for this more systematically. Every finding of ST398 that we have (long archive of posts here) is due to an academic research team who decided to look for the bug. None of the findings, to date, have come from any national surveillance system. (NB: Except for the first human colonizations in the Netherlands, which were found as a result of the national “search and destroy” rules in hospitals.)

Of note, the European Union is running a study now that is supposed to report ST398 prevalence at any moment (as they have been saying since 2007). It is not expected to be comprehensive, since it was piggy-backed onto another study, but it is something. The US government has not been so enterprising.

The cite is: Pomba, C. et al. First description of meticillin-resistant Staphylococcus aureus (MRSA) CC30 and CC398 from swine in Portugal. Intl J Antimicrob Agents (2009), doi: 10.1016/j.ijantimicag.2009.02.019

More news on ST398, “pig MRSA,” in Europe

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Two new papers have been posted ahead-of-print to the website of Emerging Infectious Diseases, the free journal published monthly by the CDC. (It’s a great journal. Just go.)

One, from the Austrian National Reference Center for Nosocomial Infections, reports that out of 1,098 isolates from infected or colonized hospital patients collected between 2006 and 2008, 21 were ST398, the “pig strain” that we have talked so much about here. Of the 21, 15 were colonized and 5 had actual infections (one person lost to followup, apparently); of the 5 infections, 4 were minor, and one was a very serious infection in a knee replacement in a 64-year-old farmer.

In a separate piece of math that is not fully explained, the researchers note that the prevalence of ST398 in Austria has risen to 2.5% of MRSA isolations, from 1.3% at the end of 2006 — close to double, and especially rapid given that Austria’s very first ST398 sample was found during 2006.

The second paper is much more complex; it deals with the prevalence of multiple MRSA strains in the cross-border region where Germany, Belgium and the Netherlands bump up. (Apparently EU bureaucracy calls an area like this a “Euregio.” Ah, jargon. This is the EMR, the Euregio Meuse-Rhin.) The concern here is that MRSA prevalence is very different in different EU countries; in the Netherlands, which has an active surveillance “search and destroy” policy in its hospitals, MRSA represents only 0.6% of all staph — but the rates are 13.8% in Germany and 23.6% in Belgium, which either do not do active surveillance or began to much more recently. So as people move freely across borders, from a high-prevalence area to a low-prevalence one, they could bring a resistant bug with them that then could find a foothold because there is an open ecological niche.

This study analyzed 257 MRSA isolates from hospitals in the border region that were collected between July 2005 and April 2006: 44 from Belgium, 92 from Germany, and 121 from the Netherlands. Of the Dutch isolates, according to typing, 12 (10%) were ST398. These were all from patients who were identified as colonized when they checked into hospitals practicing “search and destroy”; none represented actual infections.

So, what does this tell us? A couple of things, I think. First, it documents the continued presence of ST398 in Europe; in other words, it wasn’t a blip and doesn’t appear to be going away. Second, it underlines both that you find it when you look for it, and also that it remains a small portion of the overall MRSA picture. But, we immediately have to add, it’s a small portion that wasn’t present at all just a few years ago.

And it should underline that what we need, and are not getting in this country or in Europe, is much more comprehensive surveillance and research to understand ST398’s place in MRSA’s natural history, so that we can understand where it is only an emerging disease, or truly an emerging threat.

The cites are:
Krziwanek K, Metz-Gercek S, Mittermayer H. Methicillin-resistant Staphylococcus aureus ST398 from human patients, Upper Austria. Emerg Infect Dis. 2009 May; [Epub ahead of print]
Deurenberg RH, Nulens E, Valvatne H, et al. Cross-border dissemination of methicillin-resistant Staphylococcus aureus, Euregio Meuse-Rhin region. Emerg Infect Dis. 2009 May; [Epub ahead of print]

MRSA news from Europe – Society for General Microbiology

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The annual meeting of the UK’s Society for General Microbiology is taking place this week, so here’s a quick roundup of MRSA-related news. As with these posts from a year ago, abstracts are not online; in a few cases there are press releases from the science-news service EurekAlert.

