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

PloS One
Moez SanaaJane M Van Doren

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/).

References

Feb 8, 2014·PloS One·Pimlapas LeekitcharoenphonFrank M Aarestrup
Jan 18, 2016·Trends in Microbiology·Eduardo CorelEric Bapteste
Apr 20, 2016·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Brendan R JacksonPeter Gerner-Smidt
May 1, 2016·Nucleic Acids Research·Bruno Ribeiro-GonçalvesJoão André Carriço
Mar 30, 2017·Microbial Genomics·Silvia ArgimónDavid M Aanensen
May 26, 2017·Frontiers in Microbiology·Eric L StevensSteven Musser
Sep 20, 2017·Foodborne Pathogens and Disease·LaTonia Clay RichardsonDana Cole
Oct 17, 2017·International Journal of Food Microbiology·Heidy M W den BestenJeanne-Marie Membré
Apr 29, 2018·International Journal of Food Microbiology·Nabila HaddadMarcel H Zwietering
May 24, 2018·Bioinformatics·James HadfieldRichard A Neher

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Citations

Oct 3, 2019·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Adriana CabalAriane Pietzka
Oct 16, 2020·Genome Research·Zhemin ZhouMark Achtman
Aug 12, 2019·Microbes and Infection·Adrian EgliRoger Stephan

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Software Mentioned

VisNetwok R package
Social Network Analysis ( SNA )
Sankey Plots
igraph
IRIDA
R Shiny
PHYLOViZ Online
GenomeTrakr
GrapeTree
MSTree

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