Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages
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{"title"=>"Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages", "type"=>"journal", "authors"=>[{"first_name"=>"Mark", "last_name"=>"de Been", "scopus_author_id"=>"14832388100"}, {"first_name"=>"Val F.", "last_name"=>"Lanza", "scopus_author_id"=>"36150927700"}, {"first_name"=>"María", "last_name"=>"de Toro", "scopus_author_id"=>"36652555700"}, {"first_name"=>"Jelle", "last_name"=>"Scharringa", "scopus_author_id"=>"6602988426"}, {"first_name"=>"Wietske", "last_name"=>"Dohmen", "scopus_author_id"=>"36343400200"}, {"first_name"=>"Yu", "last_name"=>"Du", "scopus_author_id"=>"56457029900"}, {"first_name"=>"Juan", "last_name"=>"Hu", "scopus_author_id"=>"57198194124"}, {"first_name"=>"Ying", "last_name"=>"Lei", "scopus_author_id"=>"56457219900"}, {"first_name"=>"Ning", "last_name"=>"Li", "scopus_author_id"=>"57197435661"}, {"first_name"=>"Ave", "last_name"=>"Tooming-Klunderud", "scopus_author_id"=>"16317680600"}, {"first_name"=>"Dick J.J.", "last_name"=>"Heederik", "scopus_author_id"=>"7006663815"}, {"first_name"=>"Ad C.", "last_name"=>"Fluit", "scopus_author_id"=>"7006051903"}, {"first_name"=>"Marc J.M.", "last_name"=>"Bonten", "scopus_author_id"=>"55660254000"}, {"first_name"=>"Rob J.L.", "last_name"=>"Willems", "scopus_author_id"=>"7004872920"}, {"first_name"=>"Fernando", "last_name"=>"de la Cruz", "scopus_author_id"=>"22974628400"}, {"first_name"=>"Willem", "last_name"=>"van Schaik", "scopus_author_id"=>"6701570816"}], "year"=>2014, "source"=>"PLoS Genetics", "identifiers"=>{"sgr"=>"84919624825", "doi"=>"10.1371/journal.pgen.1004776", "pui"=>"601033436", "pmid"=>"25522320", "scopus"=>"2-s2.0-84919624825", "issn"=>"15537404", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "arxiv"=>"e1004776"}, "id"=>"c3aed50e-bf0e-3aee-aa62-257cf10ddb48", "abstract"=>"Third-generation cephalosporins are a class of β-lactam antibiotics that are often used for the treatment of human infections caused by Gram-negative bacteria, especially Escherichia coli. Worryingly, the incidence of human infections caused by third-generation cephalosporin-resistant E. coli is increasing worldwide. Recent studies have suggested that these E. coli strains, and their antibiotic resistance genes, can spread from food-producing animals, via the food-chain, to humans. However, these studies used traditional typing methods, which may not have provided sufficient resolution to reliably assess the relatedness of these strains. We therefore used whole-genome sequencing (WGS) to study the relatedness of cephalosporin-resistant E. coli from humans, chicken meat, poultry and pigs. One strain collection included pairs of human and poultry-associated strains that had previously been considered to be identical based on Multi-Locus Sequence Typing, plasmid typing and antibiotic resistance gene sequencing. The second collection included isolates from farmers and their pigs. WGS analysis revealed considerable heterogeneity between human and poultry-associated isolates. The most closely related pairs of strains from both sources carried 1263 Single-Nucleotide Polymorphisms (SNPs) per Mbp core genome. In contrast, epidemiologically linked strains from humans and pigs differed by only 1.8 SNPs per Mbp core genome. WGS-based plasmid reconstructions revealed three distinct plasmid lineages (IncI1- and IncK-type) that carried cephalosporin resistance genes of the Extended-Spectrum Beta-Lactamase (ESBL)- and AmpC-types. The plasmid backbones within each lineage were virtually identical and were shared by genetically unrelated human and animal isolates. Plasmid reconstructions from short-read sequencing data were validated by long-read DNA sequencing for two strains. Our findings failed to demonstrate evidence for recent clonal transmission of cephalosporin-resistant E. coli strains from poultry to humans, as has been suggested based on traditional, low-resolution typing methods. Instead, our data suggest that cephalosporin resistance genes are mainly disseminated in animals and