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
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{"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", "type"=>"journal", "authors"=>[{"first_name"=>"Brian M.", "last_name"=>"Forde", "scopus_author_id"=>"35746149500"}, {"first_name"=>"Nouri L.", "last_name"=>"Ben Zakour", "scopus_author_id"=>"23026690500"}, {"first_name"=>"Mitchell", "last_name"=>"Stanton-Cook", "scopus_author_id"=>"24382059600"}, {"first_name"=>"Minh Duy", "last_name"=>"Phan", "scopus_author_id"=>"16550508300"}, {"first_name"=>"Makrina", "last_name"=>"Totsika", "scopus_author_id"=>"10540434600"}, {"first_name"=>"Kate M.", "last_name"=>"Peters", "scopus_author_id"=>"55921088900"}, {"first_name"=>"Kok Gan", "last_name"=>"Chan", "scopus_author_id"=>"55484790300"}, {"first_name"=>"Mark A.", "last_name"=>"Schembri", "scopus_author_id"=>"7004603064"}, {"first_name"=>"Mathew", "last_name"=>"Upton", "scopus_author_id"=>"35593933700"}, {"first_name"=>"Scott A.", "last_name"=>"Beatson", "scopus_author_id"=>"6603612749"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84925470770", "doi"=>"10.1371/journal.pone.0104400", "sgr"=>"84925470770", "isbn"=>"10.1371/journal.pone.0104400", "pmid"=>"25126841", "issn"=>"19326203", "pui"=>"373772261"}, "id"=>"38665745-04bd-3f37-9f8f-da452d0900ce", "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.", "link"=>"http://www.mendeley.com/research/complete-genome-sequence-escherichia-coli-ec958-high-quality-reference-sequence-globally-disseminate-1", "reader_count"=>78, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>18, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>1, "Student > Master"=>16, "Other"=>2, "Student > Bachelor"=>12, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>18, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>1, "Student > Master"=>16, "Other"=>2, "Student > Bachelor"=>12, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>15, "Mathematics"=>1, "Agricultural and Biological Sciences"=>32, "Medicine and Dentistry"=>12, "Arts and Humanities"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Sports and Recreations"=>1, "Veterinary Science and Veterinary Medicine"=>3, "Physics and Astronomy"=>1, "Immunology and Microbiology"=>8}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>12}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>8}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>32}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>15}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>3}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>3}}, "reader_count_by_country"=>{"New Zealand"=>1, "United States"=>1, "Denmark"=>1, "Malaysia"=>1, "Kenya"=>1, "Spain"=>1}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1638187"], "description"=>"1<p>Kilobase-pairs;</p>2<p>Megabase-pairs;</p>3<p>Base-pairs.</p>", "links"=>[], "tags"=>["coli O 25b Clone Escherichia coli ST 131", "fimH 30 type 1 fimbrial adhesin", "tract infection", "coli ST 131 genome", "quality uropathogenic E", "Indian strain NA 114", "Disseminated Multidrug Resistant E", "NA 114", "bloodstream infections", "coli EC 958", "NA 114 genome", "Northwest region", "North American strain JJ 1886.", "High Quality Reference Sequence", "ST 131 strains", "coli ST 131 clonal lineage", "Pacific Biosciences platform", "tail fibre regions", "Complete Genome Sequence", "genomic islands", "characterised ST 131 strain"], "article_id"=>1141013, "categories"=>["Biological Sciences"], "users"=>["Brian M. Forde", "Nouri L. Ben Zakour", "Mitchell Stanton-Cook", "Minh-Duy Phan", "Makrina Totsika", "Kate M. Peters", "Kok Gan Chan", "Mark A. Schembri", "Mathew Upton", "Scott A. Beatson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104400.t001", "stats"=>{"downloads"=>1, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PacBio_assembly_statistics_/1141013", "title"=>"PacBio assembly statistics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-15 04:05:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1638186"], "description"=>"<p><b>A.