The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies
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{"title"=>"The salmonella in silico typing resource (SISTR): An open web-accessible tool for rapidly typing and subtyping draft salmonella genome assemblies", "type"=>"journal", "authors"=>[{"first_name"=>"Catherine E.", "last_name"=>"Yoshida", "scopus_author_id"=>"18134770600"}, {"first_name"=>"Peter", "last_name"=>"Kruczkiewicz", "scopus_author_id"=>"37002765700"}, {"first_name"=>"Chad R.", "last_name"=>"Laing", "scopus_author_id"=>"16506751500"}, {"first_name"=>"Erika J.", "last_name"=>"Lingohr", "scopus_author_id"=>"6504009048"}, {"first_name"=>"Victor P.J.", "last_name"=>"Gannon", "scopus_author_id"=>"6701704193"}, {"first_name"=>"John H.E.", "last_name"=>"Nash", "scopus_author_id"=>"7202698478"}, {"first_name"=>"Eduardo N.", "last_name"=>"Taboada", "scopus_author_id"=>"6701724305"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "doi"=>"10.1371/journal.pone.0147101", "sgr"=>"84958212710", "scopus"=>"2-s2.0-84958212710", "isbn"=>"1932-6203 (Electronic)\r1932-6203 (Linking)", "pmid"=>"26800248", "pui"=>"608240765"}, "id"=>"31780de8-9e2a-37a7-a8d6-4da6e44bbba7", "abstract"=>"For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of in silico serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploaded whole-genome assemblies, the SISTR platform incorporates a database comprising over 4,000 publicly available genomes, allowing users to place their isolates in a broader phylogenetic and epidemiological context. The resource incorporates several metadata driven visualizations to examine the phylogenetic, geospatial and temporal distribution of genome-sequenced isolates. As sequencing of Salmonella isolates at public health laboratories around the world becomes increasingly common, rapid in silico analysis of minimally processed draft genome assemblies provides a powerful approach for molecular epidemiology in support of public health investigations. Moreover, this type of integrated analysis using multiple sequence-based methods of sub-typing allows for continuity with historical serotyping data as we transition towards the increasing adoption of genomic analyses in epidemiology. The SISTR platform is freely available on the web at https://lfz.corefacility.ca/sistr-app/.", "link"=>"http://www.mendeley.com/research/salmonella-silico-typing-resource-sistr-open-webaccessible-tool-rapidly-typing-subtyping-draft-salmo", "reader_count"=>52, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Researcher"=>17, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>9, "Other"=>2, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Researcher"=>17, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>9, "Other"=>2, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Engineering"=>2, "Biochemistry, Genetics and Molecular Biology"=>14, "Agricultural and Biological Sciences"=>22, "Medicine and Dentistry"=>4, "Veterinary Science and Veterinary Medicine"=>2, "Computer Science"=>1, "Immunology and Microbiology"=>2, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>22}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>14}, "Unspecified"=>{"Unspecified"=>4}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>1, "Brazil"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2631630"], "description"=>"<p>The contribution of various types of errors contributing to observed differences between “reported” and “predicted” serovars was tabulated. From a total of 4,192 genomes retained for the analysis, 3,982 genomes had correct serovar predictions (94.99%).</p>", "links"=>[], "tags"=>["draft Salmonella genome assemblies", "Draft Genome Assemblies", "assembly", "analyses", "phylogenetic", "Subtyping Draft Salmonella Genome Assemblies", "WGS draft assemblies", "core genome MLST", "SISTR platform", "silico serovar prediction", "100 years serotyping", "analysis", "Silico Typing Resource"], "article_id"=>1640434, "categories"=>["Biological Sciences"], "users"=>["Catherine E. Yoshida", "Peter Kruczkiewicz", "Chad R. Laing", "Erika J. Lingohr", "Victor P. J. Gannon", "John H. E. Nash", "Eduardo N. Taboada"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0147101.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_sources_of_error_in_serovar_predictions_on_a_set_of_4_291_Salmonella_enterica_draft_genome_sequences_analyzed_using_the_SISTR_platform_/1640434", "title"=>"Analysis of sources of error in serovar predictions on a set of 4,291 <i>Salmonella enterica</i> draft genome sequences analyzed using the SISTR platform.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-28 12:39:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/2631631"], "description"=>"<p>Among a large cgMLST330 cluster of genomes of reported serovar Agona were found four genomes of different reported serovar (Paratyphi B, n = 2; Anatum, n = 1; Derby, n = 1). Upon closer inspection, the serovar prediction for these genomes was found to be Agona, consistent with the underlying cgMLST330 data.</p>", "links"=>[], "tags"=>["draft Salmonella genome assemblies", "Draft Genome Assemblies", "assembly", "analyses", "phylogenetic", "Subtyping Draft Salmonella Genome Assemblies", "WGS draft assemblies", "core genome MLST", "SISTR platform", "silico serovar prediction", "100 years serotyping", "analysis", "Silico Typing Resource"], "article_id"=>1640435, "categories"=>["Biological Sciences"], "users"=>["Catherine E. Yoshida", "Peter Kruczkiewicz", "Chad R. Laing", "Erika J. Lingohr", "Victor P. J. Gannon", "John H. E. Nash", "Eduardo N. Taboada"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0147101.