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Ready For It?

The University of Birmingham's Mark Pallen and Nicholas Loman discuss whether "diagnostic and public health bacteriology [are] ready to become branches of genomic medicine" in a Genome Medicine paper published online in advance this week. (Pallen has posted the text of this paper to his Pathogens: Genomes and Genomes blog.)

"In the research arena, genome sequencing has transformed … the study of bacterial pathogens," Pallen and Loman write, adding, though, that "relatively few front-line diagnostic bacteriology laboratories have embraced molecular methods." In considering the impacts of the collaborative investigation of the recent German Escherichia coli O104:H4 outbreak, the authors note "the value and utility of such [genomic epidemiology] approaches in real-world, real-time situations." However, despite the enthusiasm these studies have generated within the research community, Pallen and Loman point out caveats to their application in the clinic. Notably:

Bacterial genomic epidemiology is currently overly reliant on the identification of single nucleotide polymorphisms in draft genome sequences, largely because of the historical limitations of short-read technologies. It remains an open question whether for every bacterial lineage, SNP calling across the whole genome will always prove more informative than probing variation in the highly dynamic repetitive regions sampled by existing typing methods.

The authors also expresses concerns that the "comparability and reliability of draft genome analyses remain critically dependent on the sequencing technology and analytical pipelines that are used." Overall, though, Pallen and Loman say that "there are many rivers to cross before medical microbiology becomes simply a branch of genomic medicine, but perhaps the promised land is in sight."

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