Tuesday, January 31, 2012

99% of Dutch Chickens Contaminated with ESBL Strains

From De Telegraaf (De nummer 1 in nieuws), we have a report that 99% of retail chickens produced with intensive farming and sold in Dutch Supermarkets are contaminated with ESBL-containing bacteria.  Organic chicken appears to be far less contaminated, perhaps 1/8th as likely.  My Dutch is a little rusty, so I've provided the sources. Either way, fear the kipfilet!!

1. De Telegraaf article (Dutch)
2. Radio Netherlands Worldwide (English)
3. Consumentenbond 1/31/2012 (Dutch)

UPDATE:  Overdevest et al. (EID 2011:17(7) July) reported 80% (71/89) of chicken samples from random grocery stores collected in fall 2009 in the southern part of the Netherlands contained ESBL genes. The authors noted that "ESBL-producing Enterobacteriaceae derived from meat and hospitalized patients showed a high degree of similarity of resistance genes and MLST patterns. Genotype blaCTX-M-1 was the most frequent drug resistance gene in chicken meat and humans and the second most frequent in blood cultures."  h/t Jan Kluytmans

Monday, January 30, 2012

A New #OpenAccess Platform

F1000 Research is a new platform for immediate publication along with open, post-publication peer review and a site for raw data repository. The open review is described as a "simple formal check by invited reviewers confirming that the work is scientifically sound, with commenting optional... at any stage...any registered reader can also comment on the work and authors can respond."  Importantly, the default standard is to use the Creative Commons, CC-BY for  licenses for articles and CC0 for data.  The platform targets biology and medical studies.

The final platform model is not yet open.  It appears they are still seeking input on questions such as:
  1. How much formal refereeing is required?
  2. What is an article amendment versus an update?
  3. What incentives are required to encourage post-publication refereeing, author response and revisions, and sharing of raw but template data?
  4. What author fees are appropriate for the different types of content?
I suspect that Mike might have a comment on the last couple of questions.

F1000 Research (for Faculty of 1000)

Friday, January 27, 2012

Herd Immunity in the Jet Age

By 2012, I thought we'd already be beyond the jet age. Although, if you go by the GOP debates, determining if a "moon-colony" could apply for U.S. statehood is now our top domestic concern, so maybe we're finally getting beyond the jet age?

An idea central to controlling infectious diseases is herd immunity. This is the idea that vaccinating a proportion of the population (e.g. 80% for mumps or 95% for measles) will protect the entire population, even the unvaccinated. In a paper presented recently at the meeting of the American Mathematical Society and the Mathematical Association of America and discussed in the Economist, Petra Klepac and colleagues wanted to know how increasingly mobile populations with varying vaccination rates would impact optimal vaccination targets for infectious diseases. That is, does it make economic sense to target a herd-immunity threshold? Also, how would high-levels of varicella vaccination in the US vs. low levels in Britain interact to impact chickenpox in both countries?

Dr. Klepac and her team used a susceptible-infected-removed (SIR) mathematical model, which we frequently use in analysis of infection-control interventions. Analysis of their model determined that targeting herd immunity makes sense for an isolated country. However, when international travel was added, she found that a small rate of unvaccinated travelers would reduce the optimal vaccination below the level of herd immunity, so that targeting herd immunity becomes too expensive. Thus, we have to be tolerant of more infections.

There are some other interesting implications of her study, so head on over to the Economist Babbage blog to read more.

Thursday, January 26, 2012

Waiting for the Flu...

"Shouldn’t we all be dead by now?" is the first question that Kent Sepkowitz, card-carrying hospital epidemiologist, asks in his latest article in Newsweek.  He goes on to ponder why it's almost February and there's so little influenza activity and suggests that nothing we have done to prepare has made any difference including influenza vaccination and alcohol hand rub .  He hints that perhaps La Nina or climate could be a possibility.

He concludes by saying: "In fact, what we are seeing here is the dark secret of medicine and public health: the fact that we usually have no clue why something, good or bad, is happening...(and) should accept that we are mere spectators to an inscrutable alliance of virus, animal, and climate, a longstanding collaboration that we cannot, as yet, influence — though getting that flu shot might help."

