GeneAtlas® Microarray Identifies and Subtypes Pathogenic E. coli

Affymetrix, Inc. has a multi-genome pathogen microarray available, designed by the Food and Drug Administration's Center for Food Safety and Applied Nutrition (CFSAN) and built by Affymetrix, for the detection and identification of pathogenic E. coli during foodborne outbreaks. These high density DNA-based microarray assays, for use with the GeneAtlas® Personal Microarray System, can detect, discriminate, and uniquely identify strains of E. coli on food products, clinical samples, and environmental samples in real-time outbreak situations.

This custom designed microarray contains tens of thousands of biomarkers mined from over 250 E. coli whole genome sequences, making it a true representation of the E. coli PanGenome. In addition to containing every known E. coli gene (>40,000), the design contains over 10,000 highly informative single nucleotide polymorphism (SNP) biomarkers. As a result, this hybrid array is highly discriminatory as well as biologically and evolutionarily informative. Furthermore, by employing Affymetrix array strip technology, the microarray assay is rapid (<24 hours), high throughput, semi-automated, and affordable.

The Minimal Signature E. coli Array (FDA-ECID) is the culmination of seven years of research and development by FDA's Division of Molecular Biology. The choice of targets to include on the pathogen identification array were selected as part of a rational design strategy based in large part on data obtained from past outbreak investigations where several previous Affymetrix custom array designs were utilized; including GeneChip® E. coli Genome 2.0 Array and the FDA-E. coli-Shigella (ECSG) array.

In real-time outbreak investigations, FDA's comparative genomic studies demonstrate rapid identification and clear discrimination between clinically, temporally, and geographically distinct events.

The array is a complete package for genomic-scale molecular subtyping of foodborne pathogens. When used with FDA's Microbial ArrayTrack™ software, users will have a turn-key, customized solution for microarray data storage, analysis, and visualization.

Microbial ArrayTrack was developed by bioinformaticists at FDA's National Center for Toxicological Research (NCTR) from the ground-up as a high-end microarray data storage, analysis, and visualization package. As such, Microbial ArrayTrack now contains ECID-specific annotations in conjunction with a customized and validated data analysis and visualization solution.