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Title: FDA Bioinformatics Tool for Microbial Genomics Research on Molecular Characterization of Bacterial Foodborne Pathogens Using Microarrays

Author
item FANG, HONG - Icf International
item XU, JOSHUA - Icf International
item DING, DON - Icf International
item JACKSON, SCOTT - Us Food & Drug Administration (FDA)
item PATEL, ISHA - Us Food & Drug Administration (FDA)
item Frye, Jonathan
item ZOU, WEN - Us Food & Drug Administration (FDA)
item NAYAK, RAJESH - Us Food & Drug Administration (FDA)
item FOLEY, STEVEN - Us Food & Drug Administration (FDA)
item CHEN, JAMES - Us Food & Drug Administration (FDA)

Submitted to: BMC Bioinformatics
Publication Type: Proceedings
Publication Acceptance Date: 4/29/2010
Publication Date: 10/7/2010
Citation: Fang, H., Xu, J., Ding, D., Jackson, S.A., Patel, I.R., Frye, J.G., Zou, W., Nayak, R., Foley, S., Chen, J. 2010. FDA Bioinformatics Tool for Microbial Genomics Research on Molecular Characterization of Bacterial Foodborne Pathogens Using Microarrays. BMC Bioinformatics. 11(Suppl 6):S4:1-11.

Interpretive Summary: Microbial genomics is offering insights into the emergence and spread of foodborne pathogens during outbreaks. However it often creates a large amount of data that is difficult to understand. The Food and Drug Administration (FDA) developed ArrayTrackTM to provide researches a way to manage, analyze, and interpret genomic data for mammalian species. Recently ArrayTrackTM has been modified to manage and analyze genomics data from bacterial pathogens of human, animal, and food origin. ArrayTrack was adapted by populating it with data from public domains which facilitate the detection and characterization of microbial pathogens. ArrayTrack’s data processing and visualization tools were enhanced with analysis tools specific for bacteria of interest. These specific tools were evaluated on data generated from a custom test array (FDA-ECSG) previously developed within the FDA. The FDA-ECSG array represents 32 complete genomes of Escherichia coli and Shigella. The new tools were also used to analyze microarray data focusing on antimicrobial resistance genes from Salmonella isolates in a poultry production environment using a universal Antimicrobial Resistance Biochip developed by the United States Department of Agriculture (USDA). This demonstrated ArrayTrack‘s ability to analyze a variety of different biochip platforms, and thus will improve the ability of the FDA to rapidly identify foodborne bacteria and their genetic traits (i.e. antimicrobial resistance, virulence, etc.) during food outbreak investigations. ArrayTrackTM is free to use and available to public, private, and academic researchers.

Technical Abstract: Background: Advances in microbial genomics and bioinformatics are offering greater insights into the emergence and spread of foodborne pathogens in outbreak scenarios. The Food and Drug Administration (FDA) has developed the genomics tool ArrayTrackTM, which provides extensive functionalities to manage, analyze, and interpret genomic data for mammalian species. ArrayTrackTM has been widely adopted by the research community and used for pharmacogenomics data review in the FDA’s Voluntary Genomics Data Submission program. Results: ArrayTrackTM has been extended to manage and analyze genomics data from bacterial pathogens of human, animal, and food origin. It was populated with bioinformatics data from public domains such as NCBI, Swissprot Protein, KEGG Pathway, and Gene Ontology to facilitate pathogen detection and characterization. ArrayTrack’s data processing and visualization tools were enhanced with analysis capabilities specific for microbial genomics such as hierarchical clustering analysis (HCA), flag concordance heat maps, and mixed scatter plots. These specific functionalities were evaluated on data generated from a custom Affymetrix array (FDA-ECSG) previously developed within the FDA. The FDA-ECSG array represents 32 complete genomes of Escherichia coli and Shigella. The new functions were also used to analyze microarray data focusing on antimicrobial resistance genes from Salmonella isolates in a poultry production environment using a universal Antimicrobial Resistance Biochip developed by the United States Department of Agriculture (USDA). Conclusion: The application of ArrayTrackTM to different biochip platforms demonstrates its utility in microbial genomics research, and thus will improve the capabilities of the FDA to rapidly identify foodborne bacteria and their genetic traits (i.e. antimicrobial resistance, virulence, etc.) during outbreak investigations. ArrayTrackTM is free to use and available to public, private, and academic researchers at http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack.