{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T16:13:50Z","timestamp":1790612030471,"version":"4.1.0"},"reference-count":85,"publisher":"Microbiology Society","issue":"12","license":[{"start":{"date-parts":[[2021,12,24]],"date-time":"2021-12-24T00:00:00Z","timestamp":1640304000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,24]]},"abstract":"\n \n \n Shigella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n and enteroinvasive\n \n \n Escherichia coli<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n (EIEC) cause human bacillary dysentery with similar invasion mechanisms and share similar physiological, biochemical and genetic characteristics. Differentiation of\n \n \n Shigella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n from EIEC is important for clinical diagnostic and epidemiological investigations. However, phylogenetically,\n \n \n Shigella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n and EIEC strains are composed of multiple clusters and are different forms of\n \n \n E. coli<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n , making it difficult to find genetic markers to discriminate between\n \n \n Shigella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n and EIEC. In this study, we identified 10\n \n \n Shigella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n clusters, seven EIEC clusters and 53 sporadic types of EIEC by examining over 17000 publicly available\n \n \n Shigella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n and EIEC genomes. We compared\n \n \n Shigella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n and EIEC accessory genomes to identify cluster-specific gene markers for the 17 clusters and 53 sporadic types. The cluster-specific gene markers showed 99.64% accuracy and more than 97.02% specificity. In addition, we developed a freely available\n in silico<\/jats:italic>\n serotyping pipeline named\n \n \n Shigella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n EIEC Cluster Enhanced Serotype Finder (ShigEiFinder) by incorporating the cluster-specific gene markers and established\n \n \n Shigella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n and EIEC serotype-specific O antigen genes and modification genes into typing. ShigEiFinder can process either paired-end Illumina sequencing reads or assembled genomes and almost perfectly differentiated\n \n \n Shigella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n from EIEC with 99.70 and 99.74% cluster assignment accuracy for the assembled genomes and read mapping respectively. ShigEiFinder was able to serotype over 59\n \n \n Shigella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n serotypes and 22 EIEC serotypes and provided a high specificity of 99.40% for assembled genomes and 99.38% for read mapping for serotyping. The cluster-specific gene markers and our new serotyping tool, ShigEiFinder (installable package:\n https:\/\/github.com\/LanLab\/ShigEiFinder<\/jats:ext-link>\n , online tool:\n https:\/\/mgtdb.unsw.edu.au\/ShigEiFinder\/<\/jats:ext-link>\n ), will be useful for epidemiological and diagnostic investigations.\n <\/jats:p>","DOI":"10.1099\/mgen.0.000704","type":"journal-article","created":{"date-parts":[[2021,12,10]],"date-time":"2021-12-10T12:22:44Z","timestamp":1639138964000},"source":"Crossref","is-referenced-by-count":23,"title":["Cluster-specific gene markers enhance Shigella and enteroinvasive Escherichia coli in silico serotyping"],"prefix":"10.1099","volume":"7","author":[{"given":"Xiaomei","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1911-7033","authenticated-orcid":false,"given":"Michael","family":"Payne","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1687-2359","authenticated-orcid":false,"given":"Thanh","family":"Nguyen","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandeep","family":"Kaur","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9834-5258","authenticated-orcid":false,"given":"Ruiting","family":"Lan","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/159.6.1126"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(17)30276-1"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.1001940"},{"key":"R4","volume-title":"Guidelines for the Control of Shigellosis, Including Epidemics Due to Shigella dysenteriae Type 1","author":"World","year":"2005"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01592-18"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(18)30475-4"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(13)60844-2"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-019-4659-y"},{"key":"R9","volume-title":"Identification of Enterobacteriaceae. 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