  • MRSA-colonized patients who have been identified in a hospital by active surveillance culturing may not need to be isolated to prevent their bacteria being transmitted to other patients by healthcare workers — provided hospital staff and visitors adhere to very vigorous handwashing. (P. Wilson, University College Hospital, London; press release)
  • An engineered coating made of titanium dioxide with added nitrogen could be employed as an antibacterial surface in hospitals; exposure to ordinary white light activates the compound to kill E. coli and may be useful against MRSA also. (Z. Aiken, UCL Eastman Dental Institute; press release)
  • The natural antiseptics tea tree oil and silver nitrate enhance bacterial killing when combined, which may also allow them to be used in lower doses – important for avoiding toxicity. It may also be possible to deliver them encapsulated in engineered sphere made of lipids called liposomes. (W.L. Low, University of Wolverhampton; press release)
  • Overuse of antibiotics in farming is not only breeding resistant bugs in animals, it is also changing soil ecology and depleting nitrogen-fixing bacteria that improve soil fertility. The antibiotics are affecting soil when manure from drug-using farms is spread as fertilizer. (H. Schmitt, University of Utrecht; press release)

British newspaper discovers ST398, says no UK cases – incorrect

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The UK’s Sunday Express takes note today of “pig MRSA” ST398 (full post archive here) in a story that is both somewhat alarmist and oddly incomplete, since it misses a piece of news that I told you about here last June.

The Express story raises the alarm over ST 398 in pigs in the Netherlands, colonizing farmers and causing human illnesses. There is nothing in it that we have not already discussed here many times, but it is nevertheless worth noting because it appears to be the first report on ST398 in a year in a major UK paper. (Credit for what I think is the first mention of ST398 in the Brit press goes to the Independent.)

But here’s what’s odd about the story: It says (italics mine),

A DEADLY new form of MRSA is believed to be spreading from farm animals to humans – already the bacteria has been found in hospitals abroad.
It is the first time the bug has spread in this way and experts believe excessive use of antibiotics in factory-farmed animals may be behind its development.
“Farm animal” MRSA, as it is known, can cause a raft of illnesses including skin infections, pneumonia, bone infections and endocarditis. …
The new MRSA bug, known as ST398, could reach hospitals in the UK, causing serious illness and death among vulnerable patients. (Byline Lucy Johnstone and Martyn Halle)

However as constant readers here already know, ST398 has already has been found in UK hospitals: in three unrelated patients — one adult and two newborns — in a Scottish hospital, none of whom had any relationship to pig-farming.

Credit for pushing the story of ST398 in the UK goes to the organic/sustainable farming group the Soil Association, who have aggressively monitored and lobbied for the extremely slow reveal of ST398 by the British government. As the issue now stands, the UK tested British pigs for ST398 colonization in 2008, but has not revealed the results. It has not yet tested retail meat in the UK, some of which is imported from the Netherlands, the location where the most ST398 has been found.

While that sounds like foot-dragging, it is still ahead of the US: Except for the study published in January by Tara Smith’s team at University of Iowa (paper here, my Scientific American story here), there has been no testing of pigs in the US, certainly none by government agencies.

(Hat-tip to Pat Gardiner for alerting me to the Sunday Express article.)

Bill in Congress: “Preservation of Antibiotics for Medical Treatment” Act

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Important news for anyone concerned about the spread of “pig MRSA” ST398: Rep. Louise Slaughter (D-NY) and Sen. Edward Kennedy (D-MA) have introduced a bill that would restrict important classes of antibiotics for use against disease only, taking them out of the realm of subtherapeutic use or growth promotion in agriculture. The bill would allow the use of the antibiotic classes for disease in animals as well as in humans; the intent is to preserve the drugs’ effectiveness for as long as possible.

The text of the bill, the Preservation of Antibiotics for Medical Treatment Act of 2009, is here.

A Reuters story in which Slaughter predicts the bill will have a difficult time is here; she has introduced it several times in the past decade, but it has never made it through.

Support from the Pew Commission on Industrial Farm Animal Production is here. An earlier version was supported by the American Academy of Family Physicians here.

The National Pork Producers’ Council’s response is here.

(Hat tip to Barry Estabrook at Politics of the Plate and to Melinda Hemmelgarn, the FoodSleuth.)