Kent Sepkowitz, Newsweek/Daily Beast 1/23/2012

Forget mandates, a song will bring them in!

It never occurred to me to ask why people aren’t singing more songs about infection—but Slate’s William Weir is all over this, with an interesting piece that includes audio clips from songs about influenza, meningitis, plague and TB. For example, here are the lyrics from “Influenza”, recorded by Ace Johnson in 1939:

Influenza is a disease, makes you weak all in your knees
’Tis a fever everybody sure does dread
Puts a pain in every bone, a few days and you are gone
To a place in the ground called the grave

And definitely check out the clip from “Jesus is Coming Soon”, by Blind Willie Johnson. Play that at your staff meetings and just watch them all roll up their sleeves!

Photo: Blind Willie Johnson, public domain image from Wikipedia

New #OpenAccess Antimicrobial Resistance and Infection Control (ARIC) Journal Publishes First Papers

Andreas Voss, Jan Kluytmans and Didier Pittet have successfully started a new international, open-access journal called Antimicrobial Resistance and Infection Control (ARIC). The first batch of papers were just posted today to the ARIC website.  This event is a significant for several reasons.

The first, as I've mentioned before, is that as an open-access journal, ARIC will allow unaffiliated scientists, the general public and otherwise interested parties free full access immediately upon publication without having to wait years or pay high fees. In an editorial, accompanying the first publications, the editors highlight their views of open access including how they hope to respond to the high initial costs for authors.

They write: "ARIC's choice of "open-access" is a logical step towards its goal to be truly international and to allow the transfer of knowledge and best practices to even remote places that cannot afford printed journals. We realize that open access has financial consequence for some authors and that the standard BioMed Central rules to waive article-processing charges may not be enough. BioMed Central provides an automatic waiver to authors based in any country classified by the World Bank as low-income or lower-middle-income economies, but we intend to find solutions in the near future that will allow us to support authors from upper-middle income countries and young investigators" 

The second and I think equally important reason that ARIC's emergence is important is that we've never had an international voice in infection control. As the 1200 attendees from 84 countries at last summers ICPIC meeting can attest, international collaboration will be the key for controlling antimicrobial-resistant bacterial pathogens (think NDM-1) in the future.

I wish the editors and the ARIC journal much luck and future success!


Wednesday, January 25, 2012

Orphan-drug funding crowding out antibiotic discovery?

There's an interesting story today by AP Health writer Matthew Perrone that delves into reasons why little is spent on antimicrobial drug discovery in the US.  His hypothesis is that funding for orphan drugs is crowding out antibiotic drug discovery in the private sector, forcing the US Government into action.  The evidence offered is compelling, including the fact that 11 of the 30 new drugs approved last year were for rare medical conditions, the highest level since FDA incentives began about 30 years ago. These incentives include extra patent protections, higher pricing and a streamlined FDA review. The results speak for themselves: the first new SLE therapy in 50 years and first new Hodgkin's therapy in 30 years.

However, the evidence that this is actually spurring US-government funded antimicrobial drug discovery is weak.  We're offered the somewhat misleading fact that "since 2006, government spending on research for familiar diseases like staph infections, smallpox** and botulism** has increased more than 660 percent, from $54 million to $415 million last year." OK...so what does this have to do with antimicrobial discovery?

To further highlight the dearth of investment in antibiotic discovery, we have this quote from Dr. Anthony Fauci: "We have pushed the envelope more toward diminishing the risk for companies so that they'll be more interested in getting involved with us and developing things like vaccines and antivirals." To be fair, he cold be talking about the mythical Staph vaccine. But seriously, whatever happened to "eschew obfuscation, espouse elucidation"?

The rest of the article highlights new investment in therapies for tularemia and agents of bioterror and new flu-vaccine manufacturing techniques. I had my hopes up for a minute.

**Note: There are on average 110 cases of botulism in the US every year and zero cases of smallpox.  This compares to 19,000 DEATHS from MRSA per year, which would be at least twice that high if we included MSSA. Familar does not equal common.