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_silico_serovar_prediction_identifies_instances_of_Salmonella_genomes_with_incorrect_reported_serovar_information_/1640435", "title"=>"<i>In silico</i> serovar prediction identifies instances of <i>Salmonella</i> genomes with incorrect reported serovar information.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-28 12:39:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2631632"], "description"=>"<p>(A) The relative proportion of various error types does not change appreciably as a function of the N50 assembly quality parameter. Type 4 errors, which are related to poor cgMLST330 metrics, are only observed among genomes with lowest N50 values. (B) Although large numbers of missing cgMLST330 loci affect serovar prediction, as observed with errors of Type 4, accurate predictions were also made for genomes with as few as 296 complete cgMLST330 loci.</p>", "links"=>[], "tags"=>["draft Salmonella genome assemblies", "Draft Genome Assemblies", "assembly", "analyses", "phylogenetic", "Subtyping Draft Salmonella Genome Assemblies", "WGS draft assemblies", "core genome MLST", "SISTR platform", "silico serovar prediction", "100 years serotyping", "analysis", "Silico Typing Resource"], "article_id"=>1640436, "categories"=>["Biological Sciences"], "users"=>["Catherine E. Yoshida", "Peter Kruczkiewicz", "Chad R. Laing", "Erika J. Lingohr", "Victor P. J. Gannon", "John H. E. Nash", "Eduardo N. Taboada"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0147101.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_SISTR_serovar_prediction_logic_can_robustly_yield_accurate_predictions_for_a_range_of_genome_qualities_/1640436", "title"=>"The SISTR serovar prediction logic can robustly yield accurate predictions for a range of genome qualities.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-28 12:39:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2631633"], "description"=>"<p>The prediction accuracy was assessed for serovars with 10 or more genome representatives and based only on genomes with metadata of sufficient quality to enable extraction of serovar information and those with high cgMLST data quality (n = 4,188). Accuracy was computed based on concordance between reported and predicted serovars. The “uncorrected” prediction accuracy, which is based on the original set of input genomes (n = 4,291) is shown in red. A “corrected” prediction accuracy, which is based on reclassification of genomes with Type 1 and 2 errors, and removal of genomes with Type 3 and 4 errors, is shown in blue. (note: where distinct corrected and uncorrected concordance values are not observable, both values are identical).</p>", "links"=>[], "tags"=>["draft Salmonella genome assemblies", "Draft Genome Assemblies", "assembly", "analyses", "phylogenetic", "Subtyping Draft Salmonella Genome Assemblies", "WGS draft assemblies", "core genome MLST", "SISTR platform", "silico serovar prediction", "100 years serotyping", "analysis", "Silico Typing Resource"], "article_id"=>1640437, "categories"=>["Biological Sciences"], "users"=>["Catherine E. Yoshida", "Peter Kruczkiewicz", "Chad R. Laing", "Erika J. Lingohr", "Victor P. J. Gannon", "John H. E. Nash", "Eduardo N. Taboada"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0147101.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_high_accuracy_was_observed_for_the_SISTR_serovar_prediction_pipeline_/1640437", "title"=>"A high accuracy was observed for the SISTR serovar prediction pipeline.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-28 12:39:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/2631634"], "description"=>"<p>While a large majority of genomes analyzed in the SISTR server were predicted as Weltevreden (n = 64), the remaining four genomes were predicted to have different serovars; these predictions matched the predominant serovar of their corresponding cgMLST cluster. The percent concordance between cgMLST and serovar and cgMLST cluster size are shown in parentheses.</p>", "links"=>[], "tags"=>["draft Salmonella genome assemblies", "Draft Genome Assemblies", "assembly", "analyses", "phylogenetic", "Subtyping Draft Salmonella Genome Assemblies", "WGS draft assemblies", "core genome MLST", "SISTR platform", "silico serovar prediction", "100 years serotyping", "analysis", "Silico Typing Resource"], "article_id"=>1640438, "categories"=>["Biological Sciences"], "users"=>["Catherine E. Yoshida", "Peter Kruczkiewicz", "Chad R. Laing", "Erika J. Lingohr", "Victor P. J. Gannon", "John H. E. Nash", "Eduardo N. Taboada"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0147101.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differences_between_reported_and_predicted_serovars_for_Weltevreden_genomes_are_due_to_an_incorrect_reported_serovar_/1640438", "title"=>"Differences between reported and predicted serovars for Weltevreden genomes are due to an incorrect reported serovar.