title: Quantitative oligonucleotide microarray fingerprinting of Salmonella enterica isolates.
abstract: 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.
authors.affiliation: Statistics and Quantitative Sciences Group, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Alan
authors.initials: A
authors.lastname: Willse
authors.forename: Timothy M
authors.initials: TM
authors.lastname: Straub
authors.forename: Sharon C
authors.initials: SC
authors.lastname: Wunschel
authors.forename: Jack A
authors.initials: JA
authors.lastname: Small
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Call
authors.forename: Don S
authors.initials: DS
authors.lastname: Daly
authors.forename: Darrell P
authors.initials: DP
authors.lastname: Chandler
mesh_terms: D001499:Bayes Theorem; D016172:DNA Fingerprinting / Q000379:methods*; D003627:Data Interpretation, Statistical; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D019779:Salmonella enterica / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*