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While significant strides have been made in the understanding of the pathogenesis, few studies on the genomic content of the\n                    <jats:named-content content-type=\"genus-species\">Shigella<\/jats:named-content>\n                    species have been completed. The goal of this study was to characterize the genomic diversity of\n                    <jats:named-content content-type=\"genus-species\">Shigella<\/jats:named-content>\n                    species through sequencing of 55 isolates representing members of each of the four\n                    <jats:named-content content-type=\"genus-species\">Shigella<\/jats:named-content>\n                    species:\n                    <jats:named-content content-type=\"genus-species\">S. flexneri<\/jats:named-content>\n                    ,\n                    <jats:named-content content-type=\"genus-species\">S. sonnei<\/jats:named-content>\n                    ,\n                    <jats:named-content content-type=\"genus-species\">S. boydii<\/jats:named-content>\n                    , and\n                    <jats:named-content content-type=\"genus-species\">S. dysenteriae<\/jats:named-content>\n                    . Phylogeny inferred from 336 available\n                    <jats:named-content content-type=\"genus-species\">Shigella<\/jats:named-content>\n                    and\n                    <jats:named-content content-type=\"genus-species\">Escherichia coli<\/jats:named-content>\n                    genomes defined exclusive clades of\n                    <jats:named-content content-type=\"genus-species\">Shigella<\/jats:named-content>\n                    ; conserved genomic markers that can identify each clade were then identified. PCR assays were developed for each clade-specific marker, which was combined with an amplicon for the conserved\n                    <jats:named-content content-type=\"genus-species\">Shigella<\/jats:named-content>\n                    invasion antigen, IpaH3, into a multiplex PCR assay. This assay demonstrated high specificity, correctly identifying 218 of 221 presumptive\n                    <jats:named-content content-type=\"genus-species\">Shigella<\/jats:named-content>\n                    isolates, and sensitivity, by not identifying any of 151 diverse\n                    <jats:named-content content-type=\"genus-species\">E. coli<\/jats:named-content>\n                    isolates incorrectly as\n                    <jats:named-content content-type=\"genus-species\">Shigella<\/jats:named-content>\n                    . This new phylogenomics-based PCR assay represents a valuable tool for rapid typing of uncharacterized\n                    <jats:named-content content-type=\"genus-species\">Shigella<\/jats:named-content>\n                    isolates and provides a framework that can be utilized for the identification of novel genomic markers from genomic data.\n                  <\/jats:p>","DOI":"10.1128\/jcm.03527-14","type":"journal-article","created":{"date-parts":[[2015,1,15]],"date-time":"2015-01-15T01:40:15Z","timestamp":1421286015000},"page":"951-960","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":81,"title":["Defining the Phylogenomics of Shigella Species: a Pathway to Diagnostics"],"prefix":"10.1128","volume":"53","author":[{"given":"Jason W.","family":"Sahl","sequence":"first","affiliation":[{"name":"University of Maryland School of Medicine, Institute for Genome Sciences, Department of Microbiology and Immunology, Baltimore, Maryland, USA"},{"name":"Translational Genomics Research Institute, Flagstaff, Arizona, USA"},{"name":"Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolyn R.","family":"Morris","sequence":"additional","affiliation":[{"name":"University of Maryland School of Medicine, Institute for Genome Sciences, Department of Microbiology and Immunology, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Emberger","sequence":"additional","affiliation":[{"name":"University of Maryland School of Medicine, Institute for Genome Sciences, Department of Microbiology and Immunology, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire M.","family":"Fraser","sequence":"additional","affiliation":[{"name":"University of Maryland School of Medicine, Institute for Genome Sciences, Department of Microbiology and Immunology, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John Benjamin","family":"Ochieng","sequence":"additional","affiliation":[{"name":"KEMRI-CDC Kisumu, Kisumu, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane","family":"Juma","sequence":"additional","affiliation":[{"name":"KEMRI-CDC Kisumu, Kisumu, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barry","family":"Fields","sequence":"additional","affiliation":[{"name":"CDC Kenya, KEMRI Headquarters, Nairobi, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert F.","family":"Breiman","sequence":"additional","affiliation":[{"name":"CDC Kenya, KEMRI Headquarters, Nairobi, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Gilmour","sequence":"additional","affiliation":[{"name":"National Microbiology, Public Health Agency of Canada, Winnipeg, Manitoba, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James P.","family":"Nataro","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David A.","family":"Rasko","sequence":"additional","affiliation":[{"name":"University of Maryland School of Medicine, Institute for Genome Sciences, Department of Microbiology and Immunology, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","first-page":"133","article-title":"Shigellosis","volume":"43","author":"Niyogi SK","year":"2005","unstructured":"Niyogi SK. 2005. 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