title: Are diagnostic and public health bacteriology ready to become branches of genomic medicine?
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?
authors.affiliation: Centre for Systems Biology, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK. m.pallen@bham.ac.uk.
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Pallen
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Loman