J. Craig Venter Institute offers new Affymetrix array for faster identification of E. coli and shigella

Affymetrix, Inc. and the National Institute of Allergy and Infectious Diseases (NIAID)-supported Pathogen Functional Genomics Resource Center (PFGRC) at the J. Craig Venter Institute (JCVI) today announced the launch of the Affymetrix FDA-ECSG custom microarray for identifying and discriminating between different strains of E. coli and Shigella.

This custom array was developed for the FDA and is now available to researchers worldwide. Affymetrix and JCVI have collaborated to make this array available from the PFGRC at no cost to researchers through the NIAID-sponsored PFGRC microarray application process.

Approximately 165 million people fall ill and more than a million die worldwide each year after consuming foods contaminated with Escherichia coli (E. coli) and Shigella.¹ These pathogens’ ability to rapidly adapt to new environments requires highly parallel analysis methods to accurately assess their genomic diversity and genomic content.

A custom Affymetrix microarray was developed and validated by analysis of sequenced strains. Using this array, FDA researchers interrogated a collection of E. coli and Shigella strains that were associated with temporally and geographically diverse outbreaks, including the 2006 outbreaks of E. coli linked to lettuce and spinach. The spinach-related outbreak led to 199 infections in 26 states and contributed to three deaths.²

This array design allowed researchers to accurately detect each gene target represented on the array and differentiate closely related strains within a pathotype. While most of the isolates of E. coli O157:H7 associated with the spinach outbreak were indistinguishable, several clinical isolates contained apparent chromosomal rearrangements.

“The results of this investigation carried out by FDA Center for Food Safety and Applied Nutrition (CFSAN) researchers using the Affymetrix FDA-ECSG array demonstrate its great potential for use in evolutionary, epidemiological, and forensics studies for strain identification and discrimination,” said Robert Fleischmann of the JCVI and co-director of the PFGRC.

“We are proud of the researchers who created this custom array that enables identification and discrimination between more strains of E. coli and Shigella than traditional techniques,” said Kevin King, president and CEO of Affymetrix. “To date, Affymetrix has enabled the design of more than 750 custom arrays, and this array is significant as it enables scientists to know more about two foodborne pathogens which have a large impact on human health.”

Affymetrix FDA-ECSG custom microarrays are provided for research purposes only and are not for use in diagnostic procedures. For more information on the array, and to obtain it via the NIAID-sponsored PGFRC microarray application process, visit:

http://pfgrc.jcvi.org/index.php/microarray/affy_array_description/ecoli_shigella/version1.html

¹ Click on the following link and then on the next link for a PDF of the poster containing the FDA research:

http://pfgrc.jcvi.org/index.php/microarray/affy_array_description/ecoli_shigella/version1.html

²http://www.cdc.gov/foodborne/ecolispinach/100606.htm