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Biodefense Grant Funds Study of Salmonella Genomes
By Donna Bernstein

Researchers will profile the genomes of Salmonella strains like S. typhimurium, shown here in red invading human cells in culture.

The US National Institutes of Health has funded a study to characterize the genomes of dozens of strains of Salmonella bacteria using DNA microarray technology.

Perlegen Sciences, Inc., of Mountain View, California, will use a biodefense research grant from the National Institute of Allergy and Infectious Diseases to develop a database of genomic “fingerprints” that could potentially be used to trace the origins of Salmonella outbreaks that occur naturally in the population or as the result of a bioterrorism attack.

There are some 2,000 strains of Salmonella bacteria that can cause disease in humans. The pathogen is a leading cause of food poisoning and can cause typhoid fever. Concerns have been raised about its possible use as a bioterrorism agent because drug-resistant strains of Salmonella seem to be increasing.

Salmonella are included in the list of "agents associated with biocrimes and bioterrorism" by the US Centers for Disease Control and Prevention in Atlanta. The bacteria were used in an incident in Oregon in 1984 that left 45 people hospitalized.

According to Paul Cusenza, Perlegen's Vice President of Alliance Management, the database will initially have between 100 and 200 strains, including samples isolated from nature and those used in laboratory research. A genomic fingerprint is a unique collection of genomic variants, such as single nucleotide polymorphisms, or SNPs.

Andrew B. Sparks of Perlegen was awarded $500,000 for the study, according to an NIH Web site.

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In the event of an outbreak or an attack involving Salmonella, investigators could in a matter of minutes compare strains isolated from victims to those in the database. The information could not only help them trace the origins of an attack but also determine the most effective antidote or treatment.

To develop the genomic fingerprints, Perlegen scientists will use high-density DNA microarrays, which can differentiate between Salmonella strains that may differ by only a few single units of DNA. Microarrays, also called gene chips, contain bits of DNA that can be used to profile the content of a genome.

"The most exciting thing is being able to apply microarray technology to so many different areas, like helping to defend against terrorists," says Paul Cusenza.

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