RIPS (rapid intuitive pathogen surveillance): a tool for surveillance of genome sequence data from foodborne bacterial pathogens.

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.
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
(Copyright © 2024 Muruvanda, Rand, Pettengill and Pightling.)