“Sick as a pig” – from ST398

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Constant readers, I am at the annual meeting of the Society for Healthcare Epidemiology of America, where there is a lot of news about MRSA in hospitals. I hope to post on that over the next few days.

In the meantime, though, I want to pass on several pieces of news about ST398, the “pig strain” that we have talked so much about.

First, the Soil Association, the British organic/sustainable farming group that has done much work elucidating the spread of ST398 and making the link between that bug and antibiotic use on farms, has released an online documentary about ST398 called Sick as a Pig. You can watch it here, and here is the Soil Association’s press release:

…40% of Dutch pigs and up to 50% of Dutch pig farmers are now carrying the new strain, which is also spreading to the wider population. Although this type of MRSA was first detected in humans in the Netherlands as recently as 2003, it now causes almost one in three cases of MRSA treated in Dutch hospitals.
It is not yet known whether any British pigs are affected by the new strain of MRSA (called ST398) since the results of testing, which was required by the EU and carried out in 2008, have not been made public.
Several countries have already published the results of their own tests revealing significant levels of MRSA in national pig herds. The European Food Safety Authority has said that, ‘It seems likely that MRSA ST398 is widespread in the food animal population, most likely in all Member States with intensive animal production’.

Second, here is a paper from last fall that somehow slipped by me: in the CDC journal Emerging Infectious Diseases, a report of two cases of ST398 infection in men in Sweden. Neither had any contact with farming or animals.

The first patient, a previously healthy 36-year-old male physiotherapist, sought medical care in March 2006 for a small abscess in his axilla. Culture of the abscess grew MRSA. Presence of mecA gene was confirmed by PCR. During the next 2 months, furunculous [sic] developed twice, caused by the same strain. His youngest child, adopted from China, had been found to be MRSA positive (throat, perineum, and a small wound) a month earlier during routine screening for adopted children. During subsequent screening of the family, the older sister, adopted from South Korea, was also found positive (throat). Both parents were negative for MRSA at that time, which suggests that the father was newly infected when his abscess developed and that he had not acquired the strain abroad. Also, spa typing indicated that the children carried different strains from that of the father and from each other (t286, t1434). Subsequent screening of family members for MRSA on several occasions found only the father to be repeatedly positive.
The second patient, a 43-year-old male clerk, also previously healthy, sought medical attention during the summer of 2007 for a MRSA-infected elbow wound. Follow-up examination determined that he carried MRSA also in the perineum and in a chronic external otitis eczema. He was later hospitalized for a larger abscess that required surgical drainage. His family members reported no symptoms and were thus not screened for MRSA.

Of note, the men’s strain (ST398, t034) carried the two genes that express the toxin PVL, which is unusual in ST398, though characteristic of CA-MRSA USA300, the dominant community strain in the US. The role that PVL plays is very controversial: Some research groups believe it is responsible for the rapid tissue destruction that can accompany USA300 infection (in penumonia and some soft-tissue infections, for instance), while others vociferously disagree.

More MRSA in meat, in Austria

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There’s a new publication out that I haven’t been able to lay my hands on yet, except for the abstract. But here’s what I know: A group from the Austrian Agency for Health and Food Safety and two Austrian national reference laboratories have published a paper saying that ST 398, the “pig strain” of MRSA that we have been talking about here for a year now, has surfaced in Austria in environmental samples, in humans and also in food — presumably meat, but the abstract doesn’t say that.

The abstract in Wiener Klinischer Wochenshrift (Viennese weekly clinical review, if my college German is still with me) says:

…the emergence of ST398 is not just a Dutch problem, as reports on livestock colonization and human infections are appearing worldwide. In Austria, the ST398 lineage has been detected in dust samples from pig breeding facilities and in food samples. Since the first Austrian detection of this emerging lineage in 2006, 21 human isolates, partially associated with infections, have been observed. MRSA has to be regarded as a new emerging zoonotic agent and livestock may constitute a growing reservoir of the ST398 lineage.

The University of Minnesota (where, as you all know, I work part time for the excellent infectious-disease news site CIDRAP; please go) does not have electronic access to this journal, and ILL is slow. If anyone else has a copy and would like to share, I would be grateful.

