Maryn McKenna

Journalist and Author

H1N1 and MRSA – first disclosed case

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Readers, once again there’s a lot of MRSA-related news piling up, and I’ll try to roll some of it out over the next few days. But first, today we have to deal with an event that many of us have been anticipating, though not with any pleasure: the first known report of a MRSA death secondary to H1N1 “swine” flu infection.

We’ve talked about this possibility for weeks, because bacterial pneumonia, especially due to MRSA, is a known and frequently deadly follow-on to flu infection. (Archive of posts here.) With swine flu so common, CDC has said several times that they have been looking for post-flu bacterial pneumonia, but had not seen it. And commenters to this blog have relayed rumors — or, to be more precise, stories with no names attached — of flu patients so ill with MRSA that they have to be put on an ECMO, what we used to call a “heart-lung machine,” and sometimes do not come off.

Today, however, the Buffalo News carries the story of a New York State teen’s death from MRSA pneumonia as a sequela of flu:

Matthew Davis was a healthy Buffalo teenager who participated in sports before complaining of headaches June 13.
Within a few days, the 15-year-old student at Harvey Austin School 97 on Sycamore Street arrived seriously ill at Women & Children’s Hospital and then died Saturday, making him the first known fatality in Erie County caused by swine flu, officially known as novel H1N1 influenza.
… By the time Matthew entered the hospital, he was seriously ill with the flu, as well as co-infected with a type of bacteria known as methicillin-resistant staphylococcus aureus, or MRSA, according to health officials. (Byline Henry L. Davis)

Under normal circumstances — as in, during the past flu season — the public health advice has been to protect against MRSA pneumonia by getting a flu shot, which by preventing flu prevents the microtrauma to the lungs that allows MRSA and other bacteria to gain a foothold. In this case, though, with no H1N1 vaccine available, ir’s not clear what protective actions could have been taken.

Still, it’s terribly sad.

H1N1 flu and swine surveillance – more relevance for MRSA

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Constant readers, you probably know that yesterday the World Health Organization declared the first flu pandemic in 41 years. I want to point out for you a side issue in the H1N1 story that has great relevance for MRSA, especially ST398.

As described in this article I wrote last night for CIDRAP, three medical journal articles have now pointed out that the virus, or its major components, could have been recognized in swine months to years ago. We missed it, though, because there is so little regular surveillance in pigs for diseases of potential importance to humans. As the authors of the most recent article, in Nature, said yesterday: “Despite widespread influenza surveillance in humans, the lack of systematic swine surveillance allowed for the undetected persistence and evolution of this potentially pandemic strain for many years.”

This is important for our purposes because we know that we are in the same situation with MRSA ST398: The strain was first spotted in France, and has been a particular research project in the Netherlands, but has been found pretty much wherever researchers have looked for it, throughout the European Union, in Canada, and most recently in the United States. All told, though, the scientists concerned with it are still a small community; there is no broad surveillance looking for this bug.

And that’s a problem, for MRSA, for influenza, and for any number of other potentially zonotic diseases: We cannot anticipate the movement of pathogens from animals to humans if we don’t know what’s in the animals to start with. That’s the argument behind the “One Health” movement, which has been arguing for several years now for including veterinary concerns in human health planning. (The human health side would probably say that the animal health side just wants more money. This is also true, which does not make it unimportant.)

To understand the need to look at animal health in order to forecast threats to human health, you can’t do better than the map I’ve inserted above (because Blogger, annoyingly, won’t let me put it below). It has appeared in various forms in various publications for about 10 years but originates I think from the IOM’s Emerging and Reemerging Diseases report in the early 90s. (This iteration comes from the One Health Initiative website.) It depicts the movement of new diseases from animals to humans over about 30 years. It’s up-to-date through SARS and through the 2003-05 movement of H5N1 avian flu around the world. I’m sure H1N1 will be added soon. How many of those outbreaks could we have shortcircuited if we had been warned of their threat in good time?

Antibiotics in water supplies

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Via the journal Environmental Health Perspectives comes an important, comprehensive review article by scientists from Environment Canada and the Universite de Montreal on the presence of antibiotics in water supplies and waste water.

