High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis
Creators: name: Friedrich, Torben
name: Rahmann, Sven
name: Weigel, Wilfried
name: Rabsch, Wolfgang
name: Fruth, Angelika
name: Ron, Eliora
name: Gunzer, Florian
name: Dandekar, Thomas
name: Hacker, Jörg
name: Müller, Tobias
name: Dobrindt, Ulrich
Publisher: name: Robert Koch-Institut, Infektionsepidemiologie
Year: 2010
Subjects: subject: Bacterial/genetics
subject: Regression Analysis
subject: Drug Resistance
subject: Oligonucleotide Array Sequence Analysis/methods
subject: Bacterial Typing Techniques
subject: Genome
subject: Bacterial/drug effects
subject: Anti-Infective Agents/pharmacology
subject: DNA Probes/metabolism
subject: DNA Bacterial/genetics
subject: Decision Trees
subject: Drug Resistance Bacterial/genetics
subject: Enterobacteriaceae/classification
subject: Enterobacteriaceae/drug effects
subject: Enterobacteriaceae/genetics
subject: Enterobacteriaceae/isolation &amp; purification
subject: High-Throughput Screening Assays/methods
subject: Molecular Diagnostic Techniques/methods
subject: Nucleic Acid Hybridization/drug effects
subject: 610 Medizin

description: Background: The Enterobacteriaceae comprise a large number of clinically relevant species with several individual subspecies. Overlapping virulence-associated gene pools and the high overall genome plasticity often interferes with correct enterobacterial strain typing and risk assessment. Array technology offers a fast, reproducible and standardisable means for bacterial typing and thus provides many advantages for bacterial diagnostics, risk assessment and surveillance. The development of highly discriminative broad-range microbial diagnostic microarrays remains a challenge, because of marked genome plasticity of many bacterial pathogens. Results: We developed a DNA microarray for strain typing and detection of major antimicrobial resistance genes of clinically relevant enterobacteria. For this purpose, we applied a global genome-wide probe selection strategy on 32 available complete enterobacterial genomes combined with a regression model for pathogen classification. The discriminative power of the probe set was further tested in silico on 15 additional complete enterobacterial genome sequences. DNA microarrays based on the selected probes were used to type 92 clinical enterobacterial isolates. Phenotypic tests confirmed the array-based typing results and corroborate that the selected probes allowed correct typing and prediction of major antibiotic resistances of clinically relevant Enterobacteriaceae, including the subspecies level, e.g. the reliable distinction of different E. coli pathotypes. Conclusions: Our results demonstrate that the global probe selection approach based on longest common factor statistics as well as the design of a DNA microarray with a restricted set of discriminative probes enables robust discrimination of different enterobacterial variants and represents a proof of concept that can be adopted for diagnostics of a wide range of microbial pathogens. Our approach circumvents misclassifications arising from the application of virulence markers, which are highly affected by horizontal gene transfer. Moreover, a broad range of pathogens have been covered by an efficient probe set size enabling the design of high-throughput diagnostics.