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It is essential to determine the species of <jats:italic>Shigella<\/jats:italic> in outbreaks and food safety surveillance systems. The available immunological and molecular methods for identifying <jats:italic>Shigella<\/jats:italic> species are relatively complicated, expensive and time-consuming. High resolution melting (HRM) assay is a rapid, cost-effective, and easy to perform PCR-based method that has recently been used for the differentiation of bacterial species. In this study, we designed and developed a PCR-HRM assay targeting <jats:italic>rrsA<\/jats:italic> gene to distinguish four species of 49 <jats:italic>Shigella<\/jats:italic> isolates from clinical and food samples and evaluated the sensitivity and specificity of the assay. The assay demonstrated a good analytical sensitivity with 0.01\u20130.1\u00a0ng of input DNA template and an analytical specificity of 100% to differentiate the <jats:italic>Shigella<\/jats:italic> species. The PCR-HRM assay also was able to identify the species of all 49 Shigella isolates from clinical and food samples correctly. Consequently, this rapid and user-friendly method demonstrated good sensitivity and specificity to differentiate species of the <jats:italic>Shigella<\/jats:italic> isolates from naturally contaminated samples and has the potential to be implemented in public health and food safety surveillance systems.<\/jats:p>","DOI":"10.1038\/s41598-021-04484-1","type":"journal-article","created":{"date-parts":[[2022,1,10]],"date-time":"2022-01-10T11:04:32Z","timestamp":1641812672000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Development of high-resolution melting (HRM) assay to differentiate the species of Shigella isolates from stool and food samples"],"prefix":"10.1038","volume":"12","author":[{"given":"Babak","family":"Pakbin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Afshin Akhondzadeh","family":"Basti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali","family":"Khanjari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wolfram Manuel","family":"Br\u00fcck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leila","family":"Azimi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdollah","family":"Karimi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,1,10]]},"reference":[{"key":"4484_CR1","first-page":"1","volume":"8","author":"KS Baker","year":"2018","unstructured":"Baker, K. 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