{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T21:46:48Z","timestamp":1792014408709,"version":"4.4.0"},"reference-count":22,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2017,2,1]],"date-time":"2017-02-01T00:00:00Z","timestamp":1485907200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100000272","name":"DH | National Institute for Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000272","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":[[2017,2]]},"abstract":"ABSTRACT<\/jats:title>\n \n Escherichia coli<\/jats:named-content>\n and\n Shigella<\/jats:named-content>\n species are closely related and genetically constitute the same species. Differentiating between these two pathogens and accurately identifying the four species of\n Shigella<\/jats:named-content>\n are therefore challenging. The organism-specific bioinformatics whole-genome sequencing (WGS) typing pipelines at Public Health England are dependent on the initial identification of the bacterial species by use of a kmer-based approach. Of the 1,982\n Escherichia coli<\/jats:named-content>\n and\n Shigella<\/jats:named-content>\n sp. isolates analyzed in this study, 1,957 (98.4%) had concordant results by both traditional biochemistry and serology (TB&S) and the kmer identification (ID) derived from the WGS data. Of the 25 mismatches identified, 10 were enteroinvasive\n E. coli<\/jats:named-content>\n isolates that were misidentified as\n Shigella flexneri<\/jats:named-content>\n or\n S. boydii<\/jats:named-content>\n by the kmer ID, and 8 were\n S. flexneri<\/jats:named-content>\n isolates misidentified by TB&S as\n S. boydii<\/jats:named-content>\n due to nonfunctional\n S. flexneri<\/jats:named-content>\n O antigen biosynthesis genes. Analysis of the population structure based on multilocus sequence typing (MLST) data derived from the WGS data showed that the remaining discrepant results belonged to clonal complex 288 (CC288), comprising both\n S. boydii<\/jats:named-content>\n and\n S. dysenteriae<\/jats:named-content>\n strains. Mismatches between the TB&S and kmer ID results were explained by the close phylogenetic relationship between the two species and were resolved with reference to the MLST data.\n Shigella<\/jats:named-content>\n can be differentiated from\n E. coli<\/jats:named-content>\n and accurately identified to the species level by use of kmer comparisons and MLST. Analysis of the WGS data provided explanations for the discordant results between TB&S and WGS data, revealed the true phylogenetic relationships between different species of\n Shigella<\/jats:named-content>\n , and identified emerging pathoadapted lineages.\n <\/jats:p>","DOI":"10.1128\/jcm.01790-16","type":"journal-article","created":{"date-parts":[[2017,1,5]],"date-time":"2017-01-05T18:07:02Z","timestamp":1483639622000},"page":"616-623","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":127,"title":["Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences"],"prefix":"10.1128","volume":"55","author":[{"given":"Marie A.","family":"Chattaway","sequence":"first","affiliation":[{"name":"Gastrointestinal Bacteria Reference Unit and Bioinformatics Unit, National Infection Service, Public Health England, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ulf","family":"Schaefer","sequence":"additional","affiliation":[{"name":"Gastrointestinal Bacteria Reference Unit and Bioinformatics Unit, National Infection Service, Public Health England, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rediat","family":"Tewolde","sequence":"additional","affiliation":[{"name":"Gastrointestinal Bacteria Reference Unit and Bioinformatics Unit, National Infection Service, Public Health England, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy J.","family":"Dallman","sequence":"additional","affiliation":[{"name":"Gastrointestinal Bacteria Reference Unit and Bioinformatics Unit, National Infection Service, Public Health England, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire","family":"Jenkins","sequence":"additional","affiliation":[{"name":"Gastrointestinal Bacteria Reference Unit and Bioinformatics Unit, National Infection Service, Public Health England, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","first-page":"93","volume-title":"Edwards and Ewing's identification of Enterobacteriaceae","author":"Ewing WH","year":"1986","unstructured":"Ewing WH . 1986. The genus Escherichia and the genus Shigella, p 93\u2013172. InEdwards and Ewing's identification of Enterobacteriaceae, 4th ed. 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Special publication of the Society for General Microbiology no. 13. Academic Press, London, United Kingdom."},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.2308"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp698"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.107524.110"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu033"}],"container-title":["Journal of Clinical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.01790-16","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.01790-16","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T08:49:43Z","timestamp":1646470183000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JCM.01790-16"}},"subtitle":[],"editor":[{"given":"Nathan A.","family":"Ledeboer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,2]]},"references-count":22,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2017,2]]}},"alternative-id":["10.1128\/JCM.01790-16"],"URL":"https:\/\/doi.org\/10.1128\/jcm.01790-16","relation":{},"ISSN":["0095-1137","1098-660X"],"issn-type":[{"value":"0095-1137","type":"print"},{"value":"1098-660X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,2]]},"assertion":[{"value":"2016-08-24","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2016-11-28","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-01-25","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}