The news is not good. If you are concerned about the possibility that antibiotic residues in the environment create another setting in which resistance can develop, it is worth reading. It is long (10 pages in pdf) but has a comprehensive bibliography. Also, it’s open-access.

Where do these antibiotic residues come from? From us, in some cases: We urinate out up to 90% of some drugs, wash off topical formulations, flush old prescriptions down the toilet. Sometimes from industrial residues, or from leaky hospital sewage, or from sewage treatment plants, or — of course — from industrial-scale agriculture administration and run-off.

And where do they go? According to the paper, over more than 20 years of research, 126 different antibiotics and anti-infectives have been identified in processed waste water, natural surface water and groundwater, and drinking water supplies. Among them are all the antibiotics that we are concerned about here: the drugs that MRSA is already resistant to (beta-lactams, lincosamides, macrolides) and the drugs that still work, for community MRSA at least (sulfonamides, trimethoprim, tetracycline).

Moreover, the trend is expected to get worse, the authors warn: because of increased urbanization; because many urban areas are consciously setting water-saving policies, reducing the volume of wastewater and therefore increasing the concentration of drugs in the water that remains; and because, well, CAFOs aren’t exactly going away right now, are they? As they say:

…even if our results show that high concentrations … of anti-infectives in these waters are more the exception than the rule, the existence of a few locations where these concentrations can be reached are enough to contribute to the global spreading of anti-infective resistance. Given that large populations of bacteria are being exposed to a selective pressure, environmental waters and especially wastewaters become ideal settings for the assembly and exchange of mobile genetic agents encoding for resistance in bacteria. … Anti-infectives, the miracle drugs of the 20th century, have become environmental contaminants of emerging concern in the 21st.

The cite is: Segura PA et al. Review of the Occurrence of Anti-infectives in Contaminated Wastewaters and Natural and Drinking Waters. Environmental Health Perspectives, 117 (5) May 2009.

Farm animals and antibiotics – a new campaign

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I was gobsmacked to discover today, a few days late, that the Pew Campaign on Human Health and Industrial Farming (authors of the report discussed here) have launched a marvelously in-your-face series of ads in Washington DC, aimed at bringing the issue of antibiotic use in farm animals to people who might not think about it.

The ads have been placed in the Capitol South and Union Station Metro stops, which are the stops that bracket Capitol Hill, and in Metro cars on the red and blue/orange line trains, which are the main commuter trains down to the Hill. In other words, they’ve been made to be the morning reading of the people most engaged in the health reform debate right now — and if you think those folks are not thinking about healthcare spending and the growth of antibiotic resistance, well, umm, oh never mind.

The campaign says:

The American Medical Association, the American Academy of Pediatrics and other leading medical groups agree that the growth of bacterial infections resistant to antibiotic treatment is a looming public health challenge. The groups also agree the misuse of antibiotics on industrial animal farms plays a significant role in this crisis. While antibiotics are prescribed to people for short-term disease treatment, these same critically important drugs—like tetracycline, erythromycin and ciproflaxin—are fed in low doses to large herds or flocks daily, often for the lifespan of the animal. This creates ideal conditions for the breeding of new and dangerous antibiotic-resistant bacteria.

For statistics and arguments, along with more images — cows! chickens! pills! — go to the site of the commission’s campaign, Save Antibiotics.

MRSA in pig-farm workers – very high rates

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Let’s go back for a moment to what I think of as the “third epidemic” of MRSA: ST398 and the other strains that reside in animals and cross to humans. (In my personal taxonomy, the first and second epidemics are hospital-acquired and community-associated.)

Via Emerging Infectious Diseases, the open-access journal published by the CDC (Do I have to keep telling you to read it? It’s free. It’s good. Your tax dollars pay for it.), comes a report of surveillance for MRSA colonization of pig-farm workers, conducted in Belgium by researchers from Erasmus Hospital of the Free University of Brussels, and the Veterinary and Agrochemical Research Centre of Brussels. The group persuaded 127 farm workers on 49 farms to be tested for colonization, or asymptomatic carriage, of MRSA; at the same time, they tested 30 randomly selected pigs on each farm.

