title: Increase in bacteraemia cases in the East Midlands region of the UK due to MDR Escherichia coli ST73: high levels of genomic and plasmid diversity in causative isolates.
abstract: OBJECTIVE
  The objective of this study was to determine the population structure of Escherichia coli ST73 isolated from human bacteraemia and urinary tract infections.
  
  
  METHODS
  The genomes of 22 E. coli ST73 isolates were sequenced using the Illumina HiSeq platform. High-resolution SNP typing was used to create a phylogenetic tree. Comparative genomics were also performed using a pangenome approach. In silico and S1-PFGE plasmid profiling was conducted, and isolates were checked for their ability to survive exposure to human serum.
  
  
  RESULTS
  E. coli ST73 isolates circulating in clinically unrelated episodes show a high degree of diversity at a whole-genome level, but exhibit conservation in gene content, particularly in virulence-associated gene carriage. The isolates also contain a highly diverse plasmid pool that confers MDR via carriage of CTX-M genes.
  
  
  CONCLUSIONS
  Our data show that a rise in incidence of MDR E. coli ST73 clinical isolates is not due to a circulating outbreak strain as in E. coli ST131. Rather the ST73 circulating strains are distantly related and carry a diverse set of resistance plasmids. This suggests that the evolutionary events behind emergence of drug-resistant E. coli differ between lineages.
authors.affiliation: Pathogen Research Group, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK.
authors.forename: Fahad
authors.initials: F
authors.lastname: Alhashash
authors.affiliation: Department for Infection Control, West China Medical School, Chengdu, China.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Wang
authors.affiliation: Wellcome Trust Biomedical Informatics Hub, University of Exeter, Exeter EX4 4QD, UK.
authors.forename: Konrad
authors.initials: K
authors.lastname: Paszkiewicz
authors.affiliation: Department of Microbiology, Nottingham University Hospitals NHS Trust, QMC Campus, Nottingham NG7 2UH, UK.
authors.forename: Mathew
authors.initials: M
authors.lastname: Diggle
authors.affiliation: Department for Infection Control, West China Medical School, Chengdu, China.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Zong
authors.affiliation: Pathogen Research Group, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK alan.mcnally@ntu.ac.uk.
authors.forename: Alan
authors.initials: A
authors.lastname: McNally
mesh_terms: D016470:Bacteremia / Q000453:epidemiology* / Q000382:microbiology; D019295:Computational Biology; D024901:Drug Resistance, Multiple, Bacterial; D016521:Electrophoresis, Gel, Pulsed-Field; D016021:Epidemiologic Studies; D004926:Escherichia coli / Q000145:classification* / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D004927:Escherichia coli Infections / Q000453:epidemiology* / Q000382:microbiology; D014644:Genetic Variation; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D015994:Incidence; D058889:Molecular Typing; D010957:Plasmids / Q000032:analysis; D017422:Sequence Analysis, DNA; D006113:United Kingdom / Q000453:epidemiology