{"id":"https://openalex.org/W2767349396","doi":"https://doi.org/10.1128/jcm.01374-17","title":"Direct Detection of Shigella in Stool Specimens by Use of a Metagenomic Approach","display_name":"Direct Detection of Shigella in Stool Specimens by Use of a Metagenomic Approach","publication_year":2017,"publication_date":"2017-11-08","ids":{"openalex":"https://openalex.org/W2767349396","doi":"https://doi.org/10.1128/jcm.01374-17","mag":"2767349396","pmid":"https://pubmed.ncbi.nlm.nih.gov/29118177","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/5786726"},"language":"en","primary_location":{"id":"doi:10.1128/jcm.01374-17","doi":"https://doi.org/10.1128/jcm.01374-17","is_oa":true,"landing_page_url":"https://doi.org/10.1128/jcm.01374-17","pdf_url":"https://jcm.asm.org/content/jcm/56/2/e01374-17.full.pdf","source":{"id":"https://openalex.org/S53087977","display_name":"Journal of Clinical Microbiology","issn_l":"0095-1137","issn":["0095-1137","1070-633X","1098-660X"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320263","host_organization_name":"American Society for Microbiology","host_organization_lineage":["https://openalex.org/P4310320263"],"host_organization_lineage_names":["American Society for Microbiology"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Clinical Microbiology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://jcm.asm.org/content/jcm/56/2/e01374-17.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100454205","display_name":"Jie Liu","orcid":"https://orcid.org/0000-0003-2658-5249","observed_orcids":["https://orcid.org/0000-0003-2658-5249"]},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jie Liu","raw_affiliation_strings":["Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067904253","display_name":"Mathieu Almeida","orcid":"https://orcid.org/0000-0003-4971-0049","observed_orcids":["https://orcid.org/0000-0003-4971-0049"]},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]},{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mathieu Almeida","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA","School of Medicine, University of Maryland, Baltimore, Maryland, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"School of Medicine, University of Maryland, Baltimore, Maryland, USA","institution_ids":["https://openalex.org/I126744593"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071816628","display_name":"Furqan Kabir","orcid":"https://orcid.org/0000-0001-9564-4607","observed_orcids":["https://orcid.org/0000-0001-9564-4607"]},"institutions":[{"id":"https://openalex.org/I118185606","display_name":"Aga Khan University","ror":"https://ror.org/03gd0dm95","country_code":"PK","type":"education","lineage":["https://openalex.org/I118185606","https://openalex.org/I4210114929"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Furqan Kabir","raw_affiliation_strings":["Aga Khan University, Karachi, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aga Khan University, Karachi, Pakistan","institution_ids":["https://openalex.org/I118185606"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018743845","display_name":"Sadia Shakoor","orcid":"https://orcid.org/0000-0003-1301-5239","observed_orcids":["https://orcid.org/0000-0003-1301-5239"]},"institutions":[{"id":"https://openalex.org/I118185606","display_name":"Aga Khan University","ror":"https://ror.org/03gd0dm95","country_code":"PK","type":"education","lineage":["https://openalex.org/I118185606","https://openalex.org/I4210114929"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Sadia Shakoor","raw_affiliation_strings":["Aga Khan University, Karachi, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aga Khan University, Karachi, Pakistan","institution_ids":["https://openalex.org/I118185606"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109974456","display_name":"Shahida Qureshi","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I118185606","display_name":"Aga Khan University","ror":"https://ror.org/03gd0dm95","country_code":"PK","type":"education","lineage":["https://openalex.org/I118185606","https://openalex.org/I4210114929"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Shahida Qureshi","raw_affiliation_strings":["Aga Khan University, Karachi, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aga Khan University, Karachi, Pakistan","institution_ids":["https://openalex.org/I118185606"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108525767","display_name":"Anita K. M. Zaidi","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I118185606","display_name":"Aga Khan University","ror":"https://ror.org/03gd0dm95","country_code":"PK","type":"education","lineage":["https://openalex.org/I118185606","https://openalex.org/I4210114929"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Anita Zaidi","raw_affiliation_strings":["Aga Khan University, Karachi, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aga Khan