The cite is: Springer, B. et al. Methicillin-resistant Staphylococcus aureus: A new zoonotic agent? Wien Klin Wochenschr. 2009 Feb;121(3-4):86-90. Abstract here.

New York Times takes up “pig MRSA” ST398

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Constant readers, I know that many of you are very interested in ST 398, the “pig strain” of MSRA that has caused both mild and life-threatening human infections in Europe and has been found in retail meat in Canada and on farms and in farmers here in the Midwest. So I just want to bring to your attention that New York Times columnist Nicholas Kristof takes up the topic today, in the first of two promised columns: Our Pigs, Our Food, Our Health.

In today’s piece, he describes an apparent epidemic of skin and soft-tissue infections in a pig-farming area of Indiana that caught the attention of a local family physician, who subsequently died.

What we’d need to know, of course — and may never know, given that the investigation may have ended with the doctor’s death — is what strain of MRSA those local folks had. They may have ST 398, picked up if they worked on farms, or if it migrated out of the farms via groundwater or dust or flies. Or they may have USA300, the human community-associated strain, which in some areas is astonishingly common — a fact that most people don’t appreciate if they have heard only about the invasive child-death cases or the outbreaks in sports teams.

The full archive of posts on MRSA in animals is here and stories only about ST398 are here.

MRSA and animals — an elephant, this time.

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So, constant readers, I have wrestled another chapter to the ground — and thus have a few minutes’ breathing space to talk about a story that some of you have asked about privately. I’ve been wondering whether to post on this, because the entire episode is in the book, and I don’t want to scoop myself. But it’s so interesting, and so sad, that it seems worthwhile.

This episode happened a year ago, and was reported at a couple of medical meetings last fall, but it is in the news now because it was written up last week in the CDC’s Morbidity and Mortality Weekly Report or MMWR. (Which is the best-read magazine that you have never heard of. Hundreds of thousands of people all over the world read it every week for the latest in disease news. It’s free. Go, already.)

So, the brief synopsis: In late January 2008, the San Diego Zoo’s Wild Animal Park noticed that a baby African elephant, born in late November 2007, had broken out in pustules on her ear, neck, elbow and leg. Three of her caretakers had skin infections also. The zoo launched an investigation, assisted by a CDC Epidemic Intelligence Service officer who is assigned to California; they were concerned that the caretakers had unknowingly picked up a disease from the baby, who had been born early, was not thriving and was being intensively hand-reared by the zoo staff.

But in fact, it was more complicated than that. The pustules were MRSA, of course — but they were not ST 398, the animal strain that we have talked about so much here. Instead, they were USA300, the community-associated human strain that has zoomed to dominance all over the country. But there was no MRSA in the elephant herd, which the baby had not had contact with since late December. The reconstructed chain of transmission looked more like this: from an unknowingly colonized human to the baby elephant, who was medically fragile and had been isolated from her herd, and then from the elephant to the rest of the human “herd” who were caring for her. The strain involved was USA300, In the end, five human infections and three colonizations were laboratory-confirmed, and 15 other infections were suspected but not confirmed.

The humans recovered; most of their infections were so minor as to need no treatment, though three of them took oral antibiotics. The poor little elephant was not so lucky. She had multiple other illnesses, and she was euthanized on Feb. 4, 2008. The MRSA did not cause her death — by the time she died, the infection had resolved — but as one of the zoo staff told me, “It certainly didn’t help.”

So what does this tell us? Well, for zoo personnel, it tells them what to do for next time: More complete infection control especially around vulnerable animals. For microbiologists, it’s an expansion of MRSA’s range: No one had ever seen it in an elephant before.

For animal owners, it’s a warning and reminder. We’ve known for a while that community strains can transiently colonize pets, staying in the animal’s nose or elsewhere on the body just long enough to reinfect a human — in fact, an emerging piece of advice for physicians dealing with recurrent MRSA in families is, “Check the dogs and cats, too.”

And for the rest of us, it suggests, one more time, how extremely adaptive and inventive MRSA is, and that we should never underestimate its ability to surprise.

Industrial farming, bacterial spread 2 – or: Flies. Ick.

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There’s a brand-new paper in the journal Science of the Total Environment that has some unnerving things to say about the link between very large scale farming, use of antibiotics in food animals, development of resistant organisms, and transmittal out into the larger environment.

