Maryn McKenna

Journalist and Author

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.

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.

“Pig MRSA” in New York City – via the Dominican Republic?

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Folks: Back in October, I broke the news for you of an intriguing poster presentation at the ICAAC meeting. It revealed the discovery of ST 398, the anomalous staph strain found in pigs, pig farmers and health care workers in Europe, in residents of a Dominican-immigrant neighborhood in northern Manhattan, and also in the Dominican Republic.

Because there is so much traffic back and forth between those neighborhoods, the authors theorized that people are providing an “air bridge” for the bacterium — though they were unable to say whether the bug is moving from the Dominican Republic to the United States, or vice versa.

I was unable to link to that presentation at the time, because it was a meeting poster – yes, literally a poster, the authors stand by it to discuss it with anyone who wanders by. However, now it has been published as a paper, in the CDC journal Emerging Infectious Diseases; and because it is a CDC journal, the full text is available free online here.

Just to underline, despite my headline above, the strain found in NYC was not MRSA: It actually is MSSA, drug-sensitive staph. The ST 398 found in Europe, Canada and the American Midwest is MRSA. The authors hypothesize that the NYC strain is at risk of becoming MRSA also.

To see the multiple posts in this blog about MRSA ST 398 and other strains in the food chain, food animals, and pets, go to the labels under the time stamp on this post, and click “animals” or “food.”

The cite for the paper is: Bhat M, Dumortier C, Taylor B, Miller M, Vasquez G, Yunen J, et al. Staphylococcus aureus ST398, New York City and Dominican Republic. Emerg Infect Dis. 2009 Feb; [Epub ahead of print]

MRSA in meat in Louisiana: pig meat, human strain

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On Nov. 3, I posted on an enterprising group of TV stations in the Pacific Northwest who had retail meat in four states tested for MRSA. I said at the time that it was the first finding of MRSA in meat in the US that I knew of.

Turns out that I was wrong by three days. On Oct. 31, the journal Applied and Environmental Microbiology published an electronic version of a study that they will be printing in the paper journal on some future date. Journals do this when a finding is so important or timely that it should see the light immediately, rather than wait through the additional weeks or months of print production.

And this finding is certainly timely. Shuaihua Pu, Feifei Han, and Beilei Ge of the Louisiana State University Agricultural Center have made what appears to be the first scientifically valid identification of MRSA in retail meat in the United States. But — and this is an important point — it is not the swine strain, ST 398, that has been found in meat in Canada and Europe, and in hospital patients in Scotland and the Netherlands, and in pigs in Iowa; and in humans in New York, though that strain was drug-sensitive.

Instead, what the researchers found (in 5 pork and 1 beef samples, out of 120 bought in 30 grocery stores in Baton Rouge, La. over 6 weeks in February-March 2008) was USA300, the dominant community MRSA strain, and USA100, the main hospital-infection strain. In other words, they found meat that had been contaminated during production by an infected or colonized human, not by a pig. As they say:

…the presence of MRSA in meats may pose a potential threat of infection to individuals who handle the food. … (G)reat attention needs to be taken to prevent the introduction of MRSA from human carriers onto the meats they handle and thereby spreading the pathogen.

As we’ve discussed before, the primary danger from MRSA in meat is not that people will take the bug in by mouth (though that is a danger, since S. aureus because of its toxin production can cause severe foodborne illness — and these researchers found, overall, an S. aureus contamination rate of 46% of their pork samples and 20% of their beef samples). Rather, the danger is that people handling the raw meat will be careless in preparing it, and will colonize themselves by touching the meat and then touching their own noses or mucous membranes, leading to a possible future infection. As reader Rhoda pointed out in a comment last week, people could also infect themselves directly, by getting MRSA-laden juice or blood into an abrasion or cut.

So: Be careful in the kitchen, keep meat separate from other foods, wash cutting boards and knives, and (say it with me, now) wash your hands, wash your hands, wash your hands.

The cite for the new paper: Pu, S. et al. Isolation and Characterization of Methicillin-Resistant Staphylococcus aureus from Louisiana Retail Meats. Appl. Environ. Microbiol. doi:10.1128/AEM.01110-08. Epub ahead of print 31 Oct 08.