</b> Nucleotide pairwise comparison of the EC958 chromosome (top) and a simulated EC958 chromosome assembly (EC958-sim, bottom). Linear alignments revealed extensive variations in the location and structure of mobile elements in EC958-sim when compared to EC958. Grey shading indicates nucleotide identity between sequences according to BLASTn (62%–100%). Prophage regions are annotated as blue boxes and genomic islands as green boxes. <b>B.</b> Nucleotide pairwise comparison of EC958 chromosome (top) and NA114 chromosome (bottom). <b>C.</b> Nucleotide pairwise comparison of EC958 (top), EC958-sim (centre) and NA114 (bottom) chromosomes. EC958 prophage and genomic islands misassembled in EC958-sim are similarly misassembled in the genome of NA114 (red boxes). Red boxes indicate positions in EC958-sim and NA114 where mobile genetic elements are present in EC958. The <i>dnaJ</i> gene is shown as a black triangle on each chromosome. Figure prepared using Easyfig <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104400#pone.0104400-Otto1\" target=\"_blank\">[27]</a>.</p>", "links"=>[], "tags"=>["coli O 25b Clone Escherichia coli ST 131", "fimH 30 type 1 fimbrial adhesin", "tract infection", "coli ST 131 genome", "quality uropathogenic E", "Indian strain NA 114", "Disseminated Multidrug Resistant E", "NA 114", "bloodstream infections", "coli EC 958", "NA 114 genome", "Northwest region", "North American strain JJ 1886.", "High Quality Reference Sequence", "ST 131 strains", "coli ST 131 clonal lineage", "Pacific Biosciences platform", "tail fibre regions", "Complete Genome Sequence", "genomic islands", "characterised ST 131 strain"], "article_id"=>1141012, "categories"=>["Biological Sciences"], "users"=>["Brian M. Forde", "Nouri L. Ben Zakour", "Mitchell Stanton-Cook", "Minh-Duy Phan", "Makrina Totsika", "Kate M. Peters", "Kok Gan Chan", "Mark A. Schembri", "Mathew Upton", "Scott A. Beatson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104400.g006", "stats"=>{"downloads"=>0, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nucleotide_pairwise_comparison_between_EC958_a_simulated_EC958_Illumina_assembly_and_NA114_/1141012", "title"=>"Nucleotide pairwise comparison between EC958, a simulated EC958 Illumina assembly and NA114.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-15 04:05:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1638183"], "description"=>"<p>An additional prophage element present in JJ1886 has also been annotated here as Phi8 for clarity. ST131 genomes are arranged from top to bottom as follows: JJ1886, EC958, NA114, SE15. Grey shading indicates nucleotide identity between sequences according to BLASTn (62%–100%). Figure prepared using Easyfig <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104400#pone.0104400-Otto1\" target=\"_blank\">[27]</a>.</p>", "links"=>[], "tags"=>["coli O 25b Clone Escherichia coli ST 131", "fimH 30 type 1 fimbrial adhesin", "tract infection", "coli ST 131 genome", "quality uropathogenic E", "Indian strain NA 114", "Disseminated Multidrug Resistant E", "NA 114", "bloodstream infections", "coli EC 958", "NA 114 genome", "Northwest region", "North American strain JJ 1886.", "High Quality Reference Sequence", "ST 131 strains", "coli ST 131 clonal lineage", "Pacific Biosciences platform", "tail fibre regions", "Complete Genome Sequence", "genomic islands", "characterised ST 131 strain"], "article_id"=>1141009, "categories"=>["Biological Sciences"], "users"=>["Brian M. Forde", "Nouri L. Ben Zakour", "Mitchell Stanton-Cook", "Minh-Duy Phan", "Makrina Totsika", "Kate M. Peters", "Kok Gan Chan", "Mark A. Schembri", "Mathew Upton", "Scott A. Beatson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104400.g004", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nucleotide_pairwise_comparison_of_four_E_coli_ST131_chromosomes_showing_extensive_variation_in_the_structure_and_location_of_EC958_prophage_elements_blue_and_genomic_islands_green_/1141009", "title"=>"Nucleotide pairwise comparison of four <i>E. coli</i> ST131 chromosomes showing extensive variation in the structure and location of EC958 prophage elements (blue) and genomic islands (green).