Via flies.

Not to be unscientific, but: Ick.

A team from the Bloomberg School of Public Health at Johns Hopkins (who have done a number of studies on the spread of antibiotic-resistant organisms from farms to the outside world) decided to test the links in a chain of hypothesis that goes like this:

  • Antibiotics are used in large amounts in poultry production.
  • Antibiotic-resistant organisms are produced within the birds.
  • Antibiotic-resistant organisms leave the batteries via poultry litter (“excreta, feathers, spilled feed, bedding material, soil and dead birds“).
  • Poultry litter is stored in open sheds until it can be used as a soil amendment.
  • Flies have unrestricted access to poultry litter.

The tests were: sampling poultry litter from three farms in the Delmarva Peninsula (for non-US readers, that’s a portmanteau word for contiguous areas of the states Delaware, Maryland and Virginia, home to about 600 million chickens each year); trapping flies at 8 locations within 100 meters of farm boundaries; and assaying both litter and flies for the presence of resistant organisms and resistance genes.

And the findings were: Oh, lots and lots. Litter piles at all three farms contained resistant organisms — E. faecium, E. faecalis and our particular interest, Staphylococcus (multiple species, including three strains of S. aureus) — throughout the 120-day study period. All 8 fly traps did as well. All of the litter contained enterococci and staph strains that were resistant to 3 or more antibiotic classes. Seven of the 8 fly traps yielded multi-drug resistant enterococci, and 3 yielded multi-drug resistant staph. The resistance factors identified were for drugs that the FDA classifies as “critically or highly important” to human medicine: “penicillin, tetracyclines, macrolides, lincosamides, aminoglycosides and streptogramins.” Oh, and the fly species captured in the traps had an average range of 2 miles.

Of note, among the isolates discovered was one staphylococcus with high-level resistance to vancomycin.

The authors say:

This study strongly suggests that flies in intensive poultry production areas, such as the Delmarva Peninsula, can disperse antibiotic resistant bacteria in their digestive tracts and on their exterior surfaces. Dispersion of resistant bacteria from poultry farms by flies could contribute to human exposures, although at present it is difficult to quantify the contribution of flies. Flies may also transfer bacteria from fields amended with poultry waste.

The cite is: Graham JP et al., Antibiotic resistant enterococci and staphylococci isolated from flies collected near confined poultry feeding operations, Sci Total Environ (2009), doi:10.1016/j.scitotenv.2008.11.056. The ahead-of-print abstract is here.

Industrial farming, bacterial spread – another connection

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We’ve talked a lot here about the spread of MRSA ST 398, the “pig strain,” subsequently found in other animals and in retail meats in various countries; and also about the likelihood that antibiotic use in large-scale farming fosters the growth of resistant organisms; and also about the way that resistant bacteria from large-scale industrial farms end up in the larger environment via groundwater and airborne dust. (Use these links to call up all the ST 398 stories and related agriculture and food stories.)

Here’s an emerging story that should illuminate some of the dangers we are discussing. Note, it’s not about MRSA, and it’s not about resistant organisms, but it is an object lesson on how industrial-size farms can spread bacteria through the environment.

Last year, there was an outbreak of an unusual type of E. coli — a strain called O111 — in Oklahoma. There were 341 known cases, 72 hospitalizations, one death. The outbreak centered on a Locust Grove, OK restaurant called the Country Cottage, which used a private well. Here’s the Oklahoma State Department of Health wrap-up of that outbreak; no source for the E. coli was ever identified.

Now comes the Oklahoma Attorney General to say that the source has been identified: Poultry DNA has been found in wells in the area, and the AG contends it is because of the use of poultry litter — manure, feathers, the stuff that falls to the bottom of a chicken house — as fertilizer on local fields.

Now, some cautions: There is no indication in the media reports (I’m looking for a report or release from the AG’s office but haven’t found one) that the particular E. coli strain has been found; that outbreak has burned itself out. And also, the Oklahoma AG has apparently been fighting with the poultry industry and the state of Arkansas for several years over poultry-litter pollution in the Illinois River watershed. The poultry industry, naturally, disagrees that this practice is a health threat.

