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PLoS Genet. 2016 Sep 12;12(9):e1006280. doi: 10.1371/journal.pgen.1006280. eCollection 2016 Sep.

Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations.

Author information

1
Pathogen Research Group, Nottingham Trent University, Nottingham, United Kingdom.
2
Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom.
3
Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
4
Department of Biology, National University Ireland, Maynooth, Ireland.
5
College of Medicine, University of Swansea, Swansea, United Kingdom.
6
Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
7
Departments of Pathology and Microbiology, University College Cork, Cork, Ireland.
8
Institute of Hygiene, Universitat Muenster, Muenster, Germany.
9
Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, and CEITEC VFU, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic.
10
Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universitat, Berlin, Germany.
11
Robert Koch Institute, Berlin, Germany.
12
Centre for Infectious Diseases, West China Hospital of Sichuan University, Chengdu, China.
13
Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom.
14
Department of Biostatistics, University of Oslo, Oslo, Norway.

Abstract

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.

PMID:
27618184
PMCID:
PMC5019451
DOI:
10.1371/journal.pgen.1006280
[Indexed for MEDLINE]
Free PMC Article

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