title: Array-based binary analysis for bacterial typing.
abstract: An allele-specific oligonucleotide microarray was developed for rapid typing of pathogens based on analysis of genomic variations. Using a panel of Escherichia coli strains as a model system, selected loci were sequenced to uncover differences, such as single- or multiple-nucleotide polymorphisms as well as insertion/deletions (indels). While typical genomic profiling experiments employ specific sequences targeted to genomic DNA unique to a single strain or virulent gene, the present array is designed to type bacteria based on a patterned signature response across multiple loci. In the signature concept, all strains are interrogated by hybridizing their amplified DNA to an array containing multiple probe sequences. Allele-specific oligonucleotide probe sequences targeting each of these variable regions were synthesized and included in a custom fiber-optic array. For each locus, a set of specific probe sequences is selected, such that hybridization gives a binary signal/no signal response to each of the probes. Using this strategy for multiple loci, many pathogens or microorganisms could be classified using a limited number of probes. Because of the advantages of the fiber-optic array platform over other array formats, including sensitivity and speed, the platform described in this paper is capable of supporting a high-throughput diagnostic strategy.
authors.affiliation: Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, MA 02155, USA.
authors.forename: Jason R E
authors.initials: JR
authors.lastname: Shepard
authors.forename: Yael
authors.initials: Y
authors.lastname: Danin-Poleg
authors.forename: Yechezkel
authors.initials: Y
authors.lastname: Kashi
authors.forename: David R
authors.initials: DR
authors.lastname: Walt
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods*; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA