Skip to main content

TECHNOLOGY AND CODE article

Front. Bioinform.
Sec. Data Visualization
Volume 4 - 2024 | doi: 10.3389/fbinf.2024.1415078

RIPS (Rapid Intuitive Pathogen Surveillance): a tool for surveillance of genome sequence data from foodborne bacterial pathogens

Provisionally accepted
Tim Muruvanda Tim Muruvanda *Hugh Rand Hugh Rand James Pettengill James Pettengill Arthur Pightling Arthur Pightling
  • Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, United States

The final, formatted version of the article will be published soon.

    Monitoring data submitted to the National Center for Biotechnology Information's Pathogen Detection whole-genome sequence database, which includes the foodborne bacterial pathogens Listeria monocytogenes, Salmonella enterica, and Escherichia coli, 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.

    Keywords: Whole-genome sequencing, Listeria monocytogenes, Salmonella enterica, Escherichia coli, epidemiologic surveillance, Outbreak detection, foodborne pathogens, Food Safety

    Received: 09 Apr 2024; Accepted: 30 Jul 2024.

    Copyright: © 2024 Muruvanda, Rand, Pettengill and Pightling. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Tim Muruvanda, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, 20740, Maryland, United States

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.