Source: Matthew Perrone, SFGate (AP) 1/25/2012

Monday, January 23, 2012

A change of heart on vancomycin MICs?

Last year I opined that using exact vancomycin MICs as a guide to antimicrobial selection for serious MRSA infections is not a useful exercise. This position wasn’t particularly controversial at the time, and is consistent with IDSA guidance.

However, I was just directed to this study in Clinical Infectious Diseases, in which the authors conclude that in patients infected with MRSA that have vancomycin MICs of 1.5 or 2 mcg/mL (by Etest, of course, which is the only way you’ll get an MIC of “1.5”), you should consider treatment with daptomycin rather than vancomycin. In response to this paper, apparently, a large tertiary care center lab was poised to begin testing all MRSA isolates with vancomycin MIC of 1 mcg/mL by Etest (to better detect these higher MIC strains).

Really? I will let Eli comment on the finer points if he wishes, but I’m confident stating that I wouldn’t rely on a single-center, retrospective, observational, Cubist-funded study to make a major change in laboratory or clinical practice. The potential confounders, measured and unmeasured, are legion. As a single example, ID consultation occurred twice as often in the daptomycin recipients than in the vancomycin recipients (64% vs. 32%). Now I believe that ID consultation does improve outcome—but even if it doesn’t, it’s probably associated with something that does.

Cubist is funding an RCT to address this question. I’ll be interested in seeing those results. In the meantime, I’m sticking with what I wrote last year, at least as regards the laboratory testing of MRSA.

Does #OpenAccess increase readership?

From the "I Wish I Did This Study" department.  Philip Davis and the American Physiological Society completed an RCT of the open-access publication model. All articles published in 11 APS journals between January and April 2007 were randomized into immediate free access (n=247) or normal subscription-only access for the first 12 months (n=1372). So did it work? Yes - far more downloads, same number of citations.

Article downloads: One-year after publication, open access articles received twice the number of full-text downloads and 61% more PDF downloads with more unique visitors. Fewer looked at the abstract with open-access, but why would they when they can read the whole thing? (see figure below)

Citations: Open-access articles were cited in similar numbers.  During the first year, 71% of open-access and 74% of subscription articles were cited at least once. At three years, citations averaged 10.6 per open-access and 10.7 per subscription-based article.

My only question. Why was this published in a newsletter and not a peer-reviewed journal?

Reference: PM Davis. Physiologist. 2010 Dec;53(6):197, 200-1.

Yes, I know this discussion isn't specific to infection prevention, but it is a "controversy" so I'm at least partially sticking to our mission. (insert emoticon)

#openAccess Costs Less: Think about it.

There are a few good examples as to why we continue to submit papers to non-open access journals. Sure open-access publication costs are high, but many researchers, even the under-funded hospital epidemiologist, should be able to gather up Departmental, Divisional or other resources to pay the publication costs. I think it's a matter of choice. Importantly, even if the research is called "unfunded", it is likely receiving hidden funding through paying of fellows' salaries or the opportunity-costs of less time spent actually doing "infection control." That is to say, someone is paying for the research.

"An implicit although obvious subtheme of Moneyball is that resistance to innovation is driven by job insecurity" - Nate Silver 

There is a new article in the Atlantic by Laura McKenna that further describes the situation, and I think it's worth a close read.  She describes the status quo very accurately:

1) Academic research is funded by national grants and/or subsidized through the university or hospital and the scientist is given "release time" to conduct the research.

2) The paper is then submitted to an academic (non-open access) journal.

3) These journals are housed and subsidized by universities (think ICHE and University of Michigan or AJIC and Columbia).

4) Journals are then edited by faculty members, who spend subsidized time editing the journal for not enough $$ to cover their time.

5) The "home" university provides offices for the editorial faculty and staff.

6) Papers selected for review are sent to faculty at other universities and are thus subsidized by these other universities, who support their peer-review activities.

7) If accepted, the manuscript is further reviewed by the editor and sent to the journal for publication

8) The publisher, to cover printing costs, sells the rights to JSTOR or other services and makes a tidy profit.

