Universal microarray for pattern-based bacterial species identification

ABSTRACT: Microarrays have become a powerful tool for DNA-based molecular diagnostics and identification of pathogens. However, most of them target a limited range of organisms and are generally based on only one or very few genes for organism identification. Although such microarrays are proven tools for species identification, they suffer from the fact that identification is only possible for organisms for which probes were specifically pre-developed. Furthermore, this approach often leads to problems with taxonomic-level resolution with insufficient diagnostic differences between closely related taxa found in the commonly used DNA sequences. An alternative strategy is to use the hybridisation pattern generated by many different anonymous markers distributed over the entire genome for identification based on comparison to a type database. We realised this strategy using a high density microarray containing 95,000 different 13-mer probes. Here, we demonstrate the specificity of our microarray based on results obtained with nine different bacterial species and strains. The hybridisation patterns allowed clear differentiation at the strain and even variant level. The reproducibility of our system was high as shown by high correlation coefficients between replicates, despite the occurrence of mismatch hybridisation. The results indicate the potential for identification of all bacterial taxa at the subspecies level using our universal microarray.

ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium Escherichia coli K-12 synthetic construct Pantoea stewartii Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Escherichia coli B Pantoea agglomerans Micrococcus luteus

PROVIDER: GSE15391 | GEO | 2010/03/16

SECONDARY ACCESSION(S): PRJNA117129

REPOSITORIES: GEO