Molecular characterisation of Salmonella strains by an oligonucleotide multiprobe microarray

A DNA microarray has been developed for the simultaneous characterisation and typing of Salmonella enterica subsp. enterica isolates. One-hundred and nine 35-40 mer oligonucleotides probes detect flagellar and somatic antigen encoding genes (serogroup or serotype specific), important virulence genes located within or outside the pathogenicity islands, phage-associated genes and antibiotic resistance determinants. The probes were printed on glass slides and whole genomic Cy5-labelled Salmonella DNA was hybridised to the substrate. A set of 19 different Salmonella strains and one Escherichia coli strain has been selected as positive and negative controls for each probe. The validity of the results is confirmed by gene-specific PCRs or phenotypic methods (serotyping, MIC determination for various antimicrobial agents). Of 2071 data points generated, an agreement of 97.4% has been obtained between microarray and PCR/phenotypic results. Twenty-six data points (1.3%) were classified as uncertain and, similarly, 1.3% showed a discordant result. The microarray described here is a new tool to study the epidemiology of Salmonella strains on the genotypic level and might become a powerful method in risk assessment studies.