Housekeeping note: This is the 16th post I’ve written on MRSA in food animals and/or meat. Providing all the links to the previous posts is starting to obstruct the new news. So if you are looking for all those past posts, go to the labels at the end of this post, below the time-stamp, and click on “food.” You should get something that looks like this.

Final report from ICAAC-IDSA 08 (news from ICAAC, 3)

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The ICAAC-IDSA (48th Interscience Conference on Antimicrobial Agents and Chemotherapy and 46th annual meeting of the Infectious Diseases Society of America) meeting ended a week ago, and I’m still thrashing my way through the thousands of abstracts.

Here’s my final, highly unscientific selection of papers that caught my eye:

* Evidence that the community-strain clone USA300 is a formidable pathogen: It first appeared in the San Francisco jail in 2001. By last year, it had become the sole MRSA strain found in the jail — it crowded out all others. (P. Tattevin, abstract C2-225)
* Another paper from the same UCSF research group finds that the emergence of USA300 has caused a dramatic increase in bloodstream infections, most of which are diagnosed in the ER, not after patients are admitted to the hospital. (B. Diep, abstract C2-226)
* And the CDC finds that USA300 is picking up additional resistance factors, to clindamycin, tetracycline and mupirocin, the active ingredient in the decolonization ointment Bactroban. (L. McDougal, abstract C1-166)
* An example of the complexity of “search and destroy,” the active surveillance and testing program that seeks to identify colonized patients before they transmit the bug to others in a health care institution: Patients spread the bug within hours, often before test results judging them positive have been returned from the lab. (S. Chang, abstract K-3379b)
* In addition to the report from Spain I posted on during the meeting, there is a report of emerging linezolid resistance in France. (F. Doucet-Populaire, abstract C1-188)
* And in addition to the abundant new news about MRSA in pork, and “pork-MRSA” or ST 398, in humans, over the past few days, there were reports of MRSA in milk in Brazil (W. Gebreyes, abstract C2-1829) and Turkey (S. Turkyilmaz, abstract C2-1832), and beef and chicken in Korea (YJ Kim, abstract C2-1831), as well as ST 398 itself acquiring resistance to additional drugs. (Kehrenberg, abstract C1-171)
* Echoing many earlier findings that MRSA seems most common among the poor, the poorly housed and the incarcerated, BR Makos of the University of Texas found that children are more likely to be diagnosed with the bug if they are indigent, or from the South (which I imagine is a proxy for lower socio-economic status, since the South is a more rural, more poor region). (abstract G2-1314)
* And finally, to the long list of objects (ER curtains, stethoscopes) that harbor MRSA, here are more: The ultrasound probes in emergency rooms (B. Wessman, abstract K-3377). Also: Dentures. (Ick.) (D. Ready, abstract K-3354)

TV stations find MRSA in retail pork in Pacific Northwest

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In the comments, Coilin Nunan of the UK’s Soil Association (which published the wonderful 2007 report MRSA in Farm Animals and Meat report) calls attention to a report that I also spotted over the weekend.

A network of TV stations in Washington, Idaho, Oregon and California did a joint report in which they bought 97 packages of ground pork or pork cutlets and sent them to a laboratory for testing. The lab found that three of the packages, all ground pork, contained MRSA.

I believe this is the first time anyone has found (or, perhaps, looked for) MRSA in retail pork in the US. You’ll remember that MRSA ST 398 has been found in meat in Canada and Europe, and in hospital patients in Scotland and the Netherlands, and in pigs in Iowa; and MSSA ST 398 in humans in New York City.

There are some important unanswered questions about this report:

  • We aren’t told the strain. If it’s ST 398, that would be information on the spread of ST 398 in the US. If it’s USA300, on the other hand, it could be contamination from an infected or colonized human, perhaps someone in the preparation chain.
  • We aren’t told the provenance of the pork. Was it bought from a variety of markets, or one chain of supermarkets that might have one regional supplier? Was it organic v. conventional? Small-farm versus feedlot?
  • We can’t draw any broad conclusions from this. I am a poor biostatistician, but to me, this is purely a convenience sample. (If anyone disagrees with me, please weigh in.) In other words, it’s one data point. It says: There is MRSA in these packages of pork — which is an important piece of information — but it doesn’t say: 3% of all US pork contains MRSA.

