title: The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone.
abstract: Escherichia coli ST131 is now recognised as a leading contributor to urinary tract and bloodstream infections in both community and clinical settings. Here we present the complete, annotated genome of E. coli EC958, which was isolated from the urine of a patient presenting with a urinary tract infection in the Northwest region of England and represents the most well characterised ST131 strain. Sequencing was carried out using the Pacific Biosciences platform, which provided sufficient depth and read-length to produce a complete genome without the need for other technologies. The discovery of spurious contigs within the assembly that correspond to site-specific inversions in the tail fibre regions of prophages demonstrates the potential for this technology to reveal dynamic evolutionary mechanisms. E. coli EC958 belongs to the major subgroup of ST131 strains that produce the CTX-M-15 extended spectrum β-lactamase, are fluoroquinolone resistant and encode the fimH30 type 1 fimbrial adhesin. This subgroup includes the Indian strain NA114 and the North American strain JJ1886. A comparison of the genomes of EC958, JJ1886 and NA114 revealed that differences in the arrangement of genomic islands, prophages and other repetitive elements in the NA114 genome are not biologically relevant and are due to misassembly. The availability of a high quality uropathogenic E. coli ST131 genome provides a reference for understanding this multidrug resistant pathogen and will facilitate novel functional, comparative and clinical studies of the E. coli ST131 clonal lineage.
authors.affiliation: Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, The University of Queensland, Queensland, Australia.
authors.forename: Brian M
authors.initials: BM
authors.lastname: Forde
authors.affiliation: Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, The University of Queensland, Queensland, Australia.
authors.forename: Nouri L
authors.initials: NL
authors.lastname: Ben Zakour
authors.affiliation: Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, The University of Queensland, Queensland, Australia.
authors.forename: Mitchell
authors.initials: M
authors.lastname: Stanton-Cook
authors.affiliation: Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, The University of Queensland, Queensland, Australia.
authors.forename: Minh-Duy
authors.initials: MD
authors.lastname: Phan
authors.affiliation: Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, The University of Queensland, Queensland, Australia.
authors.forename: Makrina
authors.initials: M
authors.lastname: Totsika
authors.affiliation: Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, The University of Queensland, Queensland, Australia.
authors.forename: Kate M
authors.initials: KM
authors.lastname: Peters
authors.affiliation: Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Kok Gan
authors.initials: KG
authors.lastname: Chan
authors.affiliation: Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, The University of Queensland, Queensland, Australia.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Schembri
authors.affiliation: Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, United Kingdom.
authors.forename: Mathew
authors.initials: M
authors.lastname: Upton
authors.affiliation: Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, The University of Queensland, Queensland, Australia.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Beatson
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D002876:Chromosomes, Bacterial; D019295:Computational Biology; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics; D004739:England; D004926:Escherichia coli / Q000145:classification / Q000187:drug effects / Q000235:genetics*; D004927:Escherichia coli Infections / Q000382:microbiology; D023061:Gene Order; D016680:Genome, Bacterial; D023281:Genomics; D006801:Humans; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D014552:Urinary Tract Infections / Q000382:microbiology
chemical_list: D000900:Anti-Bacterial Agents