They found very high rates of colonization, higher than have been found in patients in hospitals or residents of nursing homes: 38% of the farm workers carried MRSA ST398, the pig strain (plus, an additional 17% carried various strains of MSSA, drug-susceptible staph). There was a clear association between colonized farmers and colonized pigs: Out of 1500 pigs sampled, 44% carried ST398 — and half of the workers on farms with colonized pigs were colonized also, compared to only 3% of workers on farms where pigs did not carry the bug.

In a bit of good news, the researchers found only one farm worker who had suffered any MRSA disease from ST398, a man with a lesion on his hand. There was no invasive disease, though ST398 has been associated in the past with pneumonia and endocarditis.

Workers were more likely to acquire the bug if they had regular contact with pigs, dogs or horses, which makes intuitive sense. But in an odd finding, their odds of acquiring ST398 did not go down if they wore protective clothing — which is to say, aprons, gloves and masks did not protect them from picking up the bug, leading the researchers to wonder whether airborne spread or contaminated surfaces are playing a role in transmission.

So what does this mean? The lack of invasive disease in this population must be good news; and it’s consistent with a number of papers that have reported low rates of disease from ST398 even when colonization is present. But to me, the high rate of colonization must be bad news. The more of this bug there is (and every researcher who looks for it seems to find it), the more chance there is of the bug adapting in an unpredictable — potentialy more resistant, potentially more virulent — way. If that did happen, it could well go undetected for a while — because as swine flu has been teaching us, disease surveillance in animals is patchy at best, and new pathogens can and do arise and ciruclate for years before being detected.

For more on the paucity of surveillance in animals, see my CIDRAP colleague Lisa Schnirring’s story here. For a complete archive of posts on “pig MRSA” ST398, go here.

The cite is: Denis O, Suetens C, Hallin M, Catry B, Ramboer I, Dispas M, et al. Methicillin-resistant Staphylococcus aureus ST398 in swine farm personnel, Belgium. Emerg Infect Dis. 2009 Jul; [Epub ahead of print] DOI: 10.3201/eid1507.080652.

Infections rise, but hospital budgets – and infection control – shrink

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Bad news from the Association of Professionals in Infection Control and Epidemiology (APIC): In a survey of almost 2,000 of their 12,000 members, 41% say that their hospitals’ infection-prevention budgets have been cut due to the down economy.

According to the survey, conducted March 2009 and released Tuesday morning:

Three-quarters of those whose budgets were cut experienced decreases for the necessary education that trains healthcare personnel in preventing the transmission of healthcare-associated infections (HAIs) such as MRSA and C. difficile.
Half saw reductions in overall budgets for infection prevention, including money for technology, staff, education, products, equipment and updated resources.
Nearly 40 percent had layoffs or reduced hours, and a third experienced hiring freezes.

As we know here, there are (by CDC estimate) 1.7 million hospital-acquired infections and 99,000 deaths as a result of them, each year. These are numbers we are supposed to be trying to reduce. That is going to be less likely if less money flows toward what may already be an underfunded goal:

A third of survey respondents say that cuts in staffing and resources have reduced their capacity to focus on infection prevention activities.
A quarter of respondents have had to reduce surveillance activities to detect, track and monitor HAIs.

Disturbingly, at a time when electronic health records are such an important part of the health-reform debate, “Only one in five respondents have data-mining programs – electronic surveillance systems that allow infection preventionists to identify and investigate potential infections in real time.”(APIC press release)

The full report is here.

10 years but little progress on patient safety

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Constant readers, I’ve been away for a week — trying to get my breath back now that the chaos of the novel H1N1/swine flu is diminishing — and so I’ve missed a lot of news. Over this week, I’ll try to catch you up on it.

First up: Some of you know that, 10 years ago, the nonpartisan, Congressionally-chartered Institute of Medicine (IOM) published a groundbreaking report called To Err is Human (html here, pdf here) that jump-started examination of medical quality in the United States. That report said:

Health care in the United States is not as safe as it should be–and can be. At least 44,000 people, and perhaps as many as 98,000 people, die in hospitals each year as a result of medical errors that could have been prevented…
Preventable medical errors in hospitals exceed attributable deaths to such feared threats as motor-vehicle wrecks, breast cancer, and AIDS. …
Beyond their cost in human lives, preventable medical errors exact other significant tolls. They have been estimated to result in total costs (including the expense of additional care necessitated by the errors, lost income and household productivity, and disability) of between $17 billion and $29 billion per year in hospitals nationwide. (To Err is Human, executive summary)

The report prompted a huge groundswell of legislative interest and patient advocacy that led, years later, to the successful passage of state laws insisting on public reporting of hospital infections and more recently on disclosure of hospital-acquired MRSA.