9) JSTOR then sells the papers back to university libraries for huge fees; said to be $45,000 initially and $8500/year just for the arts and sciences collection at JSTOR. If the general public (or non-university affiliated ICP) wants to read the article, they have to pay perhaps $38 to read it.

I will directly quote from her conclusion: "Step back and think about this picture. Universities that created this academic content for free must pay to read it. Step back even further. The public -- which has indirectly funded this research with federal and state taxes that support our higher education system -- has virtually no access to this material, since neighborhood libraries cannot afford to pay those subscription costs."

I would say that ALL of these costs, both visible and hidden, dwarf the one-time publication fee and would suggest that the reason we publish is to communicate our important findings with a wide audience.  If universities can't support open-access publication fees to the extent that they already silently fund closed journals, and I would suggest if they did, the pub costs would drastically decline, then I wonder if the research is even worth doing.  We easily spend 10 times more time (and money) collecting and analyzing the data, but can't cover the publication fee?  Hogwash.

Sunday, January 22, 2012

Dollars for Doctors

The NPR show On the Media aired a very interesting story today on the pharmaceutical industry's use of gifts and payments to physicians to influence drug prescribing. What I like about this interview of ProPublica journalists is that you get a sense of how nonmedical people view this issue. You can listen to the podcast here and see ProPublica's webpage on this topic here.

In the realm of infection prevention, the industries are different (e.g., microbiologic diagnostic testing supplies and equipment, cleaning products, and antimicrobial/antiseptic coated devices), but the core issue is essentially the same--allowing industry to influence practice and policy by targeting individual practitioners, professional societies and lawmakers.

Photo: ABC News

Saturday, January 21, 2012

A silver lining?

The Journal of Infectious Diseases has a paper (free full text here) and editorial on statins and influenza. It's another observational study that finds that treatment with statins is associated with decreased mortality in persons with  influenza. Over 3,000 laboratory confirmed cases of influenza requiring hospitalization in 10 states were analyzed in this study by CDC investigators. Treatment with statins was associated with a 41% reduction in mortality when adjusted for age, race, comorbid conditions, influenza vaccination and treatment with antivirals.

So when I take my dose of simvastatin tonight, I'll try to remember that this little pill may keep me alive when the next influenza pandemic hits. And speaking of flu, it's been a very slow season so far. At my hospital we've had only 2 confirmed cases, and those were in November.

Photo: Eastern Connecticut State University

Worthing Hospital: No #MRSA for 1 year!!!

Worthing Hospital, a 500-bed District General Hospital in Worthing, West Sussex, England is celebrating a nice achievement: No MRSA for one year. How did they achieve success? According to this article, "infection control has become a priority for the trust...and has seen improvements such as an increase in cleaning rounds and extra training for the housekeeping staff, detailed root cause analysis of any MRSA case, investment in all levels of nursing and a highly qualified team of infection control specialists, who work with ward staff to ensure they always follow the best practice." The hospital also reports no C. diff in November.

For me, the article is most interesting for the picture and what they don't say. No mention is made of active surveillance cultures and they don't seem to be showing off nares swabs in their photo. It all seems rather horizontal-ish. High fives Worthing Hospital!

Friday, January 20, 2012

Antibiotic-free pork ≠ #MRSA-free pork

Ashley O'Brien in Tara Smith's UI lab has a new study out in PLoS ONE looking at MSSA and MRSA in fresh retail pork samples.  Tara has a comprehensive blog post covering this study and their prior work leading up to this paper, so check it out if you want a lot of the details.

Briefly, they collected 395 samples from 36 stores in IA, MN and NJ. 300 samples were from "conventional" pork and 95 were from pork labeled "raised without antibiotics."  S. aureus was found in 67% of conventional samples and 57% of antibiotic-free samples, while 6.3% of conventional pork and 7.4% of antibiotic-free pork were contaminated with MRSA.

This is a relatively small study, so it likely should be repeated.  Also, as Tara mentioned in her post, in the states included in this study, very few USDA-certified organic products were available unfrozen, and they targeted sampling of fresh meats.  It is hard to speculate why MSSA and MRSA didn't differ significantly between the types of pork, but contamination during processing or at retail is certainly possible.  Could it be that conventional and antibiotic-free pigs are raised in close proximity?

