PeerJ and Why Giraffes Have Short Necks

Sometimes in life you need a new perspective. In the entirety of my existence, I've always thought of giraffes as having long necks, and I bet many of you did too. But then PeerJ went live today and suddenly my view of giraffes changed.  Instead of long necks, they're more of a medium neck creature. You see, today I discovered that sauropod dinosaurs had necks 15 meters in length or 6x longer than the world record for giraffes.** And as an aside, I learned what anatomic features enabled them to have such long necks.

And it's not just my perspective on neck length that changed today, it's my perspective on open-access publishing.  Until today, if you wanted to publish in an open-access journal, it would be a high-cost affair. For example, publishing in BMC-Infectious Diseases might cost you $2055/article and publishing in PLoS One might cost you $1350/article. Starting today, you can publish your hard-earned research findings in an open-access, advertising free peer-reviewed journal for .... $99.  And that one-time only $99 "membership" will allow you to publish one article a year.  Of course there's a slight catch. Each author has to pay the $99, so if you have 5 authors, it'll cost you $495. If you usually publish with the same author group, that will be a one-time cost.

We've written frequently about the benefits of open-access publishing including increased readership of your papers and the societal benefits of free access to research findings for our tax-paying funders (thank you tax payers!). There are many perceived barriers to open-access, particularly legacy promotion/tenure committees at universities, but these can be overcome. One real barrier has always been cost, but at $99 or even $495 that barrier is slowly going away. What a nice change in perspective!

For more info see Mike Taylor's post in the Guardian Feb 12, 2013

Image source: wikipedia

COI acknowledgement: I'm an Academic Editor at PeerJ (as is Dan). I'm also a section editor at the open-access journal Antimicrobial Resistance and Infection Control, and was recently named Section Editor for SHEA's journal Infection Control and Hospital Epidemiology.

**Yes, I've seen a sauropod skeleton before but I've never thought of giraffes as having short necks. It's the juxtaposition that was refreshing, like open-access next to $99.

Daptomycin non-susceptible enterococcus

There was a time, way back in the 1990's, back before quinupristin/dalfopristin (1999), linezolid (2000) or daptomycin (2003), that we had to treat VRE with an antibiotic called chloramphenicol. You remember chloramphenicol and its association with reversible bone marrow suppression and fatal aplastic anemia. Even then, VRE developed resistance to chloramphenicol, but we didn't have many other options.

So, it was an exciting time a decade ago when we suddenly had three new treatment options for the always resistant enterococcus.  Those good times have passed us by quickly.  In a new study published in ARIC, Jeremy Storm (COI alert: an ID fellow in Dan's ID division) analyzed a case-series of daptomycin non-susceptible enterococci from a 6-year period (2005-2011) at the University of Iowa.  This is a case-series, so risk factors can't specifically be measured; however, 60% of the 25 patients had prior daptomycin exposure. I've pasted Table 3 below, so you can look at the resistance profile of the isolates. Hopefully, we won't have to dig out chloramphenicol anytime soon, but I'm brushing up on its dosing just in case.

If you need more depressing enterococcal news, you can also read about a high-prevalence (61 patients) of vanB containing E. faecium in a southwest Germany neonatal ICU.

If you're criticizing methods, your methods better be strong

This morning I innocently set out to review a new study in ARIC that looks at methodological issues in C. difficile outcomes studies assessing the association between infection and excess hospital stay.  The authors make a very important point in the paper: "The studies did not collect data concerning the time of onset of CDI; therefore, it is not possible to exclude the possibility of reverse causality, in which longer lengths of hospitalisation may have increased the risk of CDI." They then go on to discuss time-dependent bias and recommend the use of multi-state models...we've made this point before.

What caused me the emotional anguish was their Table 1 that lists the 16 studies included in the review. In column two, three of the studies are listed as retrospective case-control studies...what??!!  How can you do a case-control study with an outcome being hospital length of stay?  I'm pretty sure you can't, at least not easily.

