{"id":"https://openalex.org/W2122467784","doi":"https://doi.org/10.1371/journal.ppat.1002824","title":"Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology","display_name":"Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology","publication_year":2012,"publication_date":"2012-08-02","ids":{"openalex":"https://openalex.org/W2122467784","doi":"https://doi.org/10.1371/journal.ppat.1002824","mag":"2122467784","pmid":"https://pubmed.ncbi.nlm.nih.gov/22876174","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3410874"},"language":"en","primary_location":{"id":"doi:10.1371/journal.ppat.1002824","doi":"https://doi.org/10.1371/journal.ppat.1002824","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.ppat.1002824","pdf_url":"https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1002824&type=printable","source":{"id":"https://openalex.org/S2004986","display_name":"PLoS Pathogens","issn_l":"1553-7366","issn":["1553-7366","1553-7374"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Pathogens","raw_type":"journal-article"},"parent_works":[],"lineage":["https://openalex.org/W2122467784"],"child_works_count":0,"type":"review","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1002824&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043539340","display_name":"Claudio Umberto K\u00f6ser","orcid":"https://orcid.org/0000-0002-0232-846X","observed_orcids":["https://orcid.org/0000-0002-0232-846X"]},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I4210156194","display_name":"Addenbrooke's Hospital","ror":"https://ror.org/055vbxf86","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2802466933","https://openalex.org/I4210156194"]},{"id":"https://openalex.org/I4387154524","display_name":"Health Protection Agency","ror":"https://ror.org/022pm7h15","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827","https://openalex.org/I4387154524"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Claudio U. K\u00f6ser","raw_affiliation_strings":["Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom. cuk21@cam.ac.uk","Clinical Microbiology and Public Health Laboratory, Health Protection Agency Microbiology Services, Addenbrooke's Hospital, Cambridge, United Kingdom","Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom. cuk21@cam.ac.uk","institution_ids":["https://openalex.org/I241749","https://openalex.org/I4210156194"]},{"raw_affiliation_string":"Clinical Microbiology and Public Health Laboratory, Health Protection Agency Microbiology Services, Addenbrooke's Hospital, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I4210156194","https://openalex.org/I4387154524"]},{"raw_affiliation_string":"Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749","https://openalex.org/I4210156194"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054446643","display_name":"Matthew J. Ellington","orcid":"https://orcid.org/0000-0002-0656-3360","observed_orcids":["https://orcid.org/0000-0002-0656-3360"]},"institutions":[{"id":"https://openalex.org/I4210156194","display_name":"Addenbrooke's Hospital","ror":"https://ror.org/055vbxf86","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2802466933","https://openalex.org/I4210156194"]},{"id":"https://openalex.org/I4387154524","display_name":"Health Protection Agency","ror":"https://ror.org/022pm7h15","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827","https://openalex.org/I4387154524"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Matthew J. Ellington","raw_affiliation_strings":["Clinical Microbiology and Public Health Laboratory, Health Protection Agency Microbiology Services, Addenbrooke's Hospital, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Clinical Microbiology and Public Health Laboratory, Health Protection Agency Microbiology Services, Addenbrooke's Hospital, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I4210156194","https://openalex.org/I4387154524"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004867407","display_name":"Edward J. P. Cartwright","orcid":"https://orcid.org/0000-0001-5666-5990","observed_orcids":["https://orcid.org/0000-0001-5666-5990"]},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I4210156194","display_name":"Addenbrooke's Hospital","ror":"https://ror.org/055vbxf86","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2802466933","https://openalex.org/I4210156194"]},{"id":"https://openalex.org/I4387154524","display_name":"Health Protection Agency","ror":"https://ror.org/022pm7h15","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827","https://openalex.org/I4387154524"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Edward J. P. Cartwright","raw_affiliation_strings":["Clinical Microbiology and Public Health Laboratory, Health Protection Agency Microbiology Services, Addenbrooke's Hospital, Cambridge, United Kingdom","Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Clinical Microbiology and Public Health Laboratory, Health Protection Agency Microbiology Services, Addenbrooke's Hospital, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I4210156194","https://openalex.org/I4387154524"]},{"raw_affiliation_string":"Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749","https://openalex.org/I4210156194"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005030069","display_name":"Stephen