Swabs are evil (and other sage advice from your friendly clinical microbiologist)

The current state of infectious disease diagnostics is an Achilles’ heel to effective treatment and prevention. Despite the strides we’ve made in many areas (molecular diagnostics for viral respiratory pathogens, for example), for many serious infections our turnaround times are too long to be clinically relevant, test performance characteristics are all over the map, and sample acquisition at the bedside, clinic or OR is inconsistent (“whoa, not sure what this is….let’s stick a swab in it and send it to micro…just check all the boxes on that requisition”). One of the most important jobs of a clinical microbiologist is to communicate early and often with clinicians, to advise them on what samples to obtain, and what tests to order, to maximize the likelihood that the correct diagnosis will be made. 

That’s why I’m so happy that a bevy of clinical microbiologists decided to put as much good advice as they could into one helpful guidance document, found here: A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2013 Recommendations by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM).

Whether you’re an intern trying to decide what test to order on a patient you suspect of having filariasis, or a neurosurgeon wondering what to do when that focal brain lesion turns out to be filled with pus, this is your handy reference.

Image of E. coli growth from CDC Public Health Image Library

57 Days of Diarrhea: Iowa and Nebraska Cyclospora Outbreak

As if living out here in the heartland wasn't exciting enough, news is quickly spreading (although not as quickly as the disease and ensuing panic) of a cyclospora outbreak in Iowa and Nebraska. Recent reports suggest that there have been at least 18 cases in Nebraska and perhaps 25 in Iowa. The Iowa Department of Public Health reports that as of Monday there were 22 cases and that the outbreak seems to have begun in mid-June. No source has been identified. What's a bit interesting is the focus in the IDPH brief and subsequent media reports on a 57-days duration (if untreated).  Many folks I've talked to are focusing solely on 57 days, as the news reports make it sound like if you get cyclospora, you might as well camp out in your bathroom for a couple months.  Perhaps the IDPH and media reports could mention that trimethoprim/sulfamethoxazole (bactrim) is a readily available and effective therapy? This might reduce the panic.

Dan made a radio appearance a few days ago to discuss the outbreak - you can read the transcript here. Interestingly, the segment mentioned that prior to this outbreak there were only 10 reported cases of cyclospora over past 20 years in Iowa.

A handwashing nudge

As a hospital epidemiologist, I'm always looking for ways to nudge people to wash their hands. Nudges guide a person to do the right thing (i.e., encourage compliance) without a mandate. Here's the latest one, which was featured by NPR yesterday: the sink-urinal. This allows men to pee in the bottom part of the fixture and wash their hands in the top. It provides a constant reminder to wash your hands. It's environmentally friendly as it uses gray water (from the sink) to flush the urinal. Plus, it comes in an assortment of colors; what more could you ask for?

Photos: Ingus Bajars/Courtesy of Kaspar Jursons

The donor perspective

Today's New York Times has an interesting essay on fecal transplantation with an interesting twist: it's written by a stool donor. The recipient has inflammatory bowel disease. While there is not much evidence regarding fecal transplant for inflammatory bowel disease at this point, there is growing interest. When one compares the safety profile of fecal transplant versus those of highly immunosuppressive therapies for IBD, it's easy to see why many patients might be willing to pursue fecal transplant. I recently spoke to an internist at an academic medical center, who told me that several of his gastroenterology colleagues are informally recommending to patients that fecal transplant may be worth pursuing for IBD. Oh, the power of poo...

Graphic: Katie Scott, New York Times

More VRSA

Earlier this week, Eli posted on the first case of VRSA in Europe. Today, a posting on ProMed reports on the first VRSA case in Latin America. This is also the first time VRSA has been isolated from the blood; all previous strains were isolated from wounds. The patient was a 35 year old man from Sao Paulo, Brazil with diabetes and Sezary Syndrome. His bloodstream infection was controlled with daptomycin but he died 3 weeks after VRSA was isolated. The vanA gene was detected in the VRSA strain as well as from an Enterococcus faecalis strain isolated from the same patient.

Graphic:  Wikipedia

Epidemiologic activists

There's an excellent article in this morning's New York Times on the quest by the Cochrane group to determine the efficacy of Tamiflu, which is part of a bigger story on how pharmaceutical companies selectively release data regarding their products. It demonstrates how epidemiology can involve more than just data analysis and how political activism is sometimes required to find the data to answer basic questions.

Photo: Dr. Tom Jefferson by Chris Warde-Jones for the New York Times.

Top Infection Control Papers - ICPIC 2013 Edition

Andreas Widmer and I had the honor of presenting the "Best" Papers lectures at ICPIC this year. In case we spoke too quickly or you couldn't make it to Geneva this year, we have have posted the slides below. We wish we could have included many more papers since the quality of infection prevention research has increase immensely over the past decade (e.g. Huang's REDUCE MRSA study and Bonten's MOSAR trial).