High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and...

Area of Science:

• Microbiology and Genomics
• Molecular Diagnostics
• Bioinformatics

Background:

• Enterobacteriaceae are clinically significant bacteria with high genome plasticity, complicating strain typing and risk assessment.
• Existing methods struggle with accurate identification due to overlapping virulence genes and genomic variability.
• Array technology offers a promising solution for rapid, standardized bacterial typing and diagnostics.

Purpose of the Study:

• To develop a DNA microarray for precise strain typing of clinically relevant Enterobacteriaceae.
• To enable the detection of major antimicrobial resistance genes within these bacteria.
• To address challenges in bacterial diagnostics and risk assessment caused by genome plasticity.

Main Methods:

• A global genome-wide probe selection strategy was applied to 32 complete Enterobacteriaceae genomes.
• A regression model was used for pathogen classification, with in silico testing on 15 additional genomes.
• The developed DNA microarray was validated using 92 clinical Enterobacteriaceae isolates and phenotypic tests.

Main Results:

• The DNA microarray successfully performed strain typing and detected major antimicrobial resistance genes in clinical isolates.
• Array-based typing results were confirmed by phenotypic tests, demonstrating high accuracy.
• The technology reliably distinguished between different Enterobacteriaceae variants, including E. coli pathotypes at the subspecies level.

Conclusions:

• A global probe selection approach and a DNA microarray with discriminative probes enable robust Enterobacteriaceae discrimination.
• This method circumvents misclassifications linked to horizontal gene transfer and virulence markers.
• The developed DNA microarray serves as a proof of concept for high-throughput diagnostics of diverse microbial pathogens.