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Microorganisms 2015, 3(2), 236-267; doi:10.3390/microorganisms3020236

Tackling Drug Resistant Infection Outbreaks of Global Pandemic Escherichia coli ST131 Using Evolutionary and Epidemiological Genomics

School of Biotechnology, Faculty of Science and Health, Dublin City University, Dublin 9, Ireland
Academic Editors: Weiwen Zhang and Laurent Poirel
Received: 16 February 2015 / Revised: 28 April 2015 / Accepted: 30 April 2015 / Published: 20 May 2015
(This article belongs to the Special Issue Antibiotic Resistance Mechanisms)
View Full-Text   |   Download PDF [732 KB, uploaded 20 May 2015]   |  

Abstract

High-throughput molecular screening is required to investigate the origin and diffusion of antimicrobial resistance in pathogen outbreaks. The most frequent cause of human infection is Escherichia coli, which is dominated by sequence type 131 (ST131)—a set of rapidly radiating pandemic clones. The highly infectious clades of ST131 originated firstly by a mutation enhancing conjugation and adhesion. Secondly, single-nucleotide polymorphisms occurred enabling fluoroquinolone-resistance, which is near-fixed in all ST131. Thirdly, broader resistance through beta-lactamases has been gained and lost frequently, symptomatic of conflicting environmental selective effects. This flexible approach to gene exchange is worrying and supports the proposition that ST131 will develop an even wider range of plasmid and chromosomal elements promoting antimicrobial resistance. To stop ST131, deep genome sequencing is required to understand the origin, evolution and spread of antimicrobial resistance genes. Phylogenetic methods that decipher past events can predict future patterns of virulence and transmission based on genetic signatures of adaptation and gene exchange. Both the effect of partial antimicrobial exposure and cell dormancy caused by variation in gene expression may accelerate the development of resistance. High-throughput sequencing can decode measurable evolution of cell populations within patients associated with systems-wide changes in gene expression during treatments. A multi-faceted approach can enhance assessment of antimicrobial resistance in E. coli ST131 by examining transmission dynamics between hosts to achieve a goal of pre-empting resistance before it emerges by optimising antimicrobial treatment protocols. View Full-Text
Keywords: population genetics; bacterial infection; recombination; horizontal gene transfer; epidemic; spread; transmission; antimicrobial resistance; clone; pathogen population genetics; bacterial infection; recombination; horizontal gene transfer; epidemic; spread; transmission; antimicrobial resistance; clone; pathogen
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Downing, T. Tackling Drug Resistant Infection Outbreaks of Global Pandemic Escherichia coli ST131 Using Evolutionary and Epidemiological Genomics. Microorganisms 2015, 3, 236-267.

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