title: Interrogating genomic diversity of E. coli O157:H7 using DNA tiling arrays.
abstract: Here, we describe a novel microarray-based approach for investigating the genomic diversity of Escherichia coli O157:H7 in a semi-high throughput manner using a high density, oligonucleotide-based microarray. This microarray, designed to detect polymorphisms at each of 60,000 base-pair (bp) positions within an E. coli genome, is composed of overlapping 29-mer oligonucleotides specific for 60 equally spaced, 1000-bp loci of the E. coli O157:H7 strain EDL933 chromosome. By use of a novel 12-well microarray that permitted the simultaneous investigation of 12 strains, the genomes of 44 individual isolates of E. coli O157:H7 were interrogated. These analyses revealed more than 150 single nucleotide polymorphisms (SNPs) and several deletions and amplifications in the test strains. Pyrosequencing was used to confirm the usefulness of the novel SNPs by determining their allelic frequency among a collection of diverse isolates of E. coli O157:H7. The tiling DNA microarray system would be useful for the tracking and identification of individual strains of E. coli O157:H7 needed for forensic investigations.
authors.affiliation: Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.forename: Mark K
authors.initials: MK
authors.lastname: Mammel
authors.forename: Isha R
authors.initials: IR
authors.lastname: Patel
authors.forename: Tammy
authors.initials: T
authors.lastname: Mays
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Albert
authors.forename: J Eugene
authors.initials: JE
authors.lastname: LeClerc
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Cebula
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics; D022801:Complementarity Determining Regions / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics*; D019453:Escherichia coli O157 / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D006824:Hybridization, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017384:Sequence Deletion / Q000235:genetics
chemical_list: D022801:Complementarity Determining Regions; D004269:DNA, Bacterial