Also, while the written version of the report that I linked above isn’t bad, overall, it contains one significant error. It says:

This drug-resistant bacteria is already responsible for more deaths in the US than AIDS. What makes MRSA so potentially dangerous is the bacteria can cause sickness just by touching it.

Well, not exactly. The concern with MRSA in meat is that, if you handle it without strict cleanliness, you might become colonized with the bacteria. That is not at all the same as developing a MRSA infection, much less the invasive MRSA the first sentence of that quote refers to. And yes, colonization can lead to infection. But to say that touching MRSA-contaminated meat will inevitably cause an invasive MRSA infection is alarmist.

I’m assuming the stations undertook this because it is sweeps month. (For those who have so far been spared the internals of TV news, “sweeps” are months — usually February, May, July and November — when stations’ audiences are measured to determine market rank and advertising rates. Because it is in the stations’ interest to attract as much audience as possible during those months, sweeps is usually when news stations run big investigative projects.) Interesting that they chose this topic. I think we can take this as an indicator — again, just one data point, but an interesting one — of emerging US concern over MRSA in meat.

ST 398 in New York City – via the Dominican Republic?

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Here’s a piece of MRSA news from the ICAAC meeting (see the post just below) that is intriguing enough to deserve its own post.

US and Caribbean researchers have found preliminary evidence of the staph strain ST 398, the animal-origin strain that has caused human illness in the Netherlands and has recently been found in Ontario and Iowa, in Manhattan. How it may have arrived: Via the Dominican Republic.

Th researchers (from Columbia University and Montefiore Medical Center in New York, three institutions in the Dominican Republic and one in Martinique) examine the influence of an “air bridge” — very frequent household travel — that is bringing MRSA and methicillin-sensitive staph back and forth between the Dominican Republic and the immigrant Dominican community at the north end of Manhattan. They compared 81 staph isolates from Dominican Republic residents and 636 from Manhattan residents and, among other findings, say that 6 Dominican strains and 13 Manhattan strains were ST398.

It is the first time ST398 has been found in Manhattan or in the Dominican Republic. (Most likely also the first time anyone has looked.)

The authors observe with some understatement:

Given the history of ST398’s rapid dissemination in the Netherlands, its history of methicillin-resistance and its ability to cause infections in both hospital and community, it will be important to monitor its prevalence in these new regions.

It is important to note that these ST398s were not MRSA — they were MSSA, methicillin-sensitive. However: Earlier this year, the Dutch researchers who have delineated the emergence of ST398 in Holland commented on the diversity of ST398 they have found on different pig farms and hypothesized that the resistance element has been acquired several different times by methicillin-sensitive staph. (van Duijkeren, E. et al. Vet Microbiol 2008 Jan 25; 126(4): 383-9.)

So it is possible to hypothesize that this strain arrived in Manhattan from the more rural Dominican Republic, though with the growth of hobby urban farming in NYC, one could also make the case that transmission went the other way. And it is also possible — I emphasize possible — that this could be a precursor to ST398 MRSA emerging in Manhattan. An interesting thought.

(This research is not online, because it is a poster presented at a medical meeting. For reference, the cite is: C. DuMortier, B. Taylor, J. E. Sanchez et al. “Evidence of S. aureus Transmission Between the USA and the Dominican Republic.” Poster C2-224. 48th ICAAC-46th IDSA, Washington DC, 24-28 Oct 2008.)

Breaking MRSA news from the ICAAC meeting 1

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There are 15,000+ people at the 48th Interscience Conference on Antimicrobial Agents and Chemistry (known as ICAAC – yes, “Ick-ack”) and 46th Infectious Diseases Society of America Annual Meeting, and at least half of them seem interested in MRSA. At the keynote address last night, Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases at NIH, referred to MRSA as a “global pandemic.”