H. Gillespie","orcid":"https://orcid.org/0000-0001-6537-7712","observed_orcids":["https://orcid.org/0000-0001-6537-7712"]},"institutions":[{"id":"https://openalex.org/I16835326","display_name":"University of St Andrews","ror":"https://ror.org/02wn5qz54","country_code":"GB","type":"education","lineage":["https://openalex.org/I16835326"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Stephen H. Gillespie","raw_affiliation_strings":["The Medical School University of St. Andrews, North Haugh, St. Andrews Fife, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Medical School University of St. Andrews, North Haugh, St. Andrews Fife, United Kingdom","institution_ids":["https://openalex.org/I16835326"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082537844","display_name":"Nicholas M. Brown","orcid":"https://orcid.org/0000-0002-6657-300X","observed_orcids":["https://orcid.org/0000-0002-6657-300X"]},"institutions":[{"id":"https://openalex.org/I4210156194","display_name":"Addenbrooke's Hospital","ror":"https://ror.org/055vbxf86","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2802466933","https://openalex.org/I4210156194"]},{"id":"https://openalex.org/I4387154524","display_name":"Health Protection Agency","ror":"https://ror.org/022pm7h15","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827","https://openalex.org/I4387154524"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nicholas M. Brown","raw_affiliation_strings":["Clinical Microbiology and Public Health Laboratory, Health Protection Agency Microbiology Services, Addenbrooke's Hospital, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Clinical Microbiology and Public Health Laboratory, Health Protection Agency Microbiology Services, Addenbrooke's Hospital, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I4210156194","https://openalex.org/I4387154524"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104053083","display_name":"Mark Farrington","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210156194","display_name":"Addenbrooke's Hospital","ror":"https://ror.org/055vbxf86","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2802466933","https://openalex.org/I4210156194"]},{"id":"https://openalex.org/I4387154524","display_name":"Health Protection Agency","ror":"https://ror.org/022pm7h15","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827","https://openalex.org/I4387154524"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mark Farrington","raw_affiliation_strings":["Clinical Microbiology and Public Health Laboratory, Health Protection Agency Microbiology Services, Addenbrooke's Hospital, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Clinical Microbiology and Public Health Laboratory, Health Protection Agency Microbiology Services, Addenbrooke's Hospital, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I4210156194","https://openalex.org/I4387154524"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047037920","display_name":"Matthew T. G. Holden","orcid":"https://orcid.org/0000-0002-4958-2166","observed_orcids":["https://orcid.org/0000-0002-4958-2166"]},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Matthew T. G. Holden","raw_affiliation_strings":["The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115010691","display_name":"Gordon Dougan","orcid":"https://orcid.org/0000-0003-0022-965X","observed_orcids":["https://orcid.org/0000-0003-0022-965X","https://orcid.org/0009-0005-7776-0117"]},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Gordon Dougan","raw_affiliation_strings":["The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077742706","display_name":"Stephen D. Bentley","orcid":"https://orcid.org/0000-0001-8094-3751","observed_orcids":["https://orcid.org/0000-0001-8094-3751"]},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Stephen D. Bentley","raw_affiliation_strings":["The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084268602","display_name":"Julian Parkhill","orcid":"https://orcid.org/0000-0002-7069-5958","observed_orcids":["https://orcid.org/0000-0002-7069-5958"]},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Julian Parkhill","raw_affiliation_strings":["The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014626556","display_name":"Sharon J. Peacock","orcid":"https://orcid.org/0000-0002-1718-2782","observed_orcids":["https://orcid.org/0000-0002-1718-2782"]},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210156194","display_name":"Addenbrooke's Hospital","ror":"https://ror.org/055vbxf86","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2802466933","https://openalex.org/I4210156194"]},{"id":"https://openalex.org/I4387154524","display_name":"Health Protection Agency","ror":"https://ror.org/022pm7h15","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827","https://openalex.org/I4387154524"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sharon J. Peacock","raw_affiliation_strings":["Clinical Microbiology and Public Health Laboratory, Health