And yet: Despite all that scrutiny and activism, we are nowhere near as far as we should be in reducing medical errors. Just in the area of hospital infections, which is our greatest interest here, there is not mandatory reporting in all states, and there is no nationwide reporting.

So says the Safe Patient Project of Consumers Union, which has produced an update to the IOM report called To Err is Human — To Delay is Deadly. They conclude:

Ten years later, we don’t know if we’ve made any real progress, and efforts to reduce the harm caused by our medical care system are few and fragmented. With little transparency and no public reporting (except where hard fought state laws now require public reporting of hospital infections), scarce data does not paint a picture of real progress.
Based on our review of the scant evidence, we believe that preventable medical harm still accounts for more than 100,000 deaths each year — a million lives over the past decade. This statistic by all logic is conservative. For example, the Centers for Disease Control and Prevention (CDC) estimates that hospital-acquired infections alone kill 99,000 people each year.

The project finds that many of the reforms recommended by the IOM in 1999 have not been created:

  • Few hospitals have adopted well-known systems to prevent medication errors and the FDA rarely intervenes.While the FDA reviews new drug names for potential confusion, it rarely requires name changes of existing drugs despite high levels of documented confusion among drugs, which can result in dangerous medication errors. Computerized prescribing and dispensing systems have not been widely adopted by hospitals or doctors, despite evidence that they make patients safer.
  • A national system of accountability through transparency as recommended by the IOM has not been created. While 26 states now require public reporting of some hospital-acquired infections, the medical error reporting currently in place fails to create external pressure for change. In most cases hospital-specific information is confidential and under-reporting of errors is not curbed by systematic validation of the reported data.
  • No national entity has been empowered to coordinate and track patient safety improvements.Ten years after To Err is Human, we have no national entity comprehensively tracking patient safety events or progress in reducing medical harm and we are unable to tell if we are any better off than we were a decade ago. While the federal Agency for Healthcare Research and Quality attempts to monitor progress on patient safety, its efforts fall short of what is needed.
  • Doctors and other health professionals are not expected to demonstrate competency.There has been some piecemeal action on patient safety by peers and purchasers, but there is no evidence that physicians, nurses, and other health care providers are any more competent in patient safety practices than they were ten years ago.

The entire report is well worth reading. Its lamentable but well-supported conclusion:

We give the country a failing grade on progress on select recommendations we believe necessary to create a health-care system free of preventable medical harm.


MRSA and H1N1 "swine" flu – still not a lot of evidence

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Hello again, constant readers. It’s busy out there.

The CDC said Wednesday that new infections with the novel H1N1 virus (Formerly Known As Swine Flu) may be trending down. Nevertheless, there is still a lot of rumor and speculation out there regarding what role MRSA pneumonia may have played in serious cases.

The CDC commented on this in its May 19th press briefing:

Q: Is anybody looking for, and is anybody finding any evidence of, coinfection with MRSA?
A: We′re very interested in that question. As you know, the seasonal influenza in children we′ve been tracking pediatric deaths, and we have seen MRSA among seasonal flu cases in children at a higher rate than we had expected. MRSA is a big problem in the United States right now in terms of the community associated resistant staff or its infections. So far as we′ve been looking at the patients with the H1N1 virus, we don′t have evidence of coinfection. Not everybody has been tested for bacterial infections. But among the ones that have been tested, we aren′t seeing an important role for bacterial coinfection, including MRSA. I think this is an important issue for us to continue to follow, whether bacterial co-infections or bacterial pneumonias following the illness are featured. It′s a feature we′re interested in but haven′t seen this turn up yet.

We’ve talked a number of times before here about MRSA necrotizing pneumonia, and about the apparent importance of secondary bacterial infections to the death rates in prior flu pandemics.