University, Karachi, Pakistan","institution_ids":["https://openalex.org/I118185606"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100324705","display_name":"Shan Li","orcid":"https://orcid.org/0000-0002-3200-0393","observed_orcids":["https://orcid.org/0000-0002-3200-0393"]},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shan Li","raw_affiliation_strings":["School of Medicine, University of Maryland, Baltimore, Maryland, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Medicine, University of Maryland, Baltimore, Maryland, USA","institution_ids":["https://openalex.org/I126744593"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111920831","display_name":"Boubou Tamboura","orcid":"https://orcid.org/0000-0003-0028-4341","observed_orcids":["https://orcid.org/0000-0003-0028-4341"]},"institutions":[{"id":"https://openalex.org/I4210088409","display_name":"Centre Pour le D\u00e9veloppement des Vaccins-Mali","ror":"https://ror.org/004ymwd44","country_code":"ML","type":"other","lineage":["https://openalex.org/I4210088409"]}],"countries":["ML"],"is_corresponding":false,"raw_author_name":"Boubou Tamboura","raw_affiliation_strings":["Centre pour le D\u00e9veloppement des Vaccins, Bamako, Mali"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre pour le D\u00e9veloppement des Vaccins, Bamako, Mali","institution_ids":["https://openalex.org/I4210088409"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057901946","display_name":"Samba Ousmane Sow","orcid":"https://orcid.org/0000-0002-6335-5066","observed_orcids":["https://orcid.org/0000-0002-6335-5066"]},"institutions":[{"id":"https://openalex.org/I4210088409","display_name":"Centre Pour le D\u00e9veloppement des Vaccins-Mali","ror":"https://ror.org/004ymwd44","country_code":"ML","type":"other","lineage":["https://openalex.org/I4210088409"]}],"countries":["ML"],"is_corresponding":false,"raw_author_name":"Samba O. Sow","raw_affiliation_strings":["Centre pour le D\u00e9veloppement des Vaccins, Bamako, Mali"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre pour le D\u00e9veloppement des Vaccins, Bamako, Mali","institution_ids":["https://openalex.org/I4210088409"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030515780","display_name":"In\u00e1cio Mandomando","orcid":"https://orcid.org/0000-0002-1078-2187","observed_orcids":["https://orcid.org/0000-0002-1078-2187"]},"institutions":[{"id":"https://openalex.org/I4210118037","display_name":"Manhi\u00e7a Health Research Centre","ror":"https://ror.org/0287jnj14","country_code":"MZ","type":"facility","lineage":["https://openalex.org/I4210118037"]}],"countries":["MZ"],"is_corresponding":false,"raw_author_name":"Inacio Mandomando","raw_affiliation_strings":["Centro de Investiga\u00e7\u00e3o em Sa\u00fade da Manhi\u00e7a, Maputo, Mozambique"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro de Investiga\u00e7\u00e3o em Sa\u00fade da Manhi\u00e7a, Maputo, Mozambique","institution_ids":["https://openalex.org/I4210118037"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018831973","display_name":"Pedro Luis Alonso","orcid":"https://orcid.org/0000-0003-3292-3443","observed_orcids":["https://orcid.org/0000-0003-3292-3443"]},"institutions":[{"id":"https://openalex.org/I4210118037","display_name":"Manhi\u00e7a Health Research Centre","ror":"https://ror.org/0287jnj14","country_code":"MZ","type":"facility","lineage":["https://openalex.org/I4210118037"]}],"countries":["MZ"],"is_corresponding":false,"raw_author_name":"Pedro L. Alonso","raw_affiliation_strings":["Centro de Investiga\u00e7\u00e3o em Sa\u00fade da Manhi\u00e7a, Maputo, Mozambique"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro de Investiga\u00e7\u00e3o em Sa\u00fade da Manhi\u00e7a, Maputo, Mozambique","institution_ids":["https://openalex.org/I4210118037"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052309984","display_name":"Thandavarayan Ramamurthy","orcid":"https://orcid.org/0000-0001-7999-5036","observed_orcids":["https://orcid.org/0000-0001-7999-5036"]},"institutions":[{"id":"https://openalex.org/I4210101909","display_name":"National Institute of Cholera and Enteric Diseases","ror":"https://ror.org/018azgd14","country_code":"IN","type":"facility","lineage":["https://openalex.org/I37048141","https://openalex.org/I4210101909"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Thandavarayan Ramamurthy","raw_affiliation_strings":["National Institute of Cholera and Enteric Diseases, Kolkata, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Cholera and Enteric Diseases, Kolkata, India","institution_ids":["https://openalex.org/I4210101909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109067964","display_name":"Dipika Sur","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210101909","display_name":"National Institute of Cholera and Enteric Diseases","ror":"https://ror.org/018azgd14","country_code":"IN","type":"facility","lineage":["https://openalex.org/I37048141","https://openalex.org/I4210101909"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Dipika