Protection Agency Microbiology Services, Addenbrooke's Hospital, Cambridge, United Kingdom","Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom","Department of Pathology, University of Cambridge, Cambridge, United Kingdom","The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Clinical Microbiology and Public Health Laboratory, Health Protection Agency Microbiology Services, Addenbrooke's Hospital, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I4210156194","https://openalex.org/I4387154524"]},{"raw_affiliation_string":"Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749","https://openalex.org/I4210156194"]},{"raw_affiliation_string":"Department of Pathology, University of Cambridge, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I2802476451"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5043539340"],"corresponding_institution_ids":["https://openalex.org/I241749","https://openalex.org/I4210156194","https://openalex.org/I4387154524"],"apc_list":{"value":3043,"currency":"USD","value_usd":3043},"apc_paid":{"value":3043,"currency":"USD","value_usd":3043},"fwci":3.5973,"has_fulltext":true,"cited_by_count":556,"citation_normalized_percentile":{"value":0.94736842,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"8","issue":"8","first_page":"e1002824","last_page":"e1002824"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.8773999810218811,"subfield":{"id":"https://openalex.org/subfields/2726","display_name":"Microbiology (medical)"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.8773999810218811,"subfield":{"id":"https://openalex.org/subfields/2726","display_name":"Microbiology (medical)"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.08590000122785568,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.008200000040233135,"subfield":{"id":"https://openalex.org/subfields/2726","display_name":"Microbiology (medical)"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"whole genome sequencing","score":0.906000018119812},{"id":"https://openalex.org/keywords/microbiological-diagnosis","display_name":"microbiological diagnosis","score":0.8320000171661377},{"id":"https://openalex.org/keywords/public-health-microbiology","display_name":"public health microbiology","score":0.8859999775886536},{"id":"https://openalex.org/keywords/molecular-epidemiology","display_name":"molecular epidemiology","score":0.9110000133514404},{"id":"https://openalex.org/keywords/outbreak-investigation","display_name":"outbreak investigation","score":0.890999972820282},{"id":"https://openalex.org/keywords/antimicrobial-susceptibility-testing","display_name":"antimicrobial susceptibility testing","score":0.8650000095367432},{"id":"https://openalex.org/keywords/cost-effectiveness","display_name":"cost-effectiveness","score":0.7609999775886536},{"id":"https://openalex.org/keywords/surveillance-medicine","display_name":"surveillance (medicine)","score":0.3840000033378601},{"id":"https://openalex.org/keywords/laboratory-facilities","display_name":"laboratory facilities","score":0.39800000190734863}],"concepts":[{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.6662516593933105},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.5342900156974792},{"id":"https://openalex.org/C138816342","wikidata":"https://www.wikidata.org/wiki/Q189603","display_name":"Public health","level":2,"score":0.5140841603279114},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5047725439071655},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.48073267936706543},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4790407419204712},{"id":"https://openalex.org/C2992965680","wikidata":"https://www.wikidata.org/wiki/Q598976","display_name":"Clinical microbiology","level":2,"score":0.4435790181159973},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39484065771102905},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27789822220802307},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.23422476649284363},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18074476718902588},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.06271237134933472}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001424","descriptor_name":"Bacterial Infections","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D001424","descriptor_name":"Bacterial Infections","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.ppat.1002824","doi":"https://doi.org/10.1371/journal.ppat.1002824","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.ppat.1002824","pdf_url":"https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1002824&type=printable","source":{"id":"https://openalex.org/S2004986","display_name":"PLoS Pathogens","issn_l":"1553-7366","issn":["1553-7366","1553-7374"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Pathogens","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2419139","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3410874","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmid:22876174","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22876174","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS pathogens","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3410874","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC3410874/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Pathog","raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.787.3151","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.787.3151","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/ef/f4/ppat.1002824.PMC3410874.