GenomeGraphR: A user-friendly open-source web application for foodborne pathogen whole genome sequencing data integration, analysis, and visualization

PLoS One. 2019 Feb 28;14(2):e0213039. doi: 10.1371/journal.pone.0213039. eCollection 2019.

Abstract

Food safety risk assessments and large-scale epidemiological investigations have the potential to provide better and new types of information when whole genome sequence (WGS) data are effectively integrated. Today, the NCBI Pathogen Detection database WGS collections have grown significantly through improvements in technology, coordination, and collaboration, such as the GenomeTrakr and PulseNet networks. However, high-quality genomic data is not often coupled with high-quality epidemiological or food chain metadata. We have created a set of tools for cleaning, curation, integration, analysis and visualization of microbial genome sequencing data. It has been tested using Salmonella enterica and Listeria monocytogenes data sets provided by NCBI Pathogen Detection (160,000 sequenced isolates in 2018). GenomeGraphR presents foodborne pathogen WGS data and associated curated metadata in a user-friendly interface that allows a user to query a variety of research questions such as, transmission sources and dynamics, global reach, and persistence of genotypes associated with contamination in the food supply and foodborne illness across time or space. The application is freely available (https://fda-riskmodels.foodrisk.org/genomegraphr/).

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Databases, Genetic
  • Food Microbiology*
  • Food Safety*
  • Foodborne Diseases / epidemiology
  • Foodborne Diseases / microbiology*
  • Genome, Bacterial
  • Humans
  • Internet
  • Listeria monocytogenes / genetics
  • Listeria monocytogenes / isolation & purification
  • Listeriosis / epidemiology
  • Listeriosis / microbiology
  • Metadata
  • Molecular Epidemiology
  • Polymorphism, Single Nucleotide
  • Risk Assessment
  • Salmonella Food Poisoning / epidemiology
  • Salmonella Food Poisoning / microbiology
  • Salmonella enterica / genetics
  • Software
  • User-Computer Interface
  • Whole Genome Sequencing / statistics & numerical data*

Grants and funding

The study was supported in part by an appointment to the Research Participation Program of Francisco Garcés Vega (FGV) at the Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration (CFSAN FDA), administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the U.S. Department of Energy and FDA and in part by support through Contracts HHFS223201710033I (Versar, Inc., FGV) and HHFS223201710033I (Goldbelt C6, LLC, MS and RP).