But if the Oklahoma AG is correct, and there is evidence that poultry manure is putting pathogens into the water supply far from poultry farms, then that would be one more link in the chain of evidence that connects industrial-scale farming, agricultural antibiotic use, development of resistant organisms, presence of those organisms in the environment, and human health effects.

Bad news from Australia: MRSA in water supplies

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The Brisbane Courier-Mail reports that scientists in Australia have found MRSA and VRE from hospital sewage in rivers and lakes throughout the state of Queensland, and have been trying for two years to get their provincial government to pay attention.

Secret tests on waste water discharged from 28 Queensland hospitals and clinics revealed the widespread presence of MRSA (Methicillin resistant Staphylococcus aureus) and VRE (Vancomycin resistant Enterococci).
However there was no evidence the potentially lethal organisms had made their way into drinking water.
A Central Queensland University scientist who helped carry out the research told me 97 per cent of hospital sewage discharge lines tested positive for antibiotic resistant bacteria.
He said 70 per cent of hospital discharges tested positive for both MRSA and VRE.
“We got a lot more of those bacteria than we thought possible,” he said. … “Even though they have passed through a treatment process, the bacteria are most likely getting back into natural waterways, dams and ponds used for swimming, boating, fishing and in food production.” (Byline: Des Houghton)

The report was presented to the Queensland parliament by a member in 2007, ignored, and presented again last week. (Note for US readers who click through to the story, from my UK childhood: “Tabled,” in parliamentary parlance, means “brought forward” or “introduced” — not “postponed” as we would interpret it.)

The wastewater was treated in a sewage plant and then tested — but the usual tests look for enteric pathogens such as E. coli, not for MRSA, so the water passed testing without MRSA’s presence being detected.

There have been similar studies in Portugal, South Africa and Nigeria. In the US, MRSA and other resistant bacteria have been found in groundwater and airborne dust, but that has been due to leakage from industrial farming. I’m not aware of anyone doing this sort of study, with organisms escaping from hospitals, in this country. If anyone does know of one, and has a cite, please comment!

More MRSA, more meat – poultry, this time

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Constant readers: Fresh from the journal Emerging Infectious Diseases — posted AOP (electronic publication/ahead of print) this afternoon — comes more news of MRSA ST 398, the “pig strain,” in food animals. This time, it’s chickens, in Belgium.

The authors (from Ghent University and the Veterinary and Agrochemical Research Center in Brussels) took swabs from living chickens — laying hens and broilers — from 24 farms, 50 layers and 75 broilers total; one broiler-raising farm was sampled twice. They found no MRSA in the layers, which is important for reasons I’ll get to in a moment, and ST 398 in 8 broilers. From each chicken, they took two samples, nasal and cloacal, and in the 8 positive chickens, they got 15 MRSA isolations; one cloacal swab was negative. Of the positive chickens, several (I deduce three, but the math is a bit cloudy) were spread across the two visits to the farm that was sampled twice. Since chicken farms are depopulated between batches — yes, just what it sounds like, farms sell/kill all the birds and clean the place — that finding suggests that MRSA is persisting in the environment on that farm.

Important point: This strain was ST 398, which we here have been calling the pig strain from many previous findings, most of them in pigs. However, ST 398 is an identification using a particular technique called MLST (multi-locus sequence typing), which is used for this strain because the standard typing method, PFGE (pulsed-field gel electrophoresis), did not return a readable result when the strain was first identfied back in 2004. (Trivia: That’s why the initial reports of this strain called it NT, for “nontypeable.”) It’s becoming increasingly clear, though, that ST 398 is actually a category, not a single strain. And within that category, today’s research is a new find: a strain with the unusual spa type t1456, which has only been found 10 times in the past three years, in Germany and the Netherlands, not in Belgium. The author suggest that this particular strain may be adapting to poultry in the same manner that the ST 398 we have been talking about (different spa type — sorry, I will have to look it up) has adapted to pigs.

So, as before: Why do we care? We care for two reasons: First, because since this strain is in a food animal, the possibility exists that it could contaminate the chickens’ meat during slaughter and pass to humans. As has happened with some ST 398, the humans could be only colonized, and not become ill. But, second, any increase in colonization is a bad thing: The more strains out there, the greater the chance that they will exchange virulence and resistance factors and become something unpredictable.