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:836d90ac4e4c4417b5d4ebeb1aa89878","doi":null,"is_oa":false,"landing_page_url":"https://doaj.org/article/836d90ac4e4c4417b5d4ebeb1aa89878","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Pathogens, Vol 8, Iss 8, p e1002824 (2012)","raw_type":"article"},{"id":"pmh:oai:jupiter.its.unimelb.edu.au:11343/260024","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/11343/260024","pdf_url":null,"source":{"id":"https://openalex.org/S4377196259","display_name":"Minerva Access (University of Melbourne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I165779595","host_organization_name":"The University of Melbourne","host_organization_lineage":["https://openalex.org/I165779595"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"},{"id":"pmh:oai:research-repository.st-andrews.ac.uk:10023/3290","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/10023/3290","pdf_url":null,"source":{"id":"https://openalex.org/S4306400230","display_name":"St Andrews Research Repository (St Andrews Research Repository)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I16835326","host_organization_name":"University of St Andrews","host_organization_lineage":["https://openalex.org/I16835326"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal item"}],"best_oa_location":{"id":"doi:10.1371/journal.ppat.1002824","doi":"https://doi.org/10.1371/journal.ppat.1002824","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.ppat.1002824","pdf_url":"https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1002824&type=printable","source":{"id":"https://openalex.org/S2004986","display_name":"PLoS Pathogens","issn_l":"1553-7366","issn":["1553-7366","1553-7374"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Pathogens","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.7246000170707703}],"study_designs":[],"awards":[{"id":"https://openalex.org/G4584844266","display_name":null,"funder_award_id":"G1000803","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G5371099781","display_name":null,"funder_award_id":"G1000803","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G6569692151","display_name":null,"funder_award_id":"G1000803","funder_id":"https://openalex.org/F4320312775","funder_display_name":"United Kingdom Clinical Research Collaboration"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320312775","display_name":"United Kingdom Clinical Research Collaboration","ror":"https://ror.org/025ecp212"},{"id":"https://openalex.org/F4320313269","display_name":"Scottish Government","ror":"https://ror.org/04v2xmd71"},{"id":"https://openalex.org/F4320314594","display_name":"Cambridge Philosophical Society","ror":"https://ror.org/001ajjs72"},{"id":"https://openalex.org/F4320319990","display_name":"National Institute for Health and Care Research","ror":"https://ror.org/0187kwz08"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320323024","display_name":"Astellas Pharma","ror":"https://ror.org/01cjash87"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320333685","display_name":"Chief Scientist Office, Scottish Government Health and Social Care Directorate","ror":"https://ror.org/01613vh25"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"},{"id":"https://openalex.org/F4320336709","display_name":"NIHR Cambridge Biomedical Research Centre","ror":"https://ror.org/05m8dr349"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2122467784.pdf","grobid_xml":"https://content.openalex.org/works/W2122467784.grobid-xml"},"referenced_works_count":117,"referenced_works":["https://openalex.org/W53782703","https://openalex.org/W90080750","https://openalex.org/W125544664","https://openalex.org/W846546774","https://openalex.org/W1519781644","https://openalex.org/W1935195623","https://openalex.org/W1968225289","https://openalex.org/W1968893187","https://openalex.org/W1976819270","https://openalex.org/W1977002830","https://openalex.org/W1979573684","https://openalex.org/W1980030331","https://openalex.org/W1981833315","https://openalex.org/W1982447345","https://openalex.org/W1988533731","https://openalex.org/W1989512904","https://openalex.org/W1998108522","https://openalex.org/W2002114667","https://openalex.org/W2007807048","https://openalex.org/W2012254260","https://openalex.org/W2012848909","https://openalex.org/W2012850158","https://openalex.org/W2026769436","https://openalex.org/W2032006339","https://openalex.org/W2035907483","https://openalex.org/W2036256066","https://openalex.org/W2037083749","https://openalex.org/W2037409969","https://openalex.org/W2040424746","https://openalex.org/W2049854615","https://openalex.org/W2051381929","https://openalex.org/W2051892159","https://openalex.org/W2051903478","https://openalex.org/W2052558548","https://openalex.org/W2055200195