humans via distinct plasmids.", "link"=>"http://www.mendeley.com/research/dissemination-cephalosporin-resistance-genes-between-escherichia-coli-strains-farm-animals-humans-sp", "reader_count"=>207, "reader_count_by_academic_status"=>{"Unspecified"=>8, "Professor > Associate Professor"=>10, "Librarian"=>1, "Researcher"=>47, "Student > Doctoral Student"=>13, "Student > Ph. D. Student"=>49, "Student > Postgraduate"=>13, "Other"=>8, "Student > Master"=>34, "Student > Bachelor"=>14, "Lecturer"=>4, "Lecturer > Senior Lecturer"=>2, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>8, "Professor > Associate Professor"=>10, "Librarian"=>1, "Researcher"=>47, "Student > Doctoral Student"=>13, "Student > Ph. D. Student"=>49, "Student > Postgraduate"=>13, "Other"=>8, "Student > Master"=>34, "Student > Bachelor"=>14, "Lecturer"=>4, "Lecturer > Senior Lecturer"=>2, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>20, "Engineering"=>2, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>15, "Medicine and Dentistry"=>35, "Agricultural and Biological Sciences"=>85, "Veterinary Science and Veterinary Medicine"=>15, "Physics and Astronomy"=>2, "Chemistry"=>4, "Social Sciences"=>1, "Computer Science"=>3, "Immunology and Microbiology"=>22}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>35}, "Chemistry"=>{"Chemistry"=>4}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>22}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>85}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>15}, "Unspecified"=>{"Unspecified"=>20}, "Environmental Science"=>{"Environmental Science"=>3}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>15}}, "reader_count_by_country"=>{"Ecuador"=>2, "United States"=>1, "United Kingdom"=>2, "Portugal"=>1, "Spain"=>2, "India"=>1, "Netherlands"=>2, "Pakistan"=>1, "Denmark"=>1, "Brazil"=>1, "France"=>2, "Germany"=>2, "Estonia"=>1}, "group_count"=>11}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1846913"], "description"=>"<p>The tree was built using 18169 variable positions present in 215 core genes. The strains sequenced in this study are indicated in coloured bullets according to isolation source. Typing characteristics (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004776#pgen-1004776-t001\" target=\"_blank\">Table 1</a>) are given behind strain names. In case the MLST had not been determined before, it was determined using MLST v1.6 <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004776#pgen.1004776-Larsen1\" target=\"_blank\">[55]</a>. Clusters I–IV (see main text) are indicated behind the tree. Phylogroups are also indicated behind the tree (white text on black bars). The O104:H4 and O157:H7 branches are collapsed and represent 11 and 20 strains, respectively. Bootstrap support was implemented by running 100 bootstrap replicates. Values <75% are not displayed. SLV indicates Single Locus Variants of corresponding MLSTs.</p>", "links"=>[], "tags"=>["human", "coli strains", "cephalosporin resistance genes", "snp", "antibiotic resistance gene sequencing", "wgs", "Escherichia coli strains", "typing", "dna", "plasmid", "Antibiotic Resistance Genes", "esbl", "Mbp core genome"], "article_id"=>1274226, "categories"=>["Biological Sciences"], "users"=>["Mark de Been", "Val F. Lanza", "María de Toro", "Jelle Scharringa", "Wietske Dohmen", "Yu Du", "Juan Hu", "Ying Lei", "Ning Li", "Ave Tooming-Klunderud", "Dick J. J. Heederik", "Ad C. Fluit", "Marc J. M. Bonten", "Rob J. L. Willems", "Fernando de la Cruz", "Willem van Schaik"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004776.