But for anyone who needs a refresher, I recommend an excellent new paper by researchers at Emory University, published last week in the journal Lancet Infectious Diseases. It recounts the clinical course of two people who were treated at Atlanta’s Grady Memorial Hospital for MRSA pneumonia. Both were adults, and both survived, but their courses were complicated; the clinicians note that they did not improve until they were given additional antibiotics aimed at shutting down MRSA’s toxinproduction, a step that is not universally considered by doctors treating a MRSA patient.

The cite is: Hidron, AI et al. Emergence of community-acquired methicillin-resistant Staphylococcus aureus strain USA300 as a cause of necrotising community-acquired pneumonia. Lancet Infect Dis. 2009 Jun;9(6):384-92. The abstract is here.

MRSA in space

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No, really — but not quite the way you think. The weekly geekfest that is Aviation Week and Space Technology reports that the payload of the space shuttle Atlantis includes a MRSA experiment. The goal is to investigate whether bacteria held in the microgravity of space become more virulent — this was done earlier with salmonella — and then to determine whether any new virulence markers suggest targets for a potential staph vaccine.

A vaccine of course, is the Holy Grail of MRSA research — and it has remained frustratingly out of reach. For a great review of past research and future challenges, see this review article from March.

MRSA in the House of Lords — the silly, the serious

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Thanks to constant reader Pat Gardiner, we have the transcript of the UK House of Lords discussion on community MRSA, called there PVL-MRSA after the toxin. (Go to the linked page, and click down to the time-mark 3.16 pm.) It’s encouraging to see some members of a government taking MRSA seriously. The members are asking for

  • better surveillance
  • better infection control
  • consideration of MRSA as a notifiable disease
  • and promotion of both vaccine research and point-of-care diagnostics.

Hear, hear to Baroness Masham of Ilton for bringing it up.

To get to that discussion, though, you’ll have to click down through some silliness (the ghost of Monty Python is never far from the British government, is it?): a discussion at time-stamp 3.07 p.m. of whether a House of Lords restaurant can afford to serve British bacon, rather than Dutch bacon, given that British bacon is almost twice as expensive and Dutch pigs are associated with MRSA ST398:

Lord Hoyle: My Lords, I thank the noble Lord for that reply, although there is more than a whiff of hypocrisy about it. After all, I and many others on all sides of the House have argued that it should not be a matter of price. We have urged the British consumer to buy British bacon because of the higher welfare standards that are applied in this country. Will the noble Lord also take into account the presence in Dutch bacon of a deadly form of MRSA, ST398, which can cause skin infection, heart trouble and pneumonia? Is he not putting people in this country at risk, particularly as the strain has passed from animals to humans? Indeed, when Dutch farmers go into hospital, they go into isolation. Why is he putting the British consumer and those who buy bacon in this House at risk in this way?

The discussion quickly devolves into foolishness about British Tomato Week — but if you read carefully, you’ll see that behind the silliness, there are serious issues at stake: animal welfare, farming standards, truth in labeling (the Lord Bishop of Exeter advances the very newsworthy claim that pork imported from other countries is subsequently labeled “British” only because it is packaged in the UK) and movement of zoonotic pathogens across national borders thanks to globalized trade.

Sadly, the leader of the discussion — the Chairman of Committees, AKA Lord Brabazon of Tara (no, really) — appears not to have been keeping up with the news, since he notes of ST398:

As far as MRSA is concerned, I read the article in, I think, the Daily Express a couple of weeks ago. I do not think that it has been followed up by anybody else.

Apparently the Lord’s staff have not been keeping up, since MRSA in pigs in the EU has been covered by the Daily Mail, the Independent, comprehensively by the Soil Association, and by, ahem, us.

While taking a flu break, a MRSA round-up

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Constant readers, the H1N1 (Virus Formerly Known as Swine) Flu story remains a bit intense. I’ve missed a few MRSA stories over the past few days, so here is a round-up.

First, though, if you’re curious about what the swine flu reaction says about our ability to handle a pandemic, you might take a look at this story I wrote Friday at CIDRAP. Quick version: Over-reaction on the part of the “worried well” — and people seeking testing and not knowing where to get it — put ERs into meltdown nationwide. If we were facing a virus that was not only fast-spreading but virulent, we could be in serious trouble.