O'Brien AM et al. PLoS ONE January 2012

Thursday, January 19, 2012

Hand over your money or I'll give you #MRSA

From the truth is stranger than fiction department: A man walked into Lucky's Internet Cafe in Sharon, Pennsylvania on Monday and began touching everything in the place before walking up to the cashier.  He then threatened to give the cashier MRSA if he didn't hand over the money.

The cashier refused, the man left and was later arrested at a Rite Aid Pharmacy across the street - no doubt attempting to fill his clindamycin script. I suspect the cashier was armed with bottle of alcohol hand rub under the counter, but this is just a guess.

Washington Post 1/19/2012

Sharon Herald 1/18/2012

Wednesday, January 18, 2012

Sunshinism: Protecting Patients or Further Destroying Physician Trust?

Yesterday, Dan posted about the new rules mandating the reporting of all physician payments from drug and device manufacturers. Generally, I've been in favor of increased transparency if, as Dan said, the "information is detailed and accurate." However, I think any system like this can and will be gamed and I suspect the results will be more destructive than constructive. For example, funding for "research" is thought to be less conflicting than direct payments to physicians for giving canned talks.  However, what about "research" support that pays for each patient enrolled and what if that payment goes directly to the enrolling physicians pocket, as would be the case in private practice? Is this such a bad thing that it needs to be constrained?

I suspect there are many other examples of how we won't be able to interpret the reports that are generated from these new rules.  I even suspect that the eventual approach to determining financial conflicts will be through opening up every physician's tax return.  That way, we can look at the true financial impact to the individual.  Pharmaceutical research that goes to a university and doesn't directly increase a physician's deans-approved salary would thus not appear on a tax return.  What about physicians that own stock in Pharma?  Wouldn't that be a more important conflict? You can see where this is going.  So someday soon, all physicians will have to share their tax returns with their patients perhaps by posting them in their waiting rooms or websites.

However, do you really think this will help root out conflicts?  What are the negative externalities of such an approach?  I suspect it will root out the caring physicians who don't want to appear to be in the pocket of pharma even if they are involved in highly important clinical studies. Which gets me to why I've been moved to write this post...

In today's NYT, David Brooks and Gail Collins debate the call to release Mitt Romney's tax return.  In the column, Brooks makes some important points, which I think are worth at least pondering in regards to the new payment disclosure rules and other examples of "sunshinism."

Brooks: "...there is a misbegotten ideology haunting the land, the ideology of sunshinism. This is the belief that everything should be made public. Sunshinism is a destructive ideology. Forcing people to financially undress in public is just one of those incursions that repels decent people..."

Could these new rules further mistrust of the medical community?  Is society better off when a patient doesn't want see an ID doc because she made $5000 enrolling patients in a trial of a new antibiotic? If she won't enroll patients, who will?

Which is a greater conflict for a physician? (a) $50,000 investigator initiated grant to a University (b) $5000 direct payment for giving a canned talk (c) $5000 for enrolling patients in a trial or (d) $50,000 stock in a pharmaceutical company that won't be disclosed under the new rules?

OK, so I think I've built a solid enough straw man.

Tuesday, January 17, 2012

La Nina and Influenza Pandemics

A new study published in PNAS by Jeffrey Shaman and Marc Lipsitch finds that the four recent influenza pandemics (1918, 1957, 1968, and 2009) were all preceded by La Niña (colder sea surface) conditions in the Pacific Ocean. The authors suggest that the climate changes can alter migratory bird activity and thus possibly impact their mixing with domestic animals. They therefore hypothesize that La Niña results in a higher likelihood of divergent influenza subtypes coming together with a subsequent higher probability of emergence of novel "pandemic" influenza strains.

In an accompanying BBC story by Richard Black, professor Shaman explains the findings and also cautions that the link should not yet be used to predict pandemics. However, he is hopeful that increased influenza strain surveillance subsequent to recent novel H1N1 and avian H5N1 activity will soon be able to confirm whether their proposed hypothesis is correct.

Shaman and Lipsitch PNAS 1/17/2012


Monday, January 16, 2012

This should be interesting...

