{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T06:58:56Z","timestamp":1764053936699,"version":"3.41.2"},"reference-count":25,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,8,9]],"date-time":"2024-08-09T00:00:00Z","timestamp":1723161600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>Monitoring data submitted to the National Center for Biotechnology Information\u2019s Pathogen Detection whole-genome sequence database, which includes the foodborne bacterial pathogens <jats:italic>Listeria<\/jats:italic> monocytogenes, <jats:italic>Salmonella enterica<\/jats:italic>, and <jats:italic>Escherichia coli<\/jats:italic>, has proven effective for detecting emerging outbreaks. As part of the submission process, new sequence data are typed using a whole-genome multi-locus sequence typing scheme and clustered with sequences already in the database. Publicly available text files contain the results of these analyses. However, contextualizing and interpreting this information is complex. We present the Rapid Intuitive Pathogen Surveillance (RIPS) tool, which shows the results of the NCBI Rapid Reports, along with appropriate metadata, in a graphical, interactive dashboard. RIPS makes the information in the Rapid Reports useful for real-time surveillance of genome sequence databases.<\/jats:p>","DOI":"10.3389\/fbinf.2024.1415078","type":"journal-article","created":{"date-parts":[[2024,8,9]],"date-time":"2024-08-09T05:19:07Z","timestamp":1723180747000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["RIPS (rapid intuitive pathogen surveillance): a tool for surveillance of genome sequence data from foodborne bacterial pathogens"],"prefix":"10.3389","volume":"4","author":[{"given":"Tim","family":"Muruvanda","sequence":"first","affiliation":[]},{"given":"Hugh","family":"Rand","sequence":"additional","affiliation":[]},{"given":"James","family":"Pettengill","sequence":"additional","affiliation":[]},{"given":"Arthur","family":"Pightling","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2024,8,9]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1975","DOI":"10.1128\/JCM.00081-16","article-title":"Practical value of food pathogen traceability through building a whole-genome sequencing network and database","volume":"54","author":"Allard","year":"2016","journal-title":"J. Clin. Microbiol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1089\/fpd.2019.2650","article-title":"Interpretation of whole-genome sequencing for enteric Disease surveillance and outbreak investigation","volume":"16","author":"Besser","year":"2019","journal-title":"Foodborne Pathog. Dis."},{"key":"B3","unstructured":"Shiny: web application framework for R\n          \n          \n            \n              Chang W\n              C. 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Food Prot."},{"key":"B7","unstructured":"NCBI insights\n          \n          \n          2017"},{"key":"B8","unstructured":"Index of\/pathogen\/Results\/Escherichia_coli_Shigella\/Rapid_reports"},{"key":"B9","unstructured":"Index of\/pathogen\/Results\/Listeria\/Rapid_reports"},{"key":"B10","unstructured":"Index of\/pathogen\/Results\/Salmonella\/Rapid_reports"},{"key":"B11","unstructured":"National center for Biotechnology information pathogen detection browser"},{"key":"B12","unstructured":"README for NCBI pathogen detection"},{"key":"B13","doi-asserted-by":"publisher","first-page":"1482","DOI":"10.3389\/fmicb.2018.01482","article-title":"Interpreting whole-genome sequence analyses of foodborne bacteria for regulatory applications and outbreak investigations","volume":"9","author":"Pightling","year":"2018","journal-title":"Front. 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