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_of_Escherichia_and_Shigella_species_including_ESBL_and_AmpC_positive_strains_sequenced_for_the_purpose_of_this_study_/1274226", "title"=>"Phylogeny of <i>Escherichia</i> and <i>Shigella</i> species, including ESBL- and AmpC-positive strains sequenced for the purpose of this study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-18 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1846914"], "description"=>"<p>A high resolution core genome analysis was performed for a subset of strains which, based on an initial phylogenetic analysis (Cluster IV, <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004776#pgen-1004776-g001\" target=\"_blank\">Fig. 1</a>), included the most closely related pairs of human and poultry-associated ESBL-producing strains within our dataset. Strains within Cluster IV had previously been found to be identical with respect to MLST, ESBL gene and ESBL-carrying plasmid (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004776#pgen-1004776-t001\" target=\"_blank\">Table 1</a>). For comparative purposes, clonally related <i>E. coli</i> strains from the 2011 German EHEC outbreak <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004776#pgen.1004776-Grad1\" target=\"_blank\">[21]</a> and four potentially clonally related strains isolated from a single pig farm (Farm A) were included in this analysis. A phylogenetic tree, built from the 107919 variable positions present in the resulting 3.34 Mbp core genome alignment is shown to the left. Bootstrap support was implemented by running 1000 bootstrap replicates. Coloured bullets refer to the isolation source. The number of SNPs found in each of the three clusters (Cluster IV, EHEC outbreak, Farm A) is shown to the right.</p>", "links"=>[], "tags"=>["human", "coli strains", "cephalosporin resistance genes", "snp", "antibiotic resistance gene sequencing", "wgs", "Escherichia coli strains", "typing", "dna", "plasmid", "Antibiotic Resistance Genes", "esbl", "Mbp core genome"], "article_id"=>1274227, "categories"=>["Biological Sciences"], "users"=>["Mark de Been", "Val F. Lanza", "María de Toro", "Jelle Scharringa", "Wietske Dohmen", "Yu Du", "Juan Hu", "Ying Lei", "Ning Li", "Ave Tooming-Klunderud", "Dick J. J. Heederik", "Ad C. Fluit", "Marc J. M. Bonten", "Rob J. L. Willems", "Fernando de la Cruz", "Willem van Schaik"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004776.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_and_SNP_analysis_of_closely_related_ESBL_producing_E_coli_strains_from_human_and_poultry_/1274227", "title"=>"Phylogeny and SNP analysis of closely related ESBL-producing <i>E. coli</i> strains from human and poultry.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-18 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1846915"], "description"=>"<p>The histogram shows the total number of reconstructed plasmids corresponding to each size class (in a logarithmic scale). The plasmid size distribution shows a trimodal abundance curve. Numbers above the three peaks refer to the median size for each class. Plasmids in which a relaxase gene was detected are shown in green and those in which it was not detected are shown in grey.</p>", "links"=>[], "tags"=>["human", "coli strains", "cephalosporin resistance genes", "snp", "antibiotic resistance gene sequencing", "wgs", "Escherichia coli strains", "typing", "dna", "plasmid", "Antibiotic Resistance Genes", "esbl", "Mbp core genome"], "article_id"=>1274228, "categories"=>["Biological Sciences"], "users"=>["Mark de Been", "Val F. Lanza", "María de Toro", "Jelle Scharringa", "Wietske Dohmen", "Yu Du", "Juan Hu", "Ying Lei", "Ning Li", "Ave Tooming-Klunderud", "Dick J. J. Heederik", "Ad C. Fluit", "Marc J. M. Bonten", "Rob J. L. Willems", "Fernando de la Cruz", "Willem van Schaik"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004776.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_plasmid_sizes_in_the_collection_of_32_sequenced_E_coli_strains_/1274228", "title"=>"Distribution of plasmid sizes in the collection of 32 sequenced <i>E. coli</i> strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-18 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1846916"], "description"=>"<p>The dendrogram was constructed as explained in Methods. Reconstructed plasmids are indicated with colored bullets according to isolation source. The dendrogram construction automatically grouped plasmids into Inc families, which are shown by background colours. Mob types are also indicated. Additional columns show plasmid sizes, resistance genes and MOB subfamilies.