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Design of a Seven-Genome Escherichia coli Microarray for Comparative Genomic Profiling

Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Lyngby, Denmark,¹ Norwegian School of Veterinary Science, P.O. Box 8146 Dep., N-0033 Oslo, Norway²

Received 17 July 2006/ Accepted 28 August 2006

We describe the design and evaluate the use of a high-density oligonucleotide microarray covering seven sequenced Escherichia coli genomes in addition to several sequenced E. coli plasmids, bacteriophages, pathogenicity islands, and virulence genes. Its utility is demonstrated for comparative genomic profiling of two unsequenced strains, O175:H16 D1 and O157:H7 3538 (stx₂::cat) as well as two well-known control strains, K-12 W3110 and O157:H7 EDL933. By using fluorescently labeled genomic DNA to query the microarrays and subsequently analyze common virulence genes and phage elements and perform whole-genome comparisons, we observed that O175:H16 D1 is a K-12-like strain and confirmed that its 3538 (stx₂::cat) phage element originated from the E. coli 3538 (stx₂::cat) strain, with which it shares a substantial proportion of phage elements. Moreover, a number of genes involved in DNA transfer and recombination was identified in both new strains, providing a likely explanation for their capability to transfer 3538 (stx₂::cat) between them. Analyses of control samples demonstrated that results using our custom-designed microarray were representative of the true biology, e.g., by confirming the presence of all known chromosomal phage elements as well as 98.8 and 97.7% of queried chromosomal genes for the two control strains. Finally, we demonstrate that use of spatial information, in terms of the physical chromosomal locations of probes, improves the analysis.

Published ahead of print on 8 September 2006.