Molecular characterisation of Salmonella strains by an oligonucleotide multiprobe microarray

Area of Science:

• Microbiology
• Genomics
• Molecular Diagnostics

Background:

• Accurate characterization of Salmonella enterica subsp. enterica isolates is crucial for epidemiological studies and risk assessment.
• Existing methods for Salmonella typing can be time-consuming and may not capture a comprehensive genetic profile simultaneously.

Purpose of the Study:

• To develop and validate a DNA microarray for the simultaneous characterization and genotypic typing of Salmonella enterica subsp. enterica.
• To assess the utility of the microarray for identifying key genetic determinants including antigen, virulence, and antibiotic resistance genes.

Main Methods:

• Design and printing of 109 oligonucleotide probes targeting specific genes (antigen, virulence, phage, antibiotic resistance) on glass slides.
• Hybridization of Cy5-labeled whole genomic DNA from Salmonella isolates to the microarray.
• Validation of microarray results using gene-specific PCR and phenotypic methods (serotyping, MIC determination).

Main Results:

• High agreement (97.4%) was achieved between microarray results and confirmatory PCR/phenotypic methods across 2071 data points.
• A small percentage of uncertain (1.3%) and discordant (1.3%) results were observed, indicating high reliability of the microarray.
• The microarray successfully detected specific antigen, virulence, and antibiotic resistance genes in Salmonella strains.

Conclusions:

• The developed DNA microarray is a reliable and powerful tool for the genotypic characterization and typing of Salmonella enterica subsp. enterica.
• This microarray facilitates efficient epidemiological surveillance of Salmonella strains.
• The method holds potential for enhanced risk assessment studies involving Salmonella.