On to MRSA:

  • Therapy animals as a vector: In a letter to the Journal of Hospital Infection, Drs. J. Scott Weese and Sandra L. Lefebvre of the Ontario Veterinary College at the University of Guelph report on two therapy dogs that became transiently colonizedwith C. difficile (on its paw pads) and MRSA (on its coat; found on the hands of its handler) after visiting health care facilities, demonstrating how easily bacteria can move in and out of hospitals. Constant readers will recognize Weese’s name: He is one of the most important investigators of MRSA in food animals and pets, and among other things has written infection-control guidelines for therapy animals.
  • In the Canadan Medical Association Journal, Drs. Anne G. Matlow and Shaun K. Morris of the University of Toronto and the Hospital for Sick Children caution that while hospitals may be getting better at infection control, there is not yet as much attention to it as there should be in ambulatory-care settings: urgent care centers, surgery centers and doctors’ offices. They offer a checklist of the minimal things that a physician practice should do.
  • And in the UK, Baroness Masham of Ilton, a member of the House of Lords, offers her online notes on serious infections with community MRSA, which the Brits are calling PVL-MRSA in recognition of the toxin that the strain produces. The notes are in advance of a series of questions that she intends to pose to government ministers during a Question Time on Wednesday.

More soon.

Quick update: Yes on bacterial pneumonia and new flu

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Constant readers, I thought you;d like to know that there are a few more indications that secondary bacterial pneumonia (as discussed in this post the other day) does seem to be playing a role in the severe cases of the new flu.

That’s according to this account of the WHO’s technical briefing from Wednesday, along with this item (there are three entries, go to the bottom one) from the excellent disease-alert list ProMED.

More soon.

MRSA strains crossing borders: US CA-MRSA to Italy

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Swine flu continues to dominate the headlines, but other pathogens don’t read the papers. Case in point: New news about a US community strain being found and treated in a woman in Italy — better treated, as it turns out, than she was in California, where she was infected.

In a new letter in Emerging Infectious Diseases (a free journal published online and in print by the CDC — it’s your tax dollars at work, just read it, already), Carla Vignaroli, Pietro E. Varaldo, and Alessandro Camporese of the Polytechnic University of Marche in Ancona amd the Santa Maria degli Angeli Regional Hospital, Pordenone report the case of

a 36-year-old Italian woman (who) was seen at Pordenone Hospital (northeastern Italy) for spider-bite–like skin lesions on the face, characterized by rapid evolution to furuncles and small abscesses. The infection had started ≈1 month earlier in California, where she had spent several months on business (wine import-export), and where she had been treated empirically with amoxicillin/clavulanate for 10 days (1 g, 3×/day), with no clinical improvement.

(At this point, I know every clinician reader and everyone who has had a MRSA skin infection is shaking his or her head. Surely by now the knowledge that “spider bite” is practically diagnostic for CA-MRSA has penetrated? But apparently not, since she was given amoxicillin/clavanulate, AKA Augmentin, which is partially penicillin-based.)

When the woman’s lesions were cultured, they turned out to be caused by USA400, the original community strain, which back in the 1990s was known as MW2. That’s interesting, especially in California, since USA300 has become such a dominant strain. Nevertheless, the key point is that USA400, as with USA300, has barely been recorded in Italy:

All 3 previously reported cases of CA-MRSA infection in Italy were caused by type IV SCCmec, PVL-positive strains, none of which, however, belonged to the ST80 clonal lineage that predominates in Europe (7). The first case (in 2005) was a necrotizing pneumonia caused by an ST30 isolate; the 2 other cases (2006) were severe invasive sepsis and a neck abscess, both caused by ST8 (USA300) isolates.

The concern, of course, is that once imported, they will not remain rare:

The case we note here documents the importation of a US pathogen into a country in Europe, from an area where the pathogen is widespread and has been highly virulent since the late 1990s, to an area where its penetration in the past has been poor.

The cite is: Vignaroli C, Varaldo PE, Camporese A. Methicillin-resistant Staphylococcus aureus USA400 clone, Italy [letter]. Emerg Infect Dis. 2009 Jun; [Epub ahead of print]. DOI: 10.3201/eid1506.081632

Special bonus for disease-detection wonks

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Constant readers: Some of you know that my first book, published five years ago, was a narrative and history of the CDC’s Epidemic Intelligence Service, the young, committed corps of MDs and PhDs who give up two years of their lives to serve on front-line outbreak SWAT teams.

