The publication of a paper “Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing” has drawn a lot of attention, presumably in large part because it occurred at an NIH facility. [http://stm.sciencemag.org/content/4/148/148ra116.full.html, DOI: 10.1126/scitranslmed.3004129]
I work on the microBEnet project as a “building scientist” to help achieve the Sloan Foundation’s programs goals of bringing microbial ecology methods and techniques to the indoor and built environment scientific community. My role is largely making the connections, encouraging and facilitating collaboration.
I was looking at the Klebsiella paper for discussion of possible routes of transmission and associated environmental pathways. I saw mention of a contaminated ventilator but no other. I did see that disinfection was practiced vigorously but was not enough to prevent infection spread. In the subject paper I am interested in the role of environmental factors that may contribute to infection spread. Beyond this specific case, I am interested in trying to clarify the environmental factors that are important to the microbial ecology — “who is there and what are they doing?”
My question for the authors of the paper and readers of this blog post: retrospectively, what environmental sites should have been sampled? The ones that come to my mind are the following: Bedding, clothing, door knobs, ventilation system inlets and outlets, toilets sinks and the handles and spouts associated with them, floors, etc.
My role in a couple of hospital study proposals for Sloan funding and in other Sloan-funded projects is to identify and interpret those factors in the indoor environment that should be characterized along with the collection of samples for sequencing. The microbial ecology literature systematically de-emphasizes these factors because it is not the focus of the journals, authors, or readers of most of the journals where the studies are published. To address this, I have been assembling a body of literature and a database to identify indoor environmental factors associated with the presence of specific organisms. I am trying to mine this literature to identify the most critical factors. Of course temperature, humidity, pH, and surface material come up often. I see the skin as an important “surface” with a variety of environmental characteristics strongly affected by the indoor environment.
Please consider this question: What other surfaces or conditions in the indoor environment should be sampled or characterized along with the microbial ecology?