</p>", "links"=>[], "tags"=>["human", "coli strains", "cephalosporin resistance genes", "snp", "antibiotic resistance gene sequencing", "wgs", "Escherichia coli strains", "typing", "dna", "plasmid", "Antibiotic Resistance Genes", "esbl", "Mbp core genome"], "article_id"=>1274229, "categories"=>["Biological Sciences"], "users"=>["Mark de Been", "Val F. Lanza", "María de Toro", "Jelle Scharringa", "Wietske Dohmen", "Yu Du", "Juan Hu", "Ying Lei", "Ning Li", "Ave Tooming-Klunderud", "Dick J. J. Heederik", "Ad C. Fluit", "Marc J. M. Bonten", "Rob J. L. Willems", "Fernando de la Cruz", "Willem van Schaik"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004776.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hierarchical_clustering_dendrogram_of_reconstructed_plasmids_contained_in_the_collection_of_32_sequenced_E_coli_strains_/1274229", "title"=>"Hierarchical clustering dendrogram of reconstructed plasmids contained in the collection of 32 sequenced <i>E. coli</i> strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-18 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1846917"], "description"=>"<p>The dendrogram was constructed as explained in Methods. Reconstructed plasmids are indicated with colored bullets according to isolation source. All other (reference) plasmids were taken from public sequence repositories.</p>", "links"=>[], "tags"=>["human", "coli strains", "cephalosporin resistance genes", "snp", "antibiotic resistance gene sequencing", "wgs", "Escherichia coli strains", "typing", "dna", "plasmid", "Antibiotic Resistance Genes", "esbl", "Mbp core genome"], "article_id"=>1274230, "categories"=>["Biological Sciences"], "users"=>["Mark de Been", "Val F. Lanza", "María de Toro", "Jelle Scharringa", "Wietske Dohmen", "Yu Du", "Juan Hu", "Ying Lei", "Ning Li", "Ave Tooming-Klunderud", "Dick J. J. Heederik", "Ad C. Fluit", "Marc J. M. Bonten", "Rob J. L. Willems", "Fernando de la Cruz", "Willem van Schaik"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004776.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hierarchical_clustering_dendrogram_of_reconstructed_IncI1_and_IncK_plasmids_contained_in_the_collection_of_32_sequenced_E_coli_strains_together_with_relevant_and_similar_reference_plasmids_/1274230", "title"=>"Hierarchical clustering dendrogram of reconstructed IncI1 and IncK plasmids contained in the collection of 32 sequenced <i>E. coli</i> strains together with relevant and similar reference plasmids.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-18 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1846919"], "description"=>"<p>Phylogenetic tree of IncI1 plasmids built from 763 variable positions present in an 8.6 kbp alignment, representing 8 core proteins (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004776#pgen.1004776.s003\" target=\"_blank\">S3 Table</a>) (A). Phylogenetic tree of IncK plasmids built from 2724 variable positions present in a 19.9 kbp alignment, representing 27 core proteins (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004776#pgen.1004776.s003\" target=\"_blank\">S3 Table</a>) (B). Bootstrap support was implemented by running 1000 bootstrap replicates. Reconstructed plasmids are indicated with coloured bullets according to isolation source (plasmid names include associated strain names, followed by a unique plasmid identifier). All other plasmids were taken from public sequence repositories. Plasmid STs (for IncI1 only) and encoded β-lactamases (with the exception of TEM-1, which does not provide resistance to third generation cephalosporins) are indicated to the right of the trees. 11SLV indicates a single locus variant of ST11. pMLST negative means that the reconstructed plasmid lacks one or more pMLST loci. <i>Bla</i> genes in light grey were not connected to the reconstructed plasmid, but should be located on this plasmid according to typing data. Light grey panels indicate potential epidemic <i>bla</i><sub>CTX-M-1</sub>- and <i>bla</i><sub>CMY-2</sub>-carrying plasmids. Core genome analysis of these plasmid subsets revealed virtually identical backbones of up to 50 kbp.