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!!

Sources:
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 bla_CTX-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

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)

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.

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!

@eliowa

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