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Published online 22 March 2004

Nucleic Acids Research, 2004, Vol. 32, No. 5 1848-1856
Oxford University Press

Quantitative oligonucleotide microarray fingerprinting of Salmonella enterica isolates

Alan Willse1, Timothy M. Straub2, Sharon C. Wunschel1, Jack A. Small2, Douglas R. Call3, Don S. Daly1 and Darrell P. Chandler*,4

1 Statistics and Quantitative Sciences Group and 2 Environmental Microbiology Group, Pacific Northwest National Laboratory, Richland, WA 99352, USA, 3 Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA and 4 Biochip Technology Center, Argonne National Laboratory, Building 202, 9700 South Cass Avenue, Argonne, IL 60439, USA

*To whom correspondence should be addressed. Tel: +1 630 252 4229; Fax: +1 630 252 9155; Email: dchandler{at}anl.gov

Received November 24, 2003; Revised February 3, 2004; Accepted February 17, 2004

We report on a genome-independent microbial fingerprinting method using nucleic acid microarrays for microbial forensics and epidemiology applications and demonstrate that the microarray method provides high resolution differentiation between closely related microorganisms, using Salmonella enterica strains as the test case. In replicate trials we used a simple 192 probe nonamer array to construct a fingerprint library of 25 closely related Salmonella isolates. Controlling false discovery rate for multiple testing at {alpha} = 0.05, at least 295 of 300 pairs of S.enterica isolate fingerprints were found to be statistically distinct using a modified Hotelling T2 test. Although most pairs of Salmonella fingerprints are found to be distinct, forensic applications will also require a protocol for library construction and reliable microbial classification against a fingerprint library. We outline additional steps required to produce such a protocol.


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