New rules that mandate reporting of all physician payments from drug and device manufacturers should be out soon. I favor this transparency, provided the information is detailed and accurate. For example, receiving money from a company for doing a valid research study on one of their products is a bit different than receiving money to travel around the country on a speaker’s bureau. Let’s hope the publicly available data includes information about the reason for the payment, and the recipient of the payment (e.g. the medical school, to support Dr. X’s research study, or directly to Dr. X).

It will also be interesting to see if makers of diagnostic devices will be included—clearly the makers of devices that touch or are inserted into patients will be required to report payments, but it isn’t clear to me if the same holds true for makers of new diagnostic tests. As we’ve discussed before in this blog, such transparency is also extremely important.

Gaming of Impact Factors: New tactic or did they just get caught?

Ben Goldacre, one of this blog's favorite journalists/authors/doctors/critics, has a fascinating new post up on his secondary blog.  We all know that a journal's impact factor is largely useless for grading the quality of an individual paper. This follows from the old idiom, that you can't judge a book by it's cover. However, impact factors are also a poor way of comparing the quality of journals themselves. For one, journals that contain many review articles have higher impact factors since reviews are cited more frequently than original research. Journals game their impact scores by publishing more review articles. Now there is evidence that editors are gaming impact scores by forcing authors to cite articles from their journals before accepting the paper! Craziness.

The evidence from a revise and resubmit letter: “The Editors would also greatly appreciate you adding more than two but fewer than six references of articles published in [the Journal involved], above all articles published over the past two years.” Even more evidence that you can't judge a book by the cover.

I would write more, but I gotta go round, so I leave it to Mr. Bo Diddley...

(1) Ben Goldacre Secondary Blog - 16 January 2012
(2) F. Avanzini et al. Journal of Thrombosis and Haemostasis

Thursday, January 12, 2012

Science Friday (the 13th): TDR-TB

Maryn McKenna (@marynmck) of Superbug fame will be on Science Friday (Hour 1: 2-3pm ET) tomorrow to discuss Totally Drug-Resistant TB.  She has had some very informative posts recently on the topic, including discussion of the two earliest known patients in Italy who died in 2003.  She also reports on the latest twelve TDR-TB cases in a single Indian hospital and points us to an ahead-of-print letter in CID posted in December that discusses the diagnosis and care of the first four of these patients in India.  Turn on, tune in...

Superbug post #2: Earliest Cases of TDR-TB
Superbug post #1: Latest Cases of TDR-TB in India

(Eli @eliowa)

Wednesday, January 11, 2012

Support open access!

There is an excellent OpEd piece in today's New York Times by Michael Eisen, one of the founders of the Public Library of Science. A few years ago, the NIH mandated that any studies performed that were federally funded must be made available free of charge to citizens since they had paid for the research through their tax dollars. This obviously had an impact on journals that use the traditional business model of publishing, wherein the reader bears the cost of publication via subscription, either individually or through a library. Several years ago, the open access model of publishing emerged. In this business model, the cost of publication is borne by the author, often via funds from the research sponsor. However, papers published in this model are free to the reader.

The OpEd piece today points out that some notable journals in the traditional publishing model, including the New England Journal of Medicine, are now lobbying Congress to pass a law reversing the NIH rule so that they would no longer be required to make the papers available at no cost to readers. In response, Dr. Eisen calls on researchers to publish their studies only in open access journals and for libraries to cancel their subscriptions to journals that are not open access. The greed demonstrated by journals that are financially healthy is unpalatable. However, open access is a problem for investigators who publish papers that do not have a funding source, since the publication fees are often in excess of $1000 per paper. This is particularly a problem for hospital epidemiology, a field in which much research is unfunded, and is likely one of the reasons that the open access journal Antimicrobial Resistance and Infection Control has had a slow start. Open access is clearly a great concept and it should be maintained for studies that are federally funded. And for those of us who believe that medical and scientific research is a public good, further expanding open access by reducing or eliminating authors' fees via novel approaches is a worthy goal.

