Custom Microarray Allows Scientists to Identify Different Strains of
the Potentially Fatal Foodborne Pathogens
Affymetrix, Inc. (Nasdaq:AFFX) 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.