Sur","raw_affiliation_strings":["National Institute of Cholera and Enteric Diseases, Kolkata, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Cholera and Enteric Diseases, Kolkata, India","institution_ids":["https://openalex.org/I4210101909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025149327","display_name":"Karen L. Kotloff","orcid":"https://orcid.org/0000-0003-1808-6431","observed_orcids":["https://orcid.org/0000-0003-1808-6431"]},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karen Kotloff","raw_affiliation_strings":["School of Medicine, University of Maryland, Baltimore, Maryland, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Medicine, University of Maryland, Baltimore, Maryland, USA","institution_ids":["https://openalex.org/I126744593"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105876666","display_name":"James P. Nataro","orcid":"https://orcid.org/0000-0003-4159-0097","observed_orcids":["https://orcid.org/0000-0003-4159-0097"]},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Nataro","raw_affiliation_strings":["Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049145301","display_name":"Myron M. Levine","orcid":"https://orcid.org/0000-0002-5721-5040","observed_orcids":["https://orcid.org/0000-0002-5721-5040"]},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Myron M. Levine","raw_affiliation_strings":["School of Medicine, University of Maryland, Baltimore, Maryland, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Medicine, University of Maryland, Baltimore, Maryland, USA","institution_ids":["https://openalex.org/I126744593"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016230559","display_name":"Oscar Colin Stine","orcid":"https://orcid.org/0000-0003-3974-3752","observed_orcids":["https://orcid.org/0000-0003-3974-3752"]},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"O. Colin Stine","raw_affiliation_strings":["School of Medicine, University of Maryland, Baltimore, Maryland, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Medicine, University of Maryland, Baltimore, Maryland, USA","institution_ids":["https://openalex.org/I126744593"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007061685","display_name":"Eric R. Houpt","orcid":"https://orcid.org/0000-0003-1085-1354","observed_orcids":["https://orcid.org/0000-0003-1085-1354"]},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Eric Houpt","raw_affiliation_strings":["Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA","institution_ids":["https://openalex.org/I51556381"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5007061685","https://openalex.org/A5016230559"],"corresponding_institution_ids":["https://openalex.org/I126744593","https://openalex.org/I51556381"],"apc_list":null,"apc_paid":{"value":1944,"currency":"EUR","value_usd":2096},"fwci":2.8994,"has_fulltext":false,"cited_by_count":35,"citation_normalized_percentile":{"value":0.90498763,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"56","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10943","display_name":"Escherichia coli research studies","score":0.5907999873161316,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10943","display_name":"Escherichia coli research studies","score":0.5907999873161316,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.2395000010728836,"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/T10486","display_name":"Salmonella and Campylobacter epidemiology","score":0.061500001698732376,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/shigella","display_name":"Shigella","score":0.9769999980926514},{"id":"https://openalex.org/keywords/metagenomic-sequencing","display_name":"metagenomic sequencing","score":0.7049999833106995},{"id":"https://openalex.org/keywords/childhood-diarrhea","display_name":"childhood diarrhea","score":0.652999997138977},{"id":"https://openalex.org/keywords/qpcr-detection","display_name":"qPCR detection","score":0.5199999809265137},{"id":"https://openalex.org/keywords/fecal-dna","display_name":"fecal DNA","score":0.7049999833106995},{"id":"https://openalex.org/keywords/kraken","display_name":"Kraken","score":0.5329999923706055},{"id":"https://openalex.org/keywords/ipah","display_name":"ipaH gene","score":0.5740000009536743},{"id":"https://openalex.org/keywords/vira","display_name":"VirA","score":0.75},{"id":"https://openalex.org/keywords/virg","display_name":"virG","score":0.9549999833106995},{"id":"https://openalex.org/keywords/diagnostic-accuracy","display_name":"diagnostic accuracy","score":0.6380000114440918},{"id":"https://openalex.org/keywords/global-enteric-multicenter-study","display_name":"Global Enteric Multicenter