Are diagnostic and public health bacteriology ready to become branches of genomic medicine?

Mark J Pallen^* and Nicholas J Loman

* Corresponding author: Mark J Pallen m.pallen@bham.ac.uk

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Genome Medicine 2011, 3:53 doi:10.1186/gm269
Published: 23 August 2011

Abstract

Diagnostic medical bacteriology is a conservative discipline. When busy house officers scribble 'M, C & S' on a form, they are requesting two techniques - microscopy and culture of microorganisms - that date back to the late 17th and late 19th century, respectively. The third technique - antibiotic susceptibility testing - has changed little in a half a century. Relatively few front-line diagnostic bacteriology laboratories have embraced molecular methods; on my own campus, the hospital's medical microbiology department does not even possess a thermal cycler!

And yet in the research arena, genome sequencing has transformed almost every corner of the biomedical sciences, including the study of bacterial pathogens Furthermore, over the past 5 years, high-throughput (or 'next-generation') sequencing technologies have delivered a step change in our ability to sequence microbial genomes [1]. Since arriving in the market place, these technologies have experienced sustained technical improvement, which, twinned with lively competition between alternative platforms, has placed sequencing in a state of 'permanent revolution'.

At last, it seems that genomics has come up with a game-changer, a killer app, a disruptive technology that even those long wedded to the Gram stain and the agar plate can no longer ignore. Does this mean we are on the brink of a revolution in diagnostic and public health microbiology, in which high-throughput sequencing usurps the traditional 'M, C & S', or will the discipline's innate conservatism stand firm for decades to come?