The EIS are very important right now, because there are almost 100 CDC people in the field, in Mexico and in US cities and other countries where H1N1 swine flu is emerging.

My next book — the one for which this blog is the whiteboard — is being published by the same imprint, Free Press, part of Simon & Schuster. So because the EIS is so crucial to the outbreak investigation, FP has relaxed their rights and very graciously allowed me to fling up some parts of Beating Back the Devil on the web, for free, to my regular readers.

My web skills are not magnificent, and my site has outgrown the program I used to build it. However: If you go to this page, you’ll see a section that announces Excerpts! And in it you’ll find a prologue and two chapters in various formats. (We did this fast; it is messy. Sorry.)

I particularly recommend Chapter 13 [pdf], which is a narrative of the SARS outbreak in Asia, starting with an EIS officer named Dr. Joel Montgomery staring down a tray of blood samples in a laboratory in Vietnam. (I wrote about the importance of serology — blood-analysis — surveys to swine flu at CIDRAP tonight.) The description of that outbreak response should give you a good flavor of what the CDC investigators are doing and thinking about now. And, bonus, it talks about some little-known cases of avian flu H5N1; we did not know at the time how important those cases would turn out to be.

If you have time, there are also links to sections that FP has posted on their own site: Chapter 1, which will tell you who the EIS are and why the corps exists (Korean War veterans will know already); and the book’s Prologue, which takes you inside the first bioterror-response training that EIS members ever endured.

I hope you enjoy.

More on MRSA and the new flu

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Constant readers, I admit it: I am a bad blogger. The wave of news on the novel H1N1 (AKA the Virus Formerly Known as Swine) has been just overwhelming. Apologies for disappearing.

Out of the crashing surf, though, I picked up an interesting tidbit that speaks to our concerns about MRSA. Here’s some background: If you have been following the swine flu story, you’ll have noticed that one of the puzzles has been why the Mexican experience has been so different from the United States or from the other countries where this flu has appeared briefly. (North America so appears to be the only area in which there is sustained transmission.) Among the hypotheses:

  • There is a difference in the medical care that victims are receiving.
  • There is a statistical artifact: The serious cases are a tiny percentage of the mild cases, and the US has not seen enough cases to, probabilistically, experience significant serious cases yet.
  • Or, corollary to the above: Mexico has many more cases than its surveillance systems have been able to count, and that is why we have seen that (unknown but presumably tiny) percentage that become serious cases appear there but nowhere else.

(For more on this, here’s a CNN story from a few days ago, quoting me and people much more distinguished than me.)

But a commentary by a global-health expert raises another hypothesis, one that brings this outbreak around to our concerns: the possibility that the serious flu cases in Mexico are being complicated by secondary pneumonia caused by MRSA or other bacteria.

We’ve talked about this issue before (see this post about the importance of MRSA in a flu pandemic and this paper by, among others, Dr. Anthony Fauci, director of NIAID, and Jeff Taubenberger, PhD, co-discoverer of the virus of the 1918 flu). MRSA pneumonia secondary to flu infection is the etiology of the necrotizing pneumonia cases that kill children very quickly, and is the reason why I keep haranguing you regarding flu shots.

Is bacterial pneumonia playing a role in the current epidemic? It’s too soon to tell; there is not sufficient clinical data. But it is an interesting speculation and one that we should keep in mind as this goes forward.

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 (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.

How sewage plants birth resistant bacteria

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At the always-excellent public health blog Effect Measure, there’s a fascinating dissection of a new paper still in press at the journal Science of the Total Environment. The paper unpacks what happens to Acinetobacter in effluent as they move through sewage treatment. Answer: Many are eliminated, but the ones that survive become significantly more resistant.

I am deep in the final book chapter, so blogging will be light for a week. In the meantime, I recommend this paper and the accompanying post for explicating a little-explored aspect of antibiotic resistance in the environment (which we also talked about in this earlier post.)

The cite is: Zhang, Y. et al. Wastewater treatment contributes to selective increase of antibiotic resistance among Acinetobacter spp. Sci Tot Env doi:10.1016/j.scitotenv.2009.02.013.

Back soon.