Study","score":0.8880000114440918}],"concepts":[{"id":"https://openalex.org/C2776986154","wikidata":"https://www.wikidata.org/wiki/Q131029","display_name":"Shigella","level":4,"score":0.9698091745376587},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7548574805259705},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.6147305965423584},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.5415916442871094},{"id":"https://openalex.org/C2781217973","wikidata":"https://www.wikidata.org/wiki/Q1644417","display_name":"Shigella flexneri","level":4,"score":0.5332531332969666},{"id":"https://openalex.org/C61716771","wikidata":"https://www.wikidata.org/wiki/Q496","display_name":"Feces","level":2,"score":0.5275927186012268},{"id":"https://openalex.org/C48023723","wikidata":"https://www.wikidata.org/wiki/Q856198","display_name":"Real-time polymerase chain reaction","level":3,"score":0.4920210540294647},{"id":"https://openalex.org/C2779802037","wikidata":"https://www.wikidata.org/wiki/Q40878","display_name":"Diarrhea","level":2,"score":0.46770355105400085},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.44010335206985474},{"id":"https://openalex.org/C2779546430","wikidata":"https://www.wikidata.org/wiki/Q327298","display_name":"Shigellosis","level":5,"score":0.4224322736263275},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.36275047063827515},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24704140424728394},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10859298706054688},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.10680866241455078},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.05465087294578552}],"mesh":[{"descriptor_ui":"D001431","descriptor_name":"Bacteriological Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004405","descriptor_name":"Dysentery, Bacillary","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D004405","descriptor_name":"Dysentery, Bacillary","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012760","descriptor_name":"Shigella","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012760","descriptor_name":"Shigella","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012760","descriptor_name":"Shigella","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060888","descriptor_name":"Real-Time Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1128/jcm.01374-17","doi":"https://doi.org/10.1128/jcm.01374-17","is_oa":true,"landing_page_url":"https://doi.org/10.1128/jcm.01374-17","pdf_url":"https://jcm.asm.org/content/jcm/56/2/e01374-17.full.pdf","source":{"id":"https://openalex.org/S53087977","display_name":"Journal of Clinical Microbiology","issn_l":"0095-1137","issn":["0095-1137","1070-633X","1098-660X"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320263","host_organization_name":"American Society for Microbiology","host_organization_lineage":["https://openalex.org/P4310320263"],"host_organization_lineage_names":["American Society for Microbiology"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Clinical Microbiology","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5786726","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5786726","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":"J Clin Microbiol","raw_type":"Text"},{"id":"pmid:29118177","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29118177","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":"Journal of clinical microbiology","raw_type":"Comparative Study"},{"id":"pmh:oai:ecommons.aku.edu:pakistan_fhs_mc_women_childhealth_paediatr-1948","doi":null,"is_oa":true,"landing_page_url":"https://ecommons.aku.edu/pakistan_fhs_mc_women_childhealth_paediatr/949","pdf_url":null,"source":{"id":"https://openalex.org/S4377196301","display_name":"eCommons - AKU (Aga Khan University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I118185606","host_organization_name":"Aga Khan University","host_organization_lineage":["https://openalex.org/I118185606"],"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":"Department of Paediatrics and Child Health","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1128/jcm.01374-17","doi":"https://doi.org/10.1128/jcm.01374-17","is_oa":true,"landing_page_url":"https://doi.org/10.1128/jcm.01374-17","pdf_url":"https://jcm.asm.org/content/jcm/56/2/e01374-17.full.pdf","source":{"id":"https://openalex.org/S53087977","display_name":"Journal of Clinical Microbiology","issn_l":"0095-1137","issn":["0095-1137","1070-633X","1098-660X"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320263","host_organization_name":"American Society for Microbiology","host_organization_lineage":["https://openalex.org/P4310320263"],"host_organization_lineage_names":["American Society for Microbiology"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Clinical Microbiology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.9537000060081482,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G6409072880","display_name":"University of Virginia - to improve field sites detection of enteropathogens by facilitating high quality