Broad spectrum microarray for fingerprint-based bacterial species identification

Abstract

BackgroundMicroarrays are powerful tools for DNA-based molecular diagnostics and identification of pathogens. Most target a limited range of organisms and are based on only one or a very few genes for specific identification. Such microarrays are limited to organisms for which specific probes are available, and often have difficulty discriminating closely related taxa. We have developed an alternative broad-spectrum microarray that employs hybridisation fingerprints generated by high-density anonymous markers distributed over the entire genome for identification based on comparison to a reference database.ResultsA high-density microarray carrying 95,000 unique 13-mer probes was designed. Optimized methods were developed to deliver reproducible hybridisation patterns that enabled confident discrimination of bacteria at the species, subspecies, and strain levels. High correlation coefficients were achieved between replicates. A sub-selection of 12,071 probes, determined by ANOVA and class prediction analysis, enabled the discrimination of all samples in our panel. Mismatch probe hybridisation was observed but was found to have no effect on the discriminatory capacity of our system.ConclusionsThese results indicate the potential of our genome chip for reliable identification of a wide range of bacterial taxa at the subspecies level without laborious prior sequencing and probe design. With its high resolution capacity, our proof-of-principle chip demonstrates great potential as a tool for molecular diagnostics of broad taxonomic groups.

Metatranscriptomic Analysis of the Response of River Biofilms to Pharmaceutical Products, Using Anonymous DNA Microarrays

“…The advantages of such an approach are 2-fold: first, there is no need for previous environmental genomic knowledge; second, a large number of samples can be examined without tedious metatranscriptomic sequencing each time a new sample is analyzed. Previously, anonymous microarrays for analyses of mixed microbial communities were used mainly at the genomic level to detect or differentiate particular species (6,(16)(17)(18)27). More recently, a 2,000-probe microarray made of 2.0-kb anonymous fragments was successfully used to fingerprint a simple sludge sample (40).…”

Computational Sequence Design Techniques for DNA Microarray Technologies

“…Areas that have benefited from the use of microarrays include gene discovery (Andrews et al, 2000;Yano, Imai, Shimizu, and Hanashita, 2006), disease diagnosis (Yoo, Choi, Lee, and Yoo, 2009), species identification (Pasquer, Pelludat, Duffy, and Frey, 2010;Teletchea1, Bernillon, Duffraisse, Laudet, and Hänni, 2008) and toxico-genomics (Jang, Nde, Toghrol, and Bentley, 2008;Neumanna and Galvez, 2002).…”