Now, about those layers, here’s an interesting factor that the authors call out in their paper: Layers, unlike broilers, do not receive antibiotics. The layers did not carry MRSA. The broilers did. It’s a pretty potent argument, in case anyone needed convincing, of the effect of the selective pressure that antibiotic use in food animals exerts on these strains.

The site is: Persoons D, Van Hoorebeke S, Hermans K, Butaye P, de Kruif A, Haesebrouck F, et al. Methicillin-resistant Staphylococcus aureus in poultry. Emerg Infect Dis. 2009 Mar; [Epub ahead of print] DOI: 10.3201/eid1503.080696

More MRSA in meat, and not just pork

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In my excitement over the paper by Tara Smith and team on Friday, I failed to sufficiently emphasize an important new finding. (I included it in my story for ScientificAmerican.com, but it was toward the end.) I feel it deserves a post of its own, so here it is:

The Food and Consumer Product Safety Authority of the Netherlands has found MRSA in 12% of 2,217 samples of meat on sale in the country, including not just pork, but beef, lamb, chicken, turkey and game birds, and 85% of the bacterial isolates were the”pig strain” ST 398.

We have talked before (all posts here) about the potential risk of MRSA in meat, especially ST 398 because it seems to have found a preferred host in pigs. In this study, however, the meat most likely to carry ST 398 was not pork, but turkey, followed by chicken and then by veal, and then by pork.

So what does all this mean? It’s still probably too early to tell: Recall that the first isolations of this bug were in 2004, there have still been only a few papers on it, and this finding by Smith and team is the first identification of the strain in the United States. (Though not in North America, as it was identified in Canada in 2007.) It seems likely that ST 398 may have found a niche in other food animals, and that it contaminates the meat when the animals are slaughtered.

The consensus among the Dutch, though, is that this is an effect of the use of antibiotics in food animals. The romantic image of the Netherlands is as a cute little collection of postage-stamp family farms, but the reality, especially in the southeast of the country, is that they have substantial industrial-sized farms housing thousands of animals on relatively small properties. The only way to grow animals efficiently under such conditions is to keep very close tabs on potential illness, and liberally deploy antibiotics when necessary. (NB, I am not talking here about sub-therapeutic, growth-promoting use, but rather prophylactic antibiotics, given to an entire herd when a certain percentage of the herd shows sign of illness.) Evidence for this, according to the current study’s authors: Meat sold as “biologic” — that’s “organic,” in the US — had a much lower rate of contamination with ST 398.

There are still very few reports of human illness from ST 398, though of those reports, some are quite serious, including wound infections and endocarditis. The concern here, as the researchers interested in it have been saying from the start, is that someone will inadvertently colonize themselves with the organism by touching their eyes or nose while handling meat contaminated with ST 398. Colonization does not necessarily lead to disease, but it does lead to a far greater pool of organism potentially spreading unmonitored through human and animal populations, swapping resistance and virulence factors as it goes.

So, you know what I’m going to say: Wash your hands, wash your hands, wash your hands.

Appearing tonight at SciAm.com

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Folks, last summer I told you about the very exciting though disturbing development of ST 398 MRSA — the “untypable” Dutch strain that originated in pigs and spread to humans — being found in pigs in the US for the first time.

But here’s the brand-new second half of that story: It was found in pig handlers as well, on a set of linked farms — a closed production system that takes pigs from birth to just before slaughter — in Iowa and Illinois.

The full study has just been published, in the online Public Library of Science journal PLoS One.

And I have a story describing the research and the background — and the alarming spread of ST 398 in Europe — up tonight at ScientificAmerican.com.

The cite is: Smith, TC, Male, MJ, Harper, AL et al. Methicillin-Resistant Staphylococcus aureus (MRSA) Strain ST398 Is Present in Midwestern U.S. Swine and Swine Workers. PLoS ONE 4(1): e4258 doi:10.1371/journal.pone.0004258

UPDATE: Lead author Tara Smith talks about the paper at her own blog, Aetiology. And for good measure, her Science Blogs sibling (AKA “scibling”) Ed Yong discusses the paper at Not Exactly Rocket Science.