Tragedy of the commons: Antibiotics in Agriculture

@marynmck broke the story right before Christmas that FDA had silently posted that they are backing-off of their long-held (1977) plan to limit overuse of agricultural antibiotics. Instead of formal bans and policy change the FDA now hopes to “focus its efforts for now on the potential for voluntary reform and the promotion of the judicious use of antimicrobials in the interest of public health.”

So here is the current US policy for protecting a critical and diminishing resource for public health:  Please Please Please don't use antibiotics!  Please?  How about if I'm nice? No? Pretty Please. Sugar on top?  Perhaps we should call this the "Don't let the Pigeon Drive the Bus Policy."  I guess it kinda worked in the book. Kinda.

So after burying the bad news on a Thursday before a major holiday weekend, the FDA posted some sort of half-good news right after the new year. You guys excited?  So what was the good news?  They will limit cephalosporins (woo woo) but with so many loopholes and restrictions that it won't matter much. Today, a NYT Editorial in frustration pointed out that FDA "will ban the injection of the antibiotics into chicken eggs and halt the practice of giving large, sustained doses to cattle and pigs. But it still allows widespread use in animals like rabbits and ducks, and veterinarians will still be able to use the drugs in ways not specifically approved by the FDA."

We've written about this issue many times before.  It's amazing that we continue to squander critical antibiotics in animal populations, while at the same time barely funding efforts to develop new antibiotics or new infection prevention strategies. The NYT stated today that "it’s time for the FDA to consider the public’s health as carefully as it considers the interests of intensive agriculture and pharmaceutical companies." Hear Hear.


1) Maryn McKenna, Superbug Blog 12/23/2011
2) NYT Editorial "FDA Creeps Forward" 1/11/2012

Tuesday, January 10, 2012

Break-bone Fever in the Conch Republic

Key West by Kerne Erickson
I love Key West! With its predictably warm weather (even in January!), its lack of pretentiousness, and its welcoming attitude, what is there not to like about this little island? Well, apparently there is one thing: the latest issue of Emerging Infectious Diseases has a paper (full text here) on the reemergence of dengue in Key West.

Three clinical cases of dengue were acquired there in 2009, which prompted the CDC to investigate further. A serosurvey done in September 2009 showed that 3-5% of residents in the Old Town area had been recently infected. In 2010, an additional 63 clinical cases were reported.

I guess I'll have to take along some mosquito repellent next time I head to Margaritaville.

Monday, January 9, 2012

Hospital + fountain = trouble

Photo: Urban Review STL
A report in this month's Infection Control and Hospital Epidemiology describes an outbreak of Legionellosis involving 8 patients who ended up hospitalized at two hospitals. Via good old fashioned shoe leather epidemiology, it was determined that the only common exposure among these patients was exposure to a hospital with a wall-type water fountain in the lobby. Environmental cultures revealed that the fountain was heavily contaminated with Legionella pneumophila serogroup 1. A few years ago, Dan blogged about another Legionella outbreak associated with a indoor fountain in a hospital. If your hospital has one of these, shut it down!

Sunday, January 8, 2012

The long road to fast and accurate resistance detection

I’d like to say that molecular diagnostics will soon provide nearly instantaneous detection of antimicrobial resistance in clinical samples, allowing for rapid targeting of appropriate therapy. I’d like to say that, but I can’t. Even MRSA, a bug with a relatively simple resistance mechanism (simple relative to, say, MDR Acinetobacter), is proving to be a tough nut to crack. Remember this post of mine, about Cepheid’s recall of their Xpert SA/MRSA blood culture assay? Well, another “valued customer” notice went out last week, informing users that this product requires “additional test optimization” and “clinical re-validation”—so it will be unavailable until at least the end of 2012. Labs and hospitals that have come to rely on this test to improve their antimicrobial management of S. aureus bacteremia will now have to find another approach.

I’m posting not to knock Cepheid, but to make the point that bringing new rapid diagnostic methods to a clinical microbiology laboratory environment, and applying them to clinical care in unforgiving situations (e.g. would you like to have your MRSA bacteremia treated with nafcillin for the first 2-3 days?) is difficult! The makers of agar plates will be keeping their day jobs for a while….

