Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations

The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug–resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements.

Journeying to a journal

At a Council meeting of the newly-formed Cork Historical and Archaeological Society, 17 November 1891, the Chairman /President, Revd R.A. Canon Sheehan, 'informed the meeting that Mr. Robert Day had been generous enough to place his valuable edition of Smith's History, with notes by Dr. Caulfield and Crofton Croker, at the disposal of the Society for publication'. At a subsequent meeting Wm Ringrose Atkins expressed the Society's thanks to W.A. Copinger 'who has kindly consented to edit Smith's Cork with Mr. Robert Day'. Thus began the work of rounding out close to two and a half centuries of antiquarian endeavour in Cork and of using its synthesis as a foundation for a new medium to record and communicate the social and cultural heritage of Cork city and county.