</p>", "links"=>[], "tags"=>["human", "coli strains", "cephalosporin resistance genes", "snp", "antibiotic resistance gene sequencing", "wgs", "Escherichia coli strains", "typing", "dna", "plasmid", "Antibiotic Resistance Genes", "esbl", "Mbp core genome"], "article_id"=>1274232, "categories"=>["Biological Sciences"], "users"=>["Mark de Been", "Val F. Lanza", "María de Toro", "Jelle Scharringa", "Wietske Dohmen", "Yu Du", "Juan Hu", "Ying Lei", "Ning Li", "Ave Tooming-Klunderud", "Dick J. J. Heederik", "Ad C. Fluit", "Marc J. M. Bonten", "Rob J. L. Willems", "Fernando de la Cruz", "Willem van Schaik"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004776.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_of_reconstructed_IncI1_and_IncK_plasmids_and_their_closest_relatives_/1274232", "title"=>"Phylogeny of reconstructed IncI1 and IncK plasmids and their closest relatives.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-18 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1846920"], "description"=>"<p>For all strains that were ESBL- and IncI1 plasmid-positive or AmpC- and IncK plasmid-positive, the Inc group of the plasmid that carried the ESBL/AmpC gene had previously been determined using a transformation-based approach <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004776#pgen.1004776-LeversteinvanHall1\" target=\"_blank\">[15]</a>, <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004776#pgen.1004776-Voets1\" target=\"_blank\">[18]</a>. Identical numbers behind places of isolation indicate the exact same locations: i.e. the same retail store for chicken meat isolates, the same slaughterhouse for chicken isolates and the same farm (referred to as farms A, B, and C) for pig and pig farmer isolates.</p><p>* These ESBL genes were not found in the genome assemblies: <i>bla</i><sub>TEM-20</sub> or <i>bla</i><sub>TEM-1</sub> were found instead of <i>bla</i><sub>TEM-52</sub>.</p>†<p>This ESBL gene had previously only been typed using microarrays (no sequencing). The gene was found to belong to the CTX-M-1 group.</p>‡<p>These CMY genes were divided over two contigs that were connected on a scaffold. BLAST runs of the partial CMY-2 sequences against GenBank's nr database gave best hits with <i>bla</i><sub>CMY-2</sub> and mapping of raw Illumina reads against <i>bla</i><sub>CMY-2</sub> indicated that the full <i>bla</i><sub>CMY-2</sub> gene was present in the corresponding strain.</p><p>n.d.: not determined.</p><p><i>E. coli</i> strains sequenced in this study.</p>", "links"=>[], "tags"=>["human", "coli strains", "cephalosporin resistance genes", "snp", "antibiotic resistance gene sequencing", "wgs", "Escherichia coli strains", "typing", "dna", "plasmid", "Antibiotic Resistance Genes", "esbl", "Mbp core genome"], "article_id"=>1274233, "categories"=>["Biological Sciences"], "users"=>["Mark de Been", "Val F. Lanza", "María de Toro", "Jelle Scharringa", "Wietske Dohmen", "Yu Du", "Juan Hu", "Ying Lei", "Ning Li", "Ave Tooming-Klunderud", "Dick J. J. Heederik", "Ad C. Fluit", "Marc J. M. Bonten", "Rob J. L. Willems", "Fernando de la Cruz", "Willem van Schaik"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004776.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_E_coli_strains_sequenced_in_this_study_/1274233", "title"=>"<i>E. coli</i> strains sequenced in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-18 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1846921"], "description"=>"<p>For each strain, the type and number of reconstructed plasmids are indicated in columns 2–14. Plasmid numbering (e.g. p1) corresponds with the numbering in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004776#pgen-1004776-g004\" target=\"_blank\">Figs. 4</a>–<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004776#pgen-1004776-g006\" target=\"_blank\">6</a>, and is followed by the plasmid size (in kbp), the number of assigned scaffolds (between brackets), and assigned <i>bla</i><sub>ESBL</sub> or <i>bla</i><sub>CMY-2</sub> genes, if applicable. The same format is used for the last summarising column.