Here are some highlights — a few of very, very many — from the first two days:

  • MRSA is truly a global phenomenon: Researchers here are reporting on local epidemics in Argentina, Australia, Botswana, Canada, Colombia, Ecuador, Greece, Japan, Nigeria, Peru, South Korea, Sweden and Taiwan.
  • In the United States, USA300 — the virulent community strain that is crowding out all other community strains — continues its dominance. It first appeared in the San Francisco jail in 2001 and now is the only cause of community MRSA infections there. (Tattevin, P. et al. “What Happened After the Introduction of USA300 in Correctional Facilities?” Poster C2-225.)
  • And MRSA continues to demonstrate its protean ability to cause unexpected forms of illness: The number of cases of sinusitis caused by MRSA seen at Georgetown University tripled between 2001-03 and 2004-06. (I. Brook and J. Hausfeld. “Increase in the Frequency of Recovery of Methicillin-Resistant Staphylococcus aureus in Acute and Chronic Maxillary Sinusitis.” Poster C2-228.)
  • Meanwhile, treatment options are shrinking. Hospitalization for vancomycin-resistant pathogens (that is, resistant to vancomycin, the drug of last resort for MRSA) doubled between 2003 and 2005 according to national healthcare utilization databases. (A.M. Ramsey et al. “The Growing Burden of Vancomycin Resistance in US Hospitals, 2000-2005.” Poster K-560.)
  • But, new drugs are beginning to emerge from the pipeline. Early results from a privately held company called Paratek Pharmaceuticals (co-founded by resistance guru Dr. Stuart Levy) showed that their new tetracycline relative PTK 0796 scored as well or slightly better than linezolid (Zyvox) in safety, tolerability and adverse events, and is advancing to a full Phase 3 trial. (R.D. Arbeit et al. “Safety and Efficacy of PTK 0796.” Poster L-1515.)

More as the meeting goes on.

Closing the loop: meat, meat-eaters, health-care workers

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A posting on the international disease-alert mailing list ProMED led me to a scientific abstract presented at a European meeting this spring on the ST 398 MRSA strain. It adds another, quite unnerving piece to the emerging interplay of MRSA in pigs, humans who have close contact with pigs, humans who have contact only with pig meat, and health-care workers who treat those humans.

Brief precis: About a year ago, Dutch health authorities discovered that a patient who had come in for surgical debridement of a diabetic foot ulcer had an unrecognized MRSA strain in that ulcer. Subsequently, they discovered that four other patients and five health-care workers in the same institution were carrying the same strain. None of the patients reported any contacts with pigs (or calves, which have also been found to carry the strain). One of the health-care workers lived on a farm that raised pigs, but said that she had no contact with the animals in her daily life; nor did her partner.

The authors conclude:

While the source is not fully established it could be the HCW living on a pig farm. This outbreak makes clear that transmission on a larger scale can occur, even with NT-MRSA.

(Hat-tip to Helen Branswell of the Canadian Press for telling me about the ProMED report. And a note to loyal readers: The “MRSA in meat” story is being picked up by some US newspapers. Doesn’t it feel good to know you’ve been reading about the issue here for months? And if you’re a reader of Helen’s work, months more? Of course it does.)

One more on MRSA in meat

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It turns out that European governments — in contrast to the United States — are taking very seriously the emergence of MRSA in food animals and its potential for transfer to humans. (For background, posts here, here, here and here.)

How seriously? They’re doing a sampling survey of pigs on farms across the European Union, at a cost of about $3 million in EC funds, with matching funds expected from each government.

The MRSA survey piggybacks (sorry) on a year-long survey of Salmonella incidence that the EC called for in September 2007. But in December, following publication of several significant papers about the ST 398 MRSA strain in pigs and pig farmers, the EC Directorate-General for Health and Consumer Protection pushed for an addition to the Salmonella study: a same-time sampling for the presence of MRSA strains in pig operations across 29 countries.

The sampling is taking place from January to December of this year, with results mandated by mid-2009, though individual country authorities may release data earlier if they choose. (In the wake of the finding of three ST 398 cases apparently caused by retail meat in the UK, the Soil Association has called on the British government to release whatever data it has ASAP. Before the EC decision, the UK government had refused to test its pigs; cf. these House of Lords minutes.)

Of note: The Soil Association is pressing the argument that ST 398 has developed in the setting of widespread use of antibiotics in food animals, and contends the strain’s arising in the Netherlands is especially alarming because they have some of the lowest animal-antibiotic use rates in the EC it illustrates the difficulties that even a society conscientious about antibiotic overuse can have keeping track of veterinary applications. The Netherlands has been successful limiting overuse in humans, but has found controlling veterinary use much more of a struggle. (Thanks to the Soil Association for correcting my misunderstanding!)