","https://openalex.org/W2061068281","https://openalex.org/W2061069912","https://openalex.org/W2062297053","https://openalex.org/W2063678249","https://openalex.org/W2064641442","https://openalex.org/W2066321034","https://openalex.org/W2070562450","https://openalex.org/W2076151007","https://openalex.org/W2076808352","https://openalex.org/W2078627432","https://openalex.org/W2080072974","https://openalex.org/W2080347313","https://openalex.org/W2081291022","https://openalex.org/W2081763928","https://openalex.org/W2084775171","https://openalex.org/W2089216231","https://openalex.org/W2096094352","https://openalex.org/W2098207011","https://openalex.org/W2100068729","https://openalex.org/W2100863401","https://openalex.org/W2103291998","https://openalex.org/W2105651846","https://openalex.org/W2105787356","https://openalex.org/W2107828572","https://openalex.org/W2110388384","https://openalex.org/W2111744339","https://openalex.org/W2112515389","https://openalex.org/W2112907188","https://openalex.org/W2113672069","https://openalex.org/W2114810739","https://openalex.org/W2114903401","https://openalex.org/W2116740461","https://openalex.org/W2116980203","https://openalex.org/W2118380724","https://openalex.org/W2119182236","https://openalex.org/W2119284644","https://openalex.org/W2119404698","https://openalex.org/W2120419610","https://openalex.org/W2121538804","https://openalex.org/W2122810526","https://openalex.org/W2127285340","https://openalex.org/W2130164103","https://openalex.org/W2131071075","https://openalex.org/W2132050166","https://openalex.org/W2137985139","https://openalex.org/W2139122528","https://openalex.org/W2139311359","https://openalex.org/W2140050267","https://openalex.org/W2140176358","https://openalex.org/W2140268713","https://openalex.org/W2141881393","https://openalex.org/W2142042648","https://openalex.org/W2142898494","https://openalex.org/W2143130884","https://openalex.org/W2144889117","https://openalex.org/W2146434926","https://openalex.org/W2146878319","https://openalex.org/W2147356875","https://openalex.org/W2147571700","https://openalex.org/W2149405576","https://openalex.org/W2153947793","https://openalex.org/W2153955036","https://openalex.org/W2154326381","https://openalex.org/W2157612734","https://openalex.org/W2159568419","https://openalex.org/W2161350984","https://openalex.org/W2162549023","https://openalex.org/W2162767575","https://openalex.org/W2163562836","https://openalex.org/W2164631357","https://openalex.org/W2168086802","https://openalex.org/W2169002484","https://openalex.org/W2169035256","https://openalex.org/W2169790816","https://openalex.org/W2170058018","https://openalex.org/W2318653171","https://openalex.org/W2403231568","https://openalex.org/W4236922424","https://openalex.org/W4248726629","https://openalex.org/W4255310200","https://openalex.org/W4297585095","https://openalex.org/W4392145873"],"related_works":["https://openalex.org/W2042898051","https://openalex.org/W1996792558","https://openalex.org/W4386780798","https://openalex.org/W2108703442","https://openalex.org/W2791994023","https://openalex.org/W2766658767","https://openalex.org/W4389493717","https://openalex.org/W2443422886","https://openalex.org/W2941802690"],"abstract_inverted_index":{"Whole":[0],"genome":[1],"sequencing":[2],"(WGS)":[3],"promises":[4],"to":[5,44,66,89,109],"be":[6,63,110],"transformative":[7],"for":[8,74,84,96,107],"the":[9,15,36,53,92,102],"practice":[10],"of":[11,40,55,98],"clinical":[12],"microbiology,":[13],"and":[14,19,32,76,79,100,104],"rapidly":[16],"falling":[17],"cost":[18],"turnaround":[20],"time":[21],"mean":[22],"that":[23,70,86],"this":[24,41,108],"will":[25],"become":[26],"a":[27,47,56],"viable":[28],"technology":[29],"in":[30,35,52],"diagnostic":[31,58],"reference":[33],"laboratories":[34],"near":[37],"future.The":[38],"objective":[39],"article":[42],"is":[43],"consider":[45],"at":[46],"very":[48],"practical":[49],"level":[50],"where,":[51],"context":[54],"modern":[57],"microbiology":[59],"laboratory,":[60],"WGS":[61],"might":[62],"costeffective":[64],"compared":[65],"current":[67],"alternatives.We":[68],"propose":[69],"molecular":[71],"epidemiology":[72],"performed":[73],"surveillance":[75],"outbreak":[77],"investigation":[78],"genotypic":[80],"antimicrobial":[81],"susceptibility":[82],"testing":[83],"microbes":[85],"are":[87],"difficult":[88],"grow":[90],"represent":[91],"most":[93],"immediate":[94],"areas":[95],"application":[97],"WGS,":[99],"discuss":[101],"technical":[103],"infrastructure":[105],"requirements":[106],"implemented.":[111]},"counts_by_year":[{"year":2026,"cited_by_count":26},{"year":2025,"cited_by_count":22},{"year":2024,"cited_by_count":23},{"year":2023,"cited_by_count":21},{"year":2022,"cited_by_count":20},{"year":2021,"cited_by_count":37},{"year":2020,"cited_by_count":31},{"year":2019,"cited_by_count":44},{"year":2018,"cited_by_count":43},{"year":2017,"cited_by_count":56},{"year":2016,"cited_by_count":59},{"year":2015,"cited_by_count":53},{"year":2014,"cited_by_count":69},{"year":2013,"cited_by_count":47},{"year":2012,"cited_by_count":5}],"updated_date":"2026-11-14T11:04:58.165337","created_date":"2016-06-24T00:00:00"}