multiplexed molecular diagnostics through manageable protocols, sp...","funder_award_id":"OPP1019093","funder_id":"https://openalex.org/F4320306137","funder_display_name":"Bill and Melinda Gates Foundation"}],"funders":[{"id":"https://openalex.org/F4320306137","display_name":"Bill and Melinda Gates Foundation","ror":"https://ror.org/0456r8d26"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2767349396.pdf"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1703384511","https://openalex.org/W1753053867","https://openalex.org/W2003347102","https://openalex.org/W2012807335","https://openalex.org/W2080723443","https://openalex.org/W2088651787","https://openalex.org/W2088976222","https://openalex.org/W2098916578","https://openalex.org/W2106303448","https://openalex.org/W2114053580","https://openalex.org/W2116593462","https://openalex.org/W2118442768","https://openalex.org/W2123349167","https://openalex.org/W2131960275","https://openalex.org/W2139817179","https://openalex.org/W2143285077","https://openalex.org/W2159954944","https://openalex.org/W2162351073","https://openalex.org/W2166293389","https://openalex.org/W2169792847","https://openalex.org/W2184291903","https://openalex.org/W2255167279","https://openalex.org/W2287849783","https://openalex.org/W2336330109","https://openalex.org/W2337747100","https://openalex.org/W2418082614","https://openalex.org/W2521607002","https://openalex.org/W2614986146","https://openalex.org/W2951176108"],"related_works":["https://openalex.org/W2088976222","https://openalex.org/W4411211869","https://openalex.org/W2269986178","https://openalex.org/W4393167147","https://openalex.org/W2780866427","https://openalex.org/W2080723443","https://openalex.org/W2091849359","https://openalex.org/W4392895531","https://openalex.org/W2327924310","https://openalex.org/W6907992102"],"abstract_inverted_index":{"ABSTRACT":[0],"The":[1,127,175],"underestimation":[2],"of":[3,9,31,39,129,178,242,270],"Shigella":[4,32,53,121,130,243,262,271,275,287],"species":[5,254],"as":[6,281],"a":[7,34],"cause":[8],"childhood":[10],"diarrhea":[11],"disease":[12],"has":[13],"become":[14],"increasingly":[15],"apparent":[16],"with":[17],"quantitative":[18],"PCR":[19],"(qPCR)-based":[20],"diagnostic":[21],"methods":[22],"versus":[23,235],"culture.":[24],"We":[25,109],"sought":[26],"to":[27,113,119,268],"confirm":[28],"qPCR-based":[29],"detection":[30],"via":[33],"metagenomics":[35],"approach.":[36],"Three":[37],"groups":[38,218,227],"samples":[40,151,265,273],"were":[41,104,152,204,244],"selected":[42],"from":[43,46,162,221],"diarrheal":[44],"cases":[45],"the":[47,115,124,163,208,222,247,253],"Global":[48],"Enteric":[49],"Multicenter":[50],"Study:":[51],"nine":[52,63,74],"culture-positive":[54,272],"and":[55,73,76,143,160,201,213,219,240],"qPCR-positive":[56,66,264],"(culture":[57,67,78],"+":[58,60,70,137,139,147,210,212,217],"qPCR":[59,69,80,138,146,166,188,211,216,225,280],")":[61,71,82],"samples,":[62,72],"culture-negative":[64,75],"but":[65,250],"\u2212":[68,79,81,145,165,167,215,224,226],"qPCR-negative":[77],"samples.":[83],"Fecal":[84],"DNA":[85],"was":[86],"sequenced":[87],"using":[88],"paired-end":[89],"Illumina":[90],"HiSeq,":[91],"whereby":[92],"3.26":[93],"\u00d7":[94,99],"10":[95,100],"8":[96],"\u00b1":[97,141,149,170],"5.6":[98],"7":[101],"high-quality":[102],"reads":[103,134],"generated":[105],"for":[106,285],"each":[107],"sample.":[108],"used":[110],"Kraken":[111,232],"software":[112],"compare":[114],"read":[116,176],"counts":[117,177],"specific":[118],"\u201c":[120],"\u201d":[122],"among":[123],"three":[125],"groups.":[126],"proportions":[128],"-specific":[131],"nonhuman":[132],"sequence":[133,276],"between":[135,207],"culture":[136,144,164,209,214,223],"(0.65":[140],"0.42%)":[142],"(0.55":[148],"0.31%)":[150],"similar":[153,206,267],"(Mann-Whitney":[154],"U":[155],"test,":[156],"P":[157,172,229],"=":[158],"0.627)":[159],"distinct":[161,220],"group":[168],"(0.17":[169],"0.15%,":[171],"<":[173,230],"0.05).":[174],"sequences":[179],"previously":[180],"targeted":[181],"by":[182],"Shigella/":[183],"enteroinvasive":[184],"Escherichia":[185],"coli":[186],"(EIEC)":[187],"assays,":[189],"namely,":[190],"ipaH":[191],",":[192,194,196,198,200,203],"virA":[193],"virG":[195],"ial":[197],"ShET2":[199],"ipaH3":[202],"also":[205],"(":[228],"0.001).":[231],"performed":[233],"well":[234],"other":[236],"methods:":[237],"its":[238],"precision":[239],"recall":[241],"excellent":[245],"at":[246,252],"genus":[248],"level":[249],"variable":[251],"level.":[255],"In":[256],"summary,":[257],"metagenomic":[258],"sequencing":[259],"indicates":[260],"that":[261],"/EIEC":[263],"are":[266],"those":[269],"in":[274],"composition,":[277],"thus":[278],"supporting":[279],"an":[282],"accurate":[283],"method":[284],"detecting":[286],".":[288]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":5}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2017-11-17T00:00:00"}