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-15 04:05:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1638181"], "description"=>"<p>The tree is rooted using the out-group species <i>E. fergusonii</i> ATCC35469. The phylogenetic relationships were inferred with the use of 261,214 SNPs identified between the genomes of the 22 <i>Escherichia</i> strains and 1000 bootstrap replicates. The major <i>E. coli</i> phylogroups are coloured as follows; phylogroup B2-ST131: SE15, NA114, JJ1886, EC958 (red); other phylogroup B2: APEC-01, S88, 536, UTI89, CFT073, ED1A (orange); phylogroup D: UMN026 (yellow); phylogroup F: IAI39 (yellow); phylogroup A: BW2952, MG1655, W3110, HS (green); phylogroup B1: SE11, IAI1 (aquamarine); phylogroup E: O157 EDL933, O157 Sakai (blue). Red nodes have 100% bootstrap support from 1000 replicates.</p>", "links"=>[], "tags"=>["coli O 25b Clone Escherichia coli ST 131", "fimH 30 type 1 fimbrial adhesin", "tract infection", "coli ST 131 genome", "quality uropathogenic E", "Indian strain NA 114", "Disseminated Multidrug Resistant E", "NA 114", "bloodstream infections", "coli EC 958", "NA 114 genome", "Northwest region", "North American strain JJ 1886.", "High Quality Reference Sequence", "ST 131 strains", "coli ST 131 clonal lineage", "Pacific Biosciences platform", "tail fibre regions", "Complete Genome Sequence", "genomic islands", "characterised ST 131 strain"], "article_id"=>1141007, "categories"=>["Biological Sciences"], "users"=>["Brian M. Forde", "Nouri L. Ben Zakour", "Mitchell Stanton-Cook", "Minh-Duy Phan", "Makrina Totsika", "Kate M. Peters", "Kok Gan Chan", "Mark A. Schembri", "Mathew Upton", "Scott A. Beatson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104400.g002", "stats"=>{"downloads"=>7, "page_views"=>207, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_likelihood_phylogenetic_comparison_of_4_ST131_and_17_representative_E_coli_isolates_/1141007", "title"=>"Maximum likelihood phylogenetic comparison of 4 ST131 and 17 representative <i>E. coli</i> isolates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-15 04:05:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1638182"], "description"=>"<p><b>A.</b> Visualisation of the EC958 genome compared with three <i>E. coli</i> ST131 genomes and 16 other <i>E. coli</i> genomes using BLASTn. EC958 prophage (Phi1 – Phi7) and genomic islands (GI-<i>thrW</i>, GI-<i>pheV</i>, GI-<i>selC</i>, GI-<i>leuX</i>) are represented by black boxes in the outermost circle. The innermost circles represent the GC content (black) and GC skew (green/purple) of EC958. The remaining circles display BLASTn searches against the genome of EC958. <b>B.</b> A BRIG visualisation of the EC958 mobile elements compared with the 19 <i>E. coli</i> genomes. BLASTn searches of the 19 genomes against the EC958 prophage and genomic islands show that the EC958 GIs and prophage are well conserved in the ST131 clade C genomes but largely absent from the genomes of SE15 and the other 16 <i>E. coli</i> genomes, which are arranged inner to outer as follows: Group E strains O157 EDL933, O157 Sakai (blue); group B1 strains SE11, IAI1 (aquamarine); group A strains BW2952, MG1655, W3110, HS (green); group D strains UMN026, IAI39 (yellow); group B2 strains APEC-01, S88, 536, UTI89, CFT073, ED1A (orange); group B2 ST131 strains SE15, NA114, JJ1886, EC958 (red). Figure prepared using BRIG <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104400#pone.0104400-Touchon1\" target=\"_blank\">[28]</a>.