</p><p>* Inconsistency between plasmid typing data and WGS data/PLACNET (typing data is between brackets below): 320 (<i>bla</i><sub>TEM-52</sub> on IncI1): <i>bla</i><sub>TEM-52</sub> not found in assembly and thus not linked to an IncI1 plasmid; 681 (<i>bla</i><sub>TEM-52</sub> on IncI1): <i>bla</i><sub>TEM-52</sub> not found in assembly and thus not linked to an IncI1 plasmid; 38.34 (<i>bla</i><sub>TEM-52</sub> on IncI1): <i>bla</i><sub>TEM-52</sub> not found in assembly and thus not linked to an IncI1 plasmid; 1350 (<i>bla</i><sub>CTX-M-1</sub> on IncI1): <i>bla</i><sub>CTX-M-1</sub> found in assembly, but not linked to an IncI1 plasmid; 1365 (<i>bla</i><sub>CTX-M-1</sub> on IncI1): <i>bla</i><sub>CTX-M-1</sub> found in assembly, but not linked to an IncI1 plasmid; 1047 (<i>bla</i><sub>CTX-M-1</sub> on IncI1): <i>bla</i><sub>CTX-M-1</sub> found in assembly, but not linked to an IncI1 plasmid; 1047 (<i>bla</i><sub>CMY-2</sub> on IncK): <i>bla</i><sub>CMY-2</sub> found in assembly, but no IncK plasmid reconstructed; 38.52 (<i>bla</i><sub>CTX-M-1</sub> on IncI1): <i>bla</i><sub>CTX-M-1</sub> found in assembly, but not linked to an IncI1 plasmid.</p><p>Plasmids reconstructed using PLACNET.</p>", "links"=>[], "tags"=>["human", "coli strains", "cephalosporin resistance genes", "snp", "antibiotic resistance gene sequencing", "wgs", "Escherichia coli strains", "typing", "dna", "plasmid", "Antibiotic Resistance Genes", "esbl", "Mbp core genome"], "article_id"=>1274234, "categories"=>["Biological Sciences"], "users"=>["Mark de Been", "Val F. Lanza", "María de Toro", "Jelle Scharringa", "Wietske Dohmen", "Yu Du", "Juan Hu", "Ying Lei", "Ning Li", "Ave Tooming-Klunderud", "Dick J. J. Heederik", "Ad C. Fluit", "Marc J. M. Bonten", "Rob J. L. Willems", "Fernando de la Cruz", "Willem van Schaik"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004776.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Plasmids_reconstructed_using_PLACNET_/1274234", "title"=>"Plasmids reconstructed using PLACNET.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-18 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1846922"], "description"=>"<p>* Note that the region of the PacBio plasmid that was recovered can exceed the reconstructed plasmid size because of repetitive elements, which are collapsed in Illumina assemblies, but are uncollapsed in PacBio assemblies. For each reconstructed plasmid the PLACNET precision rate was calculated by the formula [(assembly size of all correctly assigned scaffolds/assembly size of all correctly+incorrectly assigned scaffolds)×100%]. Sensitivity reflects the percentage of each plasmid sequence (assembled using PacBio data) that was correctly reconstructed in the PLACNET analysis. The sensitivity rate was calculated by the formula [(total nr. of non-overlapping aligning residues/size of the plasmid that was assembled using PacBio data)×100%].</p><p>PLACNET precision and sensitivity rates for seven reconstructed plasmids.</p>", "links"=>[], "tags"=>["human", "coli strains", "cephalosporin resistance genes", "snp", "antibiotic resistance gene sequencing", "wgs", "Escherichia coli strains", "typing", "dna", "plasmid", "Antibiotic Resistance Genes", "esbl", "Mbp core genome"], "article_id"=>1274235, "categories"=>["Biological Sciences"], "users"=>["Mark de Been", "Val F. Lanza", "María de Toro", "Jelle Scharringa", "Wietske Dohmen", "Yu Du", "Juan Hu", "Ying Lei", "Ning Li", "Ave Tooming-Klunderud", "Dick J. J. Heederik", "Ad C. Fluit", "Marc J. M. Bonten", "Rob J. L. Willems", "Fernando de la Cruz", "Willem van Schaik"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004776.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PLACNET_precision_and_sensitivity_rates_for_seven_reconstructed_plasmids_/1274235", "title"=>"PLACNET precision and sensitivity rates for seven reconstructed plasmids.