{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T11:15:32Z","timestamp":1790248532453,"version":"4.1.0"},"reference-count":47,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2019,3,28]],"date-time":"2019-03-28T00:00:00Z","timestamp":1553731200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Belgian Ministry of Social Affairs"},{"name":"Contractual Research (RCO) of the Federal Public Service in Belgium","award":["RF_16\/6302"],"award-info":[{"award-number":["RF_16\/6302"]}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["MicrobiologyOpen"],"published-print":{"date-parts":[[2019,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The phylogenetically closely related <jats:italic>Shigella<\/jats:italic> species and enteroinvasive <jats:italic>Escherichia coli<\/jats:italic> (EIEC) are responsible for millions of episodes of bacterial dysenteriae worldwide. Given its distinct epidemiology and public health relevance, only <jats:italic>Shigellae<\/jats:italic> are subject to mandatory reporting and follow\u2010up by public health authorities. However, many clinical laboratories struggle to differentiate non\u2010EIEC, EIEC, and <jats:italic>Shigella<\/jats:italic> in their current workflows, leading to inaccuracies in surveillance and rising numbers of misidentified <jats:italic>E.\u00a0coli<\/jats:italic> samples at the National Reference Centre (NRC). In this paper, we describe two novel tools to enhance <jats:italic>Shigella<\/jats:italic> surveillance. First, we developed a low\u2010cost Luminex\u2010based multiplex assay combining five genetic markers for species identification with 11 markers for serotype prediction for <jats:italic>S.\u00a0sonnei<\/jats:italic> and <jats:italic>S.\u00a0flexneri<\/jats:italic> isolates. Using a test panel of 254 clinical samples, this assay has a sensitivity of 100% in differentiation of EIEC\/<jats:italic>Shigella<\/jats:italic> pathotype from non\u2010EIEC strains, and 68.7% success rate in distinction of Shigella and EIEC. A novel, and particularly successful marker was a <jats:italic>Shigella<\/jats:italic>\u2010specific deletion in the spermidine acetyltransferase gene <jats:italic>speG<\/jats:italic>, reflecting its metabolic decay. For <jats:italic>Shigella<\/jats:italic> serotype prediction, the multiplex assay scored a sensitivity and specificity of 96.6% and 98.4%, respectively. All discrepancies were analyzed with whole\u2010genome sequencing and shown to be related to causative mutations (stop codons, indels, and promoter mutations) in glycosyltransferase genes. This observation spurred the development of an in silico workflow which extracts the <jats:italic>Shigella<\/jats:italic> serotype from Next\u2010Generation Sequencing (NGS) data, taking into account gene functionality. Both tools will be implemented in the workflow of the NRC, and will play a major role in the shift from phenotypic to genotyping\u2010based surveillance of shigellosis in Belgium.<\/jats:p>","DOI":"10.1002\/mbo3.807","type":"journal-article","created":{"date-parts":[[2019,3,29]],"date-time":"2019-03-29T04:11:18Z","timestamp":1553832678000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Shifting national surveillance of Shigella infections toward geno\u2010serotyping by the development of a tailored Luminex assay and NGS workflow"],"prefix":"10.1002","volume":"8","author":[{"given":"Eleonora","family":"Ventola","sequence":"first","affiliation":[{"name":"National Reference Centre of Salmonella and Shigella Brussels Belgium"},{"name":"Department of Biology and Biotechnology \u201cC. Darwin\u201d \u201cSapienza\u201d Universit\u00e0 di Roma Rome Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bert","family":"Bogaerts","sequence":"additional","affiliation":[{"name":"Transversal activities in Applied Genomics Brussels Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sigrid C. J.","family":"De Keersmaecker","sequence":"additional","affiliation":[{"name":"Transversal activities in Applied Genomics Brussels Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Vanneste","sequence":"additional","affiliation":[{"name":"Transversal activities in Applied Genomics Brussels Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nancy H. 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