</p>", "links"=>[], "tags"=>["coli O 25b Clone Escherichia coli ST 131", "fimH 30 type 1 fimbrial adhesin", "tract infection", "coli ST 131 genome", "quality uropathogenic E", "Indian strain NA 114", "Disseminated Multidrug Resistant E", "NA 114", "bloodstream infections", "coli EC 958", "NA 114 genome", "Northwest region", "North American strain JJ 1886.", "High Quality Reference Sequence", "ST 131 strains", "coli ST 131 clonal lineage", "Pacific Biosciences platform", "tail fibre regions", "Complete Genome Sequence", "genomic islands", "characterised ST 131 strain"], "article_id"=>1141008, "categories"=>["Biological Sciences"], "users"=>["Brian M. Forde", "Nouri L. Ben Zakour", "Mitchell Stanton-Cook", "Minh-Duy Phan", "Makrina Totsika", "Kate M. Peters", "Kok Gan Chan", "Mark A. Schembri", "Mathew Upton", "Scott A. Beatson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104400.g003", "stats"=>{"downloads"=>2, "page_views"=>176, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_EC958_mobile_genetic_elements_in_E_coli_/1141008", "title"=>"Distribution of EC958 mobile genetic elements in <i>E. coli</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-15 04:05:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1638180"], "description"=>"<p><b>A.</b> Alignment of the Phi1 alternative contig that contains the inversion of the tail fibre region to the genome of EC958. Phage tail fibre genes are coloured from dark green to light green. Phage DNA invertase genes are coloured orange. 26 bp crossover sites are indicated by black arrows. Red shading indicates nucleotide identity in the same orientation. Blue shading indicates nucleotide identity in the opposite orientation, highlighting the inversion in the phage tail fibre region. <b>B.</b> Genetic loci map of the tail fibre gene region of EC958 phages (Phi1, Phi2 and Phi4) and the location of recombination sites for DNA invertase. The major tail fibre gene is formed by a fusion of the stable 5′ region (dark green), encoding a series of Phage_fibre_2 tandem repeats (Pfam03406), with the invertible 3′ region (green) that encodes a Phage Tail Collar domain (Pfam07484). Downstream and presumably co-transcribed with the major tail fibre gene is a minor tail fibre gene (green). The alternate alleles form a mirror image of this arrangement, immediately downstream of the functional phage tail genes (lime green), enabling a new major tail fibre gene (and cognate minor tail fibre gene) to be formed by inversion of a 2–3 kb DNA segment. DNA invertase genes are coloured orange. The Phi4 prophage encodes a truncated DNA invertase (EC958_1582) that lacks the characteristic helix-turn-helix resolvase domain (PF02796). Invertible regions are highlighted in yellow. Figure prepared using Easyfig <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104400#pone.0104400-Otto1\" target=\"_blank\">[27]</a>.</p>", "links"=>[], "tags"=>["coli O 25b Clone Escherichia coli ST 131", "fimH 30 type 1 fimbrial adhesin", "tract infection", "coli ST 131 genome", "quality uropathogenic E", "Indian strain NA 114", "Disseminated Multidrug Resistant E", "NA 114", "bloodstream infections", "coli EC 958", "NA 114 genome", "Northwest region", "North American strain JJ 1886.", "High Quality Reference Sequence", "ST 131 strains", "coli ST 131 clonal lineage", "Pacific Biosciences platform", "tail fibre regions", "Complete Genome Sequence", "genomic islands", "characterised ST 131 strain"], "article_id"=>1141006, "categories"=>["Biological Sciences"], "users"=>["Brian M. Forde", "Nouri L. Ben Zakour", "Mitchell Stanton-Cook", "Minh-Duy Phan", "Makrina Totsika", "Kate M. Peters", "Kok Gan Chan", "Mark A. Schembri", "Mathew Upton", "Scott A. Beatson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104400.g001", "stats"=>{"downloads"=>1, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prophage_tail_fibre_allele_switching_in_EC958_/1141006", "title"=>"Prophage tail fibre allele switching in EC958.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-15 04:05:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1638189"], "description"=>"1<p>Nucleotide position (or range) in complete PacBio EC958 genome.