Tuesday, January 31, 2012
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
The final platform model is not yet open. It appears they are still seeking input on questions such as:
- How much formal refereeing is required?
- What is an article amendment versus an update?
- What incentives are required to encourage post-publication refereeing, author response and revisions, and sharing of raw but template data?
- What author fees are appropriate for the different types of content?
F1000 Research (for Faculty of 1000)
Friday, January 27, 2012
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
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
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!
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
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
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.
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)
"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
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
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
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
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
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
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
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
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.
Monday, January 16, 2012
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
Superbug post #2: Earliest Cases of TDR-TB
Superbug post #1: Latest Cases of TDR-TB in India
Wednesday, January 11, 2012
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.
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
|Key West by Kerne Erickson|
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
|Photo: Urban Review STL|
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
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.
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)|
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
|Photo: 2old2play. com|
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.