Mike the Mad Biologist

In this story about the use of rapid genomic sequencing to monitor a hospital outbreak of multi-drug resistant Klebsiella pneumoniae (more details here), this end bit is interesting (italics mine):

“In the E. coli outbreak, we had enough E. coli reference strains and knew enough about E. coli biology to quickly identify a set of genes for specific diagnostics before we had the whole genome sequence,” says Dag Harmsen, a microbiologist at the University of M√ľnster who was involved in sequencing efforts during both outbreaks. “But we don’t have as much experience with Klebsiella, so this time we really needed the whole genome,” he says.

“I think every large hospital will soon have a benchtop whole genome sequencer,” says Harmsen. But rapid science can only help when there is rapid recognition of a threat. The director of the Maasstad hospital, Paul Smits, resigned on 9 August following condemnation of his hospital’s slow response to the outbreak.


I’ve always opposed (in the U.S.) a lawsuit-based approach, since most lawyers and judges are stone-cold ignorant of biology (patenting the sun, for instance). But making hospitals–and those who run them–responsible for what is essentially ‘epidemiological malpractice’ is a good idea. Mind you, I’m not talking about firing someone because an outbreak happens infrequently–this, unfortunately, happens. But when there’s a pattern of recurrent hospital outbreaks, or an incredibly inept response, then this needs to be treated in the same way that egregious surgical or prescription malpractice would be (or should be, anyway).