</p>2<p>Name, position of variant and length of 454 contig from draft 454 assembly.</p>3<p>“Homopolymeric tract” indicates that variant falls within tract of 5 or more nucleotides of same type.</p>", "links"=>[], "tags"=>["coli O 25b Clone Escherichia coli ST 131", "fimH 30 type 1 fimbrial adhesin", "tract infection", "coli ST 131 genome", "quality uropathogenic E", "Indian strain NA 114", "Disseminated Multidrug Resistant E", "NA 114", "bloodstream infections", "coli EC 958", "NA 114 genome", "Northwest region", "North American strain JJ 1886.", "High Quality Reference Sequence", "ST 131 strains", "coli ST 131 clonal lineage", "Pacific Biosciences platform", "tail fibre regions", "Complete Genome Sequence", "genomic islands", "characterised ST 131 strain"], "article_id"=>1141015, "categories"=>["Biological Sciences"], "users"=>["Brian M. Forde", "Nouri L. Ben Zakour", "Mitchell Stanton-Cook", "Minh-Duy Phan", "Makrina Totsika", "Kate M. Peters", "Kok Gan Chan", "Mark A. Schembri", "Mathew Upton", "Scott A. Beatson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104400.t002", "stats"=>{"downloads"=>2, "page_views"=>32, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_complete_PacBio_EC958_genome_with_draft_454_EC958_genome_/1141015", "title"=>"Comparison of complete PacBio EC958 genome with draft 454 EC958 genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-15 04:05:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1638190"], "description"=>"<div><p><i>Escherichia coli</i> 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 <i>E. coli</i> 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. <i>E. coli</i> 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 <i>fimH30</i> 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 <i>E. coli</i> ST131 genome provides a reference for understanding this multidrug resistant pathogen and will facilitate novel functional, comparative and clinical studies of the <i>E. coli</i> ST131 clonal lineage.</p></div>", "links"=>[], "tags"=>["coli O 25b Clone Escherichia coli ST 131", "fimH 30 type 1 fimbrial adhesin", "tract infection", "coli ST 131 genome", "quality uropathogenic E", "Indian strain NA 114", "Disseminated Multidrug Resistant E", "NA 114", "bloodstream infections", "coli EC 958", "NA 114 genome", "Northwest region", "North American strain JJ 1886.", "High Quality Reference Sequence", "ST 131 strains", "coli ST 131 clonal lineage", "Pacific Biosciences platform", "tail fibre regions", "Complete Genome Sequence", "genomic islands", "characterised ST 131 strain"], "article_id"=>1141016, "categories"=>["Biological Sciences"], "users"=>["Brian M. Forde", "Nouri L. Ben Zakour", "Mitchell Stanton-Cook", "Minh-Duy Phan", "Makrina Totsika", "Kate M. Peters", "Kok Gan Chan", "Mark A. Schembri", "Mathew Upton", "Scott A. Beatson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104400", "stats"=>{"downloads"=>3, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/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/1141016", "title"=>"The Complete Genome Sequence of <i>Escherichia coli</i> EC958: A High Quality Reference Sequence for the Globally Disseminated Multidrug Resistant <i>E. coli</i> O25b:H4-ST131 Clone", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-15 04:05:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1638188"], "description"=>"1<p>Predicted binding site for DNA invertase shown in capital letters; site of strand exchange is indicated by underlined central dinucleotide with ∧ indicating downstream staggered cut; nucleotides in bold are consistent with the previously determined consensus DNA invertase crossover site <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104400#pone.0104400-Blattner1\" target=\"_blank\">[42]</a>; square brackets indicate boundaries of larger imperfect inverted repeats that encode the crossover sites.