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-28 12:39:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2631635"], "description"=>"<p>The concordance was based on the proportion of genomes in a cgMLST cluster that belonged to the predominant predicted serovar in the group. The cgMLST clusters were defined at a similarity threshold of 85%; only clusters with four or more members are shown.</p>", "links"=>[], "tags"=>["draft Salmonella genome assemblies", "Draft Genome Assemblies", "assembly", "analyses", "phylogenetic", "Subtyping Draft Salmonella Genome Assemblies", "WGS draft assemblies", "core genome MLST", "SISTR platform", "silico serovar prediction", "100 years serotyping", "analysis", "Silico Typing Resource"], "article_id"=>1640439, "categories"=>["Biological Sciences"], "users"=>["Catherine E. Yoshida", "Peter Kruczkiewicz", "Chad R. Laing", "Erika J. Lingohr", "Victor P. J. Gannon", "John H. E. Nash", "Eduardo N. Taboada"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0147101.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_high_level_of_concordance_observed_between_cgMLST_cluster_and_serovar_/1640439", "title"=>"A high level of concordance observed between cgMLST cluster and serovar.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-28 12:39:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/2631636"], "description"=>"<p>Minimum Spanning Tree visualization of cgMLST phylogeny for a set of <i>Salmonella enterica</i> genomes (n = 2,002) created in the SISTR server. The predicted serovar for Newport and Agona genomes has been projected onto the tree to highlight the contrast between a polyphyletic serovar (Newport) and a monophyletic serovar (Agona).</p>", "links"=>[], "tags"=>["draft Salmonella genome assemblies", "Draft Genome Assemblies", "assembly", "analyses", "phylogenetic", "Subtyping Draft Salmonella Genome Assemblies", "WGS draft assemblies", "core genome MLST", "SISTR platform", "silico serovar prediction", "100 years serotyping", "analysis", "Silico Typing Resource"], "article_id"=>1640440, "categories"=>["Biological Sciences"], "users"=>["Catherine E. Yoshida", "Peter Kruczkiewicz", "Chad R. Laing", "Erika J. Lingohr", "Victor P. J. Gannon", "John H. E. Nash", "Eduardo N. Taboada"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0147101.g007", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evidence_from_cgMLST_supports_the_polyphyletic_origin_of_Salmonella_Newport_/1640440", "title"=>"Evidence from cgMLST supports the polyphyletic origin of <i>Salmonella</i> Newport.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-28 12:39:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/2631637", "https://ndownloader.figshare.com/files/2631638"], "description"=>"<div><p>For nearly 100 years serotyping has been the gold standard for the identification of <i>Salmonella</i> serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the <i>Salmonella In Silico</i> Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous <i>in silico</i> analyses for several leading subtyping methods on draft <i>Salmonella</i> genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of <i>in silico</i> serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploaded whole-genome assemblies, the SISTR platform incorporates a database comprising over 4,000 publicly available genomes, allowing users to place their isolates in a broader phylogenetic and epidemiological context. The resource incorporates several metadata driven visualizations to examine the phylogenetic, geospatial and temporal distribution of genome-sequenced isolates. As sequencing of <i>Salmonella</i> isolates at public health laboratories around the world becomes increasingly common, rapid <i>in silico</i> analysis of minimally processed draft genome assemblies provides a powerful approach for molecular epidemiology in support of public health investigations. Moreover, this type of integrated analysis using multiple sequence-based methods of sub-typing allows for continuity with historical serotyping data as we transition towards the increasing adoption of genomic analyses in epidemiology. The SISTR platform is freely available on the web at <a href=\"https://lfz.corefacility.ca/sistr-app/\" target=\"_blank\">https://lfz.corefacility.ca/sistr-app/</a>.</p></div>", "links"=>[], "tags"=>["draft Salmonella genome assemblies", "Draft Genome Assemblies", "assembly", "analyses", "phylogenetic", "Subtyping Draft Salmonella Genome Assemblies", "WGS draft assemblies", "core genome MLST", "SISTR platform", "silico serovar prediction", "100 years serotyping", "analysis", "Silico Typing Resource"], "article_id"=>1640441, "categories"=>["Biological Sciences"], "users"=>["Catherine E. Yoshida", "Peter Kruczkiewicz", "Chad R. Laing", "Erika J. Lingohr", "Victor P. J. Gannon", "John H. E. Nash", "Eduardo N. Taboada"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0147101.s001", "https://dx.doi.org/10.1371/journal.pone.0147101.s002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Salmonella_In_Silico_Typing_Resource_SISTR_An_Open_Web_Accessible_Tool_for_Rapidly_Typing_and_Subtyping_Draft_Salmonella_Genome_Assemblies/1640441", "title"=>"The <i>Salmonella In Silico</i> Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft <i>Salmonella</i> Genome Assemblies", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2016-01-28 12:39:28"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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