The Pathogen-annotated Tracking Resource Network (PATRN) system: A web-based resource to aid food safety, regulatory science, and investigations of foodborne pathogens and disease G. Gopinath a , K. Hari d , R. Jain d , M.K. Mammel a , M.H. Kothary a , A.A. Franco a , C.J. Grim a, c , K.G. Jarvis a, c , V. Sathyamoorthy a , L. Hu a, c , A.R. Datta a , I.R. Patel a , S.A. Jackson a , J. Gangiredla a , M.L. Kotewicz a , J.E. LeClerc a, b , M. Wekell a , B.A. McCardell a , M.D. Solomotis a , B.D. Tall a, * a CFSAN, FDA, Laurel, MD 20708, USA b CFSAN, FDA, College Park, MD 20740, USA c Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA d cBio, Inc. Fremont, CA, USA article info Article history: Received 17 September 2012 Received in revised form 23 December 2012 Accepted 7 January 2013 Available online 23 January 2013 Keywords: Pathogen data analysis platform Web-based pathogen tracking database system abstract Investigation of foodborne diseases requires the capture and analysis of time-sensitive information on microbial pathogens that is derived from multiple analytical methods and sources. The web-based Pathogen-annotated Tracking Resource Network (PATRN) system (www.patrn.net) was developed to address the data aggregation, analysis, and communication needs important to the global food safety community for the investigation of foodborne disease. PATRN incorporates a standard vocabulary for describing isolate metadata and provides a representational schema for a prototypic data exchange standard using a novel data loading wizard for aggregation of assay and attribution information. PATRN currently houses expert-curated, high-quality “foundational datasets” consisting of published exper- imental results from conventional assays and next generation analysis platforms for isolates of Escher- ichia coli, Listeria monocytogenes, and Salmonella, Shigella, Vibrio and Cronobacter species. A suite of computational tools for data mining, clustering, and graphical representation is available. Within PATRN, the public curated data repository is complemented by a secure private workspace for user-driven an- alyses, and for sharing data among collaborators. To demonstrate the data curation, loading wizard features, and analytical capabilities of PATRN, three use-case scenarios are presented. Use-case scenario one is a comparison of the distribution and prevalence of plasmid-encoded virulence factor genes among 249 Cronobacter strains with similar attributes to that of nine Cronobacter isolates from recent cases obtained between March and October, 2010e2011. To highlight PATRN’s data management and trend finding tools, analysis of datasets, stored in PATRN as part of an ongoing surveillance project to identify the predominant molecular serogroups among Cronobacter sakazakii isolates observed in the USA is shown. Use-case scenario two demonstrates the secure workspace available for private users to upload and analyze sensitive data, and for collating cross-platform datasets to identify and validate congruent datapoints. SNP datasets from WGS assemblies and pan-genome microarrays are analyzed in a combi- natorial fashion to determine relatedness of 33 Salmonella enterica strains to six strains collected as part of an outbreak investigation. Use-case scenario three utilizes published surveillance results that describe the incidence and sources of O157:H7 E. coli isolates associated with a produce pre-harvest surveillance study that occurred during 2002e2006. In summary, PATRN is a web-based integrated platform con- taining tools for the management, analysis and visualization of data about foodborne pathogens. Published by Elsevier Ltd. 1. Introduction For purposes of optimal resource allocation, and for prioritizing research and intervention strategies, accurate information about the number of foodborne illnesses and their causative pathogens is * Corresponding author. Room 3607, MOD 1 Facility, Virulence Mechanisms Branch, (HFS-025), Division of Virulence Assessment, OARSA, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 MuirKirk Rd., Laurel, MD 20708, USA. Tel.: þ1 301 210 7880. E-mail addresses: ben.tall@fda.hhs.gov, shakee2326@aol.com (B.D. Tall). Contents lists available at SciVerse ScienceDirect Food Microbiology journal homepage: www.elsevier.com/locate/fm 0740-0020/$ e see front matter Published by Elsevier Ltd. http://dx.doi.org/10.1016/j.fm.2013.01.001 Food Microbiology 34 (2013) 303e318