Detection of genetic elements carrying glycopeptide resistance clusters in Enterococcus by DNA microarrays

Glycopeptide resistance in enterococci is conferred by discrete genetic elements, which can carry mutations, deletions, and partial disruptions. We developed a custom DNA microarray as a tool for typing glycopeptide resistant enterococci. Oligonucleotide DNA microarrays were produced targeting the genes of enterococcal glycopeptide resistance gene clusters. A total of 105 probes selective for 42 genes were designed. The microarrays were validated on DNA extracted from reference strains and used to type 24 enterococcal strains belonging to various species and with different resistance phenotype, detecting all the genes of the resistance clusters which were actually present in each control and study strain. Moreover, this technique was capable of identifying the presence of additional resistant elements masked by a higher or similar resistance phenotype, and also of correcting an erroneous assignment made on the basis of phenotype alone. The use of our microarrays provided additional and complementary information compared to the phenotype alone. Our screening technique compares favourably, in aggregate terms of turnaround time, costs and convenience with other molecular biology techniques such as amplification and sequencing when applied to the study of complex genetic elements composed of several genes, such as glycopeptide resistance elements in enterococci.