You see, a case-control study requires identifying an outcome and looking back for risk-factors associated with the outcome. For example, you could look at 50 people that died (and 100 that didn't die) and see how many had CDI, to determine if CDI was a risk-factor for death.  For length of stay, I can't even make up a good way to do a case-control study.  Would you find patients who stay >14 days and compare them to patients that stay <14 days? The three studies listed MUST have been cohort studies, so why did the authors of the ARIC paper seeking to teach us about proper methods for outcomes studies list them as case-control studies? Perhaps they pasted them from the individual studies' methods sections?

Just to confirm this, I looked at all three papers: (Ananthakrishnan (2008), Bajaj (2010), Pepin 2005).

Pepin: from the Methods  - "We compared mortality and total length of hospital stay among inpatients in whom nosocomial CDAD developed and among control subjects without CDAD."  This is a cohort study - exposed and unexposed to CDAD, looking forward to outcomes.  Just because they incorrectly use the word control, doesn't make this a case-control study. (Strike 1)

Ananthakrishnan: "Our primary case group (C difficile–IBD group) included patients who had a primary diagnosis of C difficile colitis and a secondary diagnosis of either Chrohn's Disease (CD) or Ulcerative Colitis (UC). Patients admitted to hospital with a primary diagnosis of CD or UC without a diagnosis of C. difficile colitis formed one of our comparison groups (IBD group)." Another cohort study - defined by the exposure to C. difficile and not by the outcome. (Strike 2)

Bajaj: "Among the cohort of hospitalized patients with any diagnosis of cirrhosis, co-existing diagnosis of C. difficile was associated with significantly greater in-hospital mortality."(Strike 3)

The error of incorrectly describing cohort studies as case-control studies is very common - enough to be a pandemic.  The journal CID is one of the worst offenders. One of my favorite examples is this recent VAP treatment cohort study described as a case-control study in the title!  When I've mentioned the problem to CID editors, they suggest I write a letter.  You can't write letters for each issue.

OK: Cohort - exposed/unexposed look forward in time to the outcome. Case-control - find outcomes and look back for exposures. Got it?  EOR

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

Open Source ARIC Journal: Now Open!

As we mentioned back in June, there's a new open-source BMC journal titled - Antimicrobial Resistance and Infection Control (ARIC).  The website for submissions is NOW active. Per Andreas Voss, the Editor-in-Chief, manuscripts are being accepted and the "under construction" sign will be removed after the first paper is published. In addition to Andreas, Jan Kluytmans is the Deputy Editor and Didier Pittet is the Executive Editor, so this will be an excellent addition to our field and the benefits of having an open-source option can't be over emphasized. Submit your manuscripts here and read more about what types of papers they are looking for here.

Journal website: www.aricjournal.com/

Infection Control Journals - Hooray!!!

Hanging out at the 1st ICPIC, yesterday.  Pretty exciting with ~1100 attendees from the whole world. Save the date for the next conference in Geneva - June 25-28, 2013.

While wandering about, I got a cool text message from Preeti Malani, an Associate Editor at ICHE, who informed me that the ICHE journal impact score is up to 3.751 - that's quite a huge jump in 1 year.  I suspect it will be even higher next year given the size of the 1-year jump.  Independent of how you feel about impact scores, it is still very good news for those of us that publish in this excellent and well-focused journal.  Given that promotion and tenure of medical school faculty often depend on publication in high impact journals, this is a big deal for academic types. Three cheers to the entire ICHE editorial board and especially Suzanne Bradley, whose tireless efforts should now be fully appreciated.

...and to emphasize that you can never rest on your laurels...Andreas Voss, the ICPIC co-chair, just announced a new BMC journal titled - Antimicrobial Resistance and Infection Control (ARIC).  The website for submissions is not yet active, but I will post the info when it becomes available.