Blog | Monday, November 11, 2013

Everything old is new again, with whole genome sequencing

As we’ve pointed out, whole genome sequencing (WGS) is the hottest new tool to help us decipher the epidemiology of healthcare-associated pathogens. The New England Journal of Medicine included a study using WGS to investigate the molecular epidemiology of Clostridium difficile disease (CDD) in Oxfordshire, UK. In a 3.6 year study that included 1,223 CDD patient isolates, the investigators found that only 333 were genetically related to at least one previously obtained isolate. Of those 333, only 126 (38%) had nosocomial exposure to the earlier patient. And the finding receiving the most attention was that 45% of strains isolated were genetically distinct from all previous isolates.

The take home point? In current hospital settings (where we isolate every known CDD patient and use enhanced environmental measures to try to eradicate their C. difficile spores), symptomatic CDD cases are no longer the major reservoir for C. difficile acquisition. Focusing only on transmission prevention, then, will have a limited impact (antimicrobial stewardship, anyone?). Most obviously, further work is clearly needed to identify other sources of exposure and acquisition of C. difficile.

This may come as news to many, but probably not to Matt Samore, who made a similar observation … in 1994.

Daniel J. Diekema, MD, FACP, practices infectious diseases, clinical microbiology, and hospital epidemiology in Iowa City, Iowa, splitting time between seeing patients with infectious diseases, diagnosing infections in the microbiology laboratory, and trying to prevent infections in the hospital. This post originally appeared at the blog Controversies in Hospital Infection Prevention.