R-051. Design and Development of a Novel High Density Microarray Representative of over 75 Complete Genome Sequences of Salmonella and Escherichia coli: Identifying Genes and SNPs

S. A. Jackson, M. Mammel, I. Patel, J. E. LeClerc, T. A. Cebula;
US FDA, Laurel, MD.

Background: Escherichia coli and Salmonellae are recognized as two of the major bacterial foodborne pathogens in the United States, causing a combined total of over 2 million cases of illness and 600 deaths annually. The ability of these pathogens to rapidly adapt to novel environmental niches has recently been made apparent by their contamination of foods not traditionally associated with enteric illness, such as fresh produce. More problematic is the fact that multidrug resistance (MDR) is being increasingly identified among numerous E. coli pathotypes and Salmonella serotypes, potentially compromising antimicrobial therapy. To investigate their genomic diversity and evolutionary history, we have developed a comprehensive DNA microarray for analysis of these enteric pathogens. Methods: An Affymetrix DNA microarray containing over 2.5 million features was developed. It represents sequences of 178,000 genes from 28 whole genomes and 46 plasmids of E. coli and 10 whole genomes and 16 plasmids of Shigella; 177,000 genes from 35 whole genomes and 58 plasmids/integrons of Salmonella; 13,000 intragenic regions; and 2400 antibiotic resistance genes and 2200 virulence genes from various bacterial sources (GenBank references and Los Alamos Virulence Database). Sequence analysis identified over 60,000 unique genes, each of which is represented on the array using 11 independent 25-mer probe pairs. Additionally, a tiling strategy was utilized to identify genomic changes at the single-nucleotide level in approximately 2400 core genes highly conserved in Salmonella and E. coli. Whole genome sequenced strains, including pairs of MDR and susceptible strains in the case of Salmonella, were used to validate this array. Results and Conclusions: The results demonstrate the usefulness of a comprehensive DNA microarray representing pangenomic elements for identification and characterization of foodborne pathogens. The array serves as a diagnostic tool for identification of strains important to public health, as well as providing a means to delimit the core genes of a pathogenic group or to identify genes that specify the particular ‘personality’ of strains.