{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T00:49:38Z","timestamp":1789865378571,"version":"4.0.1"},"reference-count":29,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2018,1,24]],"date-time":"2018-01-24T00:00:00Z","timestamp":1516752000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2018,2,1]],"date-time":"2018-02-01T00:00:00Z","timestamp":1517443200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1019093"],"award-info":[{"award-number":["OPP1019093"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2018,2]]},"abstract":"ABSTRACT<\/jats:title>\n \n The underestimation of\n Shigella<\/jats:named-content>\n species as a cause of childhood diarrhea disease has become increasingly apparent with quantitative PCR (qPCR)-based diagnostic methods versus culture. We sought to confirm qPCR-based detection of\n Shigella<\/jats:named-content>\n via a metagenomics approach. Three groups of samples were selected from diarrheal cases from the Global Enteric Multicenter Study: nine\n Shigella<\/jats:named-content>\n culture-positive and qPCR-positive (culture\n +<\/jats:sup>\n qPCR\n +<\/jats:sup>\n ) samples, nine culture-negative but qPCR-positive (culture\n \u2212<\/jats:sup>\n qPCR\n +<\/jats:sup>\n ) samples, and nine culture-negative and qPCR-negative (culture\n \u2212<\/jats:sup>\n qPCR\n \u2212<\/jats:sup>\n ) samples. Fecal DNA was sequenced using paired-end Illumina HiSeq, whereby 3.26 \u00d7 10\n 8<\/jats:sup>\n \u00b1 5.6 \u00d7 10\n 7<\/jats:sup>\n high-quality reads were generated for each sample. We used Kraken software to compare the read counts specific to \u201c\n Shigella<\/jats:named-content>\n \u201d among the three groups. The proportions of\n Shigella<\/jats:named-content>\n -specific nonhuman sequence reads between culture\n +<\/jats:sup>\n qPCR\n +<\/jats:sup>\n (0.65 \u00b1 0.42%) and culture\n \u2212<\/jats:sup>\n qPCR\n +<\/jats:sup>\n (0.55 \u00b1 0.31%) samples were similar (Mann-Whitney U test,\n P<\/jats:italic>\n = 0.627) and distinct from the culture\n \u2212<\/jats:sup>\n qPCR\n \u2212<\/jats:sup>\n group (0.17 \u00b1 0.15%,\n P<\/jats:italic>\n < 0.05). The read counts of sequences previously targeted by\n Shigella\/<\/jats:italic>\n enteroinvasive\n Escherichia coli<\/jats:named-content>\n (EIEC) qPCR assays, namely,\n ipaH<\/jats:italic>\n ,\n virA<\/jats:italic>\n ,\n virG<\/jats:italic>\n ,\n ial<\/jats:italic>\n ,\n ShET2<\/jats:italic>\n , and\n ipaH3<\/jats:italic>\n , were also similar between the culture\n +<\/jats:sup>\n qPCR\n +<\/jats:sup>\n and culture\n \u2212<\/jats:sup>\n qPCR\n +<\/jats:sup>\n groups and distinct from the culture\n \u2212<\/jats:sup>\n qPCR\n \u2212<\/jats:sup>\n groups (\n P<\/jats:italic>\n < 0.001). Kraken performed well versus other methods: its precision and recall of\n Shigella<\/jats:named-content>\n were excellent at the genus level but variable at the species level. In summary, metagenomic sequencing indicates that\n Shigella<\/jats:named-content>\n \/EIEC qPCR-positive samples are similar to those of\n Shigella<\/jats:named-content>\n culture-positive samples in\n Shigella<\/jats:named-content>\n sequence composition, thus supporting qPCR as an accurate method for detecting\n Shigella<\/jats:named-content>\n .\n <\/jats:p>","DOI":"10.1128\/jcm.01374-17","type":"journal-article","created":{"date-parts":[[2017,11,8]],"date-time":"2017-11-08T16:25:48Z","timestamp":1510158348000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":29,"title":["Direct Detection of Shigella in Stool Specimens by Use of a Metagenomic Approach"],"prefix":"10.1128","volume":"56","author":[{"given":"Jie","family":"Liu","sequence":"first","affiliation":[{"name":"Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mathieu","family":"Almeida","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA"},{"name":"School of Medicine, University of Maryland, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Furqan","family":"Kabir","sequence":"additional","affiliation":[{"name":"Aga Khan University, Karachi, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sadia","family":"Shakoor","sequence":"additional","affiliation":[{"name":"Aga Khan University, Karachi, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shahida","family":"Qureshi","sequence":"additional","affiliation":[{"name":"Aga Khan University, Karachi, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anita","family":"Zaidi","sequence":"additional","affiliation":[{"name":"Aga Khan University, Karachi, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shan","family":"Li","sequence":"additional","affiliation":[{"name":"School of Medicine, University of Maryland, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Boubou","family":"Tamboura","sequence":"additional","affiliation":[{"name":"Centre pour le D\u00e9veloppement des Vaccins, Bamako, Mali"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samba O.","family":"Sow","sequence":"additional","affiliation":[{"name":"Centre pour le D\u00e9veloppement des Vaccins, Bamako, Mali"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Inacio","family":"Mandomando","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Sa\u00fade da Manhi\u00e7a, Maputo, Mozambique"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro L.","family":"Alonso","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Sa\u00fade da Manhi\u00e7a, Maputo, Mozambique"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thandavarayan","family":"Ramamurthy","sequence":"additional","affiliation":[{"name":"National Institute of Cholera and Enteric Diseases, Kolkata, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dipika","family":"Sur","sequence":"additional","affiliation":[{"name":"National Institute of Cholera and Enteric Diseases, Kolkata, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen","family":"Kotloff","sequence":"additional","affiliation":[{"name":"School of Medicine, University of Maryland, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Nataro","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Myron M.","family":"Levine","sequence":"additional","affiliation":[{"name":"School of Medicine, University of Maryland, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"O. 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Polymerase chain reaction method for the rapid detection of virulent Shigella spp. Int J Mol Clin Microbiol 2:134\u2013137.","journal-title":"Int J Mol Clin Microbiol"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.37.11.3608-3611.1999"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2016.10"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep19233"}],"container-title":["Journal of Clinical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.01374-17","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.01374-17","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T10:12:35Z","timestamp":1646475155000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JCM.01374-17"}},"subtitle":[],"editor":[{"given":"Andrew B.","family":"Onderdonk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,2]]},"references-count":29,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2018,2]]}},"alternative-id":["10.1128\/JCM.01374-17"],"URL":"https:\/\/doi.org\/10.1128\/jcm.01374-17","relation":{},"ISSN":["0095-1137","1098-660X"],"issn-type":[{"value":"0095-1137","type":"print"},{"value":"1098-660X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,2]]},"assertion":[{"value":"2017-08-28","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-11-02","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2018-01-24","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01374-17"}}