</p>2<p>Coordinates refer to start and end of 26 bp crossover site in EC958 complete genome; 5prime/3prime orientation is relative to the complete prophage tail fibre gene and prophage genome; c = complement.</p>3<p>Phi1 and Phi4 5prime and 3prime 26 bp crossover sites differ by only 2 and 1 mismatches, respectively.</p>", "links"=>[], "tags"=>["coli O 25b Clone Escherichia coli ST 131", "fimH 30 type 1 fimbrial adhesin", "tract infection", "coli ST 131 genome", "quality uropathogenic E", "Indian strain NA 114", "Disseminated Multidrug Resistant E", "NA 114", "bloodstream infections", "coli EC 958", "NA 114 genome", "Northwest region", "North American strain JJ 1886.", "High Quality Reference Sequence", "ST 131 strains", "coli ST 131 clonal lineage", "Pacific Biosciences platform", "tail fibre regions", "Complete Genome Sequence", "genomic islands", "characterised ST 131 strain"], "article_id"=>1141014, "categories"=>["Biological Sciences"], "users"=>["Brian M. Forde", "Nouri L. Ben Zakour", "Mitchell Stanton-Cook", "Minh-Duy Phan", "Makrina Totsika", "Kate M. Peters", "Kok Gan Chan", "Mark A. Schembri", "Mathew Upton", "Scott A. Beatson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104400.t003", "stats"=>{"downloads"=>2, "page_views"=>29, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sites_of_DNA_inversion_within_EC958_prophage_genomes_as_determined_by_PacBio_assembly_of_alternate_alleles_/1141014", "title"=>"Sites of DNA inversion within EC958 prophage genomes as determined by PacBio assembly of alternate alleles.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-15 04:05:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1638185"], "description"=>"<p>Grey shading indicates nucleotide identity between sequences according to BLASTn (62%–100%). Coding regions immediately upstream of <i>dnaJ</i> are highlighted in purple. This region is well conserved in 19 of 20 <i>E. coli</i> genomes examined. However, a large insertion in the genome of NA114 located immediately upstream of <i>dnaJ</i> is clearly evident (white). <i>E. coli</i> genomes are arranged from top to bottom as follows: group B2 ST131 strains JJ1886, EC958, NA114, SE15 (red); group B2 strains ED1A, CFT073, UTI89, 536, S88, APEC-01 (orange); group F strain: IAI39 (yellow); group D strain UMN026 (yellow); group A strains HS, W3110, MG1655, BW2952 (green); group B1 strains IAI1, SE11 (aquamarine); group E strains O157 Sakai, O157 EDL933 (blue). Figure prepared using Easyfig <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104400#pone.0104400-Otto1\" target=\"_blank\">[27]</a>.</p>", "links"=>[], "tags"=>["coli O 25b Clone Escherichia coli ST 131", "fimH 30 type 1 fimbrial adhesin", "tract infection", "coli ST 131 genome", "quality uropathogenic E", "Indian strain NA 114", "Disseminated Multidrug Resistant E", "NA 114", "bloodstream infections", "coli EC 958", "NA 114 genome", "Northwest region", "North American strain JJ 1886.", "High Quality Reference Sequence", "ST 131 strains", "coli ST 131 clonal lineage", "Pacific Biosciences platform", "tail fibre regions", "Complete Genome Sequence", "genomic islands", "characterised ST 131 strain"], "article_id"=>1141011, "categories"=>["Biological Sciences"], "users"=>["Brian M. Forde", "Nouri L. Ben Zakour", "Mitchell Stanton-Cook", "Minh-Duy Phan", "Makrina Totsika", "Kate M. Peters", "Kok Gan Chan", "Mark A. Schembri", "Mathew Upton", "Scott A. Beatson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104400.g005", "stats"=>{"downloads"=>1, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nucleotide_pairwise_comparison_of_a_200_kb_region_thrA_to_degP_from_the_genomes_of_the_four_ST131_and_16_other_representative_E_coli_strains_/1141011", "title"=>"Nucleotide pairwise comparison of a 200 kb region (<i>thrA</i> to <i>degP</i>) from the genomes of the four ST131 and 16 other representative <i>E. coli</i> strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-15 04:05:59"}

PMC Usage Stats | Further Information

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