Friday, January 25, 2013

Carl Zimmer just wrote a wonderful article describing the use of microbiology, DNA sequencing, bioinformatics, and phylogenetic analysis to explain a carbapenem-resistant Klebsiella pneumoniae outbreak in Wired:
On September 19, 2011, Evan Snitkin sat staring at a computer monitor, its screen cluttered with Perl script and row after row of 0s sprinkled with the occasional 1. To Snitkin, a bioinformatician at the National Institutes of Health, it read like a medical thriller. In this raw genetic-sequencing data, he could see the hidden history of a deadly outbreak that was raging just a few hundred yards from where he sat. 
And further on:
As word of the outbreak circulated among the NIH staff, Snitkin and his boss, Julie Segre, approached the Clinical Center with an unusual offer. In their jobs at the NIH’s National Human Genome Research Institute, the two scientists had previously sequenced genomes from a bacterial outbreak long after it had died out. But today, sequencing technology had become so fast and so cheap. Why not analyze the bacteria in the middle of an outbreak? By tracking the bug’s transmission route through the hospital, they might be able to isolate it and stop its lethal spread. 
Zimmer did an excellent job in this article translating an overwhelming amount of lab techniques and jargon into easily understandable explanations.  This story of Bethesda, Maryland's Klebsiella outbreak is a long, but excellent read, for anyone curious about what "real science" is all about.

I only have one constructive disagreement with Zimmer, and it's on the following.  He claims:
It’s unlikely that most US hospitals will be able to fight their superbug outbreaks the way that Tara Palmore, Julie Segre, and Evan Snitkin fought theirs—at least not anytime soon. The NIH Clinical Center had access to a scientific brain trust and a massive genome sequencing center to go with it. For now, smaller hospitals don’t have a labful of sequencing equipment, let alone the necessary expertise.
He emphasizes a lack of equipment, but machines aren't the limiting factor: it's having the people capable of doing Snitkin's kind of molecular detective work.  I probably know over a hundred people (I'm not kidding) that could be taught how to do this in a few weeks.  Genomics-based public health approaches are easily within reach, almost anywhere in North America, today.

DNA samples from future outbreaks in small hospitals can simply be couriered to sequencing centers and data can be put into a scientist's hands in a few days, if need be. But ultimately, scientifically minded people must be readily available to do something with it!