An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays.
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 a genomics tool, ArrayTrack™, which provides extensive functionalities to manage, analyze, and interpret genomic data for mammalian species. ArrayTrack™ has been widely adopted by the research community and used for pharmacogenomics data review in the FDA's Voluntary Genomics Data Submission program.


RESULTS
ArrayTrack™ 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 databases such as NCBI, Swiss-Prot, KEGG Pathway, and Gene Ontology to facilitate pathogen detection and characterization. ArrayTrack™'s data processing and visualization tools were enhanced with analysis capabilities designed specifically for microbial genomics including flag-based 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 microarray developed by the United States Department of Agriculture (USDA).


CONCLUSIONS
The application of ArrayTrack™ to different microarray 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 (e.g., antimicrobial resistance, virulence, etc.) during outbreak investigations. ArrayTrack™ is free to use and available to public, private, and academic researchers at http://www.fda.gov/ArrayTrack.
Fang
Hong
H
Z-Tech Corporation, ICF International Company at National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA.
Xu
Joshua
J
Ding
Don
D
Jackson
Scott A
SA
Patel
Isha R
IR
Frye
Jonathan G
JG
Zou
Wen
W
Nayak
Rajesh
R
Foley
Steven
S
Chen
James
J
Su
Zhenqiang
Z
Ye
Yanbin
Y
Turner
Steve
S
Harris
Steve
S
Zhou
Guangxu
G
Cerniglia
Carl
C
Tong
Weida
W
D030541:Databases, Genetic; D030562:Databases, Protein; D005517:Foodborne Diseases / Q000382:microbiology; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software; D014481:United States; D014486:United States Food and Drug Administration