Thursday, January 5, 2012

Quote of the Day

Ezekiel Emanual (U Penn) wrote an Editorial in this weeks JAMA titled "Where are the Health Care Cost Savings?" where he suggests that there are not enough aggregate savings in targeting malpractice costs, insurance profits, drug costs, and the "million dollar babies" to make a significant impact in US medical expenditures.

Where does he think the savings are:

"One estimate suggested that as much as 22% of all health care expenditures is related to potentially avoidable complications...reducing avoidable complications by 10% could save more than $40 billion per year."

The reference for the 22% estimate is a 2009 article by François de Brantes et al in the NEJM. What was the preventable complication example in the 2009 article? A readmission for a harvest site SSI post-CABG.

Video of the day

Here's a short video from a great organization, Clean the World. They collect leftover soap and shampoo from hotels, recycle it, and take it to those who need it in the developing world.

Chart of the day

The graph here shows the yearly number of publications found via a PubMed search using the terms "MRSA" and "active surveillance." What this means is open to interpretation, but I do sense that some of the fervor for this practice may be waning.

Death of the Mid-Career Investigator

Now that we Iowans have failed to select a candidate in the GOP caucuses, we can turn our attention to other political pursuits.  There is an important article just released in PLoS ONE by Kristin Matthews and colleagues at Rice University that describes the aging of the biomedical-research community in the US and its potential impact. 

The authors report that the average age of an NIH investigator rose from 39 to 51 between 1980 and 2008, while the average age of a new (first time) investigator rose from 36 to 42 during the same period. They also make some interesting comparisons to the average age of Nobel Laureates to determine if the rising age barriers at NIH could impact future innovative ideas and research. They found that during the same period, 96 scientists won a Nobel Prize in medicine or chemistry for biomedical research at an average age during the awarded research of 41 and 78% completed their research before age 51. They suggest that scientists do great work early in their careers but now those early careers won't be funded.

They conclude that "if nothing is done to reverse the rising age of PIs and first-time grantees, the scientific community could lose a generation of researchers, leading to an unsustainable biomedical research infrastructure and a dearth of talent participating in NIH-funded projects in the near future." I think a similar problem exists in infectious diseases and infection prevention research.

A world filled with only postdocs  (source Matthews et al PloS ONE)
Thus, there appears to be little funding or opportunity in the early and particularly mid-career period. This results in many fine and well-trained investigators leaving biomedical research in their 40's and never returning. Sure, a few lucky people will survive this pyramid scheme, but there won't be enough senior investigators in 10-20 years to mentor the next generation.

I'm not sure what the solution is or even the exact problem.  Is it ageism in scientific review committees or the lack of tenure-track faculty positions at the University level?  I suspect both of those issues are intertwined.

Source: Matthews et al. PLoS ONE 12/28/2011

Wednesday, January 4, 2012

Hospital epidemiologists are killing pharma

Photo: 2old2play. com
A new report shows that the hospital acquired bacterial infections market for the time period 2010 through 2017 is expected to decline by a negative CAGR of 3.4% (click here if, like me, you need help understanding a CAGR). One of the major reasons cited for this decline in the market for these antibacterial drugs is a reduction in healthcare associated infections.

If you are interested in learning more about what's in this report, click here and submit your credit card information. For only $3,500 (about the same price as a course of fidaxomicin), the report can be yours.  

Tuesday, January 3, 2012

Happy New Year from #Iowa #Nice

I think infection control was also invented in Iowa...

Sunday, January 1, 2012

Treatment as prevention; or, the best defense is a good offense

The journal Science has selected this paper as their “breakthrough of the year”. As you know, the HIV Prevention Trials Network study 052 demonstrated that early antiretroviral therapy reduced heterosexual HIV transmission by 96%. The concept is intuitively obvious, but often we compartmentalize “prevention” and “treatment” without recognizing how crucial prompt and effective therapy can be to preventing pathogen transmission (and/or to preventing emergence of antimicrobial resistance). I suspect we can and will put together some excellent sessions on “treatment as prevention” at the inaugural ID Week in 2012.

Oh, and Happy January 2012 from this humble blog.