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-18 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1846923", "https://ndownloader.figshare.com/files/1846924", "https://ndownloader.figshare.com/files/1846925", "https://ndownloader.figshare.com/files/1846926"], "description"=>"<div><p>Third-generation cephalosporins are a class of β-lactam antibiotics that are often used for the treatment of human infections caused by Gram-negative bacteria, especially <i>Escherichia coli</i>. Worryingly, the incidence of human infections caused by third-generation cephalosporin-resistant <i>E. coli</i> is increasing worldwide. Recent studies have suggested that these <i>E. coli</i> strains, and their antibiotic resistance genes, can spread from food-producing animals, via the food-chain, to humans. However, these studies used traditional typing methods, which may not have provided sufficient resolution to reliably assess the relatedness of these strains. We therefore used whole-genome sequencing (WGS) to study the relatedness of cephalosporin-resistant <i>E. coli</i> from humans, chicken meat, poultry and pigs. One strain collection included pairs of human and poultry-associated strains that had previously been considered to be identical based on Multi-Locus Sequence Typing, plasmid typing and antibiotic resistance gene sequencing. The second collection included isolates from farmers and their pigs. WGS analysis revealed considerable heterogeneity between human and poultry-associated isolates. The most closely related pairs of strains from both sources carried 1263 Single-Nucleotide Polymorphisms (SNPs) per Mbp core genome. In contrast, epidemiologically linked strains from humans and pigs differed by only 1.8 SNPs per Mbp core genome. WGS-based plasmid reconstructions revealed three distinct plasmid lineages (IncI1- and IncK-type) that carried cephalosporin resistance genes of the Extended-Spectrum Beta-Lactamase (ESBL)- and AmpC-types. The plasmid backbones within each lineage were virtually identical and were shared by genetically unrelated human and animal isolates. Plasmid reconstructions from short-read sequencing data were validated by long-read DNA sequencing for two strains. Our findings failed to demonstrate evidence for recent clonal transmission of cephalosporin-resistant <i>E. coli</i> strains from poultry to humans, as has been suggested based on traditional, low-resolution typing methods. Instead, our data suggest that cephalosporin resistance genes are mainly disseminated in animals and humans via distinct plasmids.</p></div>", "links"=>[], "tags"=>["human", "coli strains", "cephalosporin resistance genes", "snp", "antibiotic resistance gene sequencing", "wgs", "Escherichia coli strains", "typing", "dna", "plasmid", "Antibiotic Resistance Genes", "esbl", "Mbp core genome"], "article_id"=>1274236, "categories"=>["Biological Sciences"], "users"=>["Mark de Been", "Val F. Lanza", "María de Toro", "Jelle Scharringa", "Wietske Dohmen", "Yu Du", "Juan Hu", "Ying Lei", "Ning Li", "Ave Tooming-Klunderud", "Dick J. J. Heederik", "Ad C. Fluit", "Marc J. M. Bonten", "Rob J. L. Willems", "Fernando de la Cruz", "Willem van Schaik"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004776.s001", "https://dx.doi.org/10.1371/journal.pgen.1004776.s002", "https://dx.doi.org/10.1371/journal.pgen.1004776.s003", "https://dx.doi.org/10.1371/journal.pgen.1004776.s004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Dissemination_of_Cephalosporin_Resistance_Genes_between_Escherichia_coli_Strains_from_Farm_Animals_and_Humans_by_Specific_Plasmid_Lineages/1274236", "title"=>"Dissemination of Cephalosporin Resistance Genes between <i>Escherichia coli</i> Strains from Farm Animals and Humans by Specific Plasmid Lineages", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-12-18 03:00:00"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"54", "full-text"=>"77", "pdf"=>"28", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2015", "month"=>"6"}
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  • {"unique-ip"=>"42", "full-text"=>"43", "pdf"=>"24", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"9", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"1"}
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Relative Metric

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