The transcriptomes of vancomycin intermediate-resistance Staphylococcus aureus (VISA) clinical isolates HIP5827 and Mu50 (MIC ؍ 8 g/ml) were compared to those of highly vancomycin-resistant S. aureus (VRSA; MIC ؍ 32 g/ml) passage derivatives by microarray. There were 35 genes with increased transcription and 16 genes with decreased transcription in common between the two VRSAs compared to those of their VISA parents. Of the 35 genes with increased transcription, 15 involved purine biosynthesis or transport, and the regulator (purR) of the major purine biosynthetic operon (purE-purD) was mutant. We hypothesize that increased energy (ATP) is required to generate the thicker cell walls that characterize resistant mutants.Vancomycin is the treatment of choice for serious infections caused by oxacillin-resistant Staphylococcus aureus, and some isolates are reported that are susceptible only to this antibiotic (8, 12). Oxacillin-resistant S. aureus isolates with reduced susceptibility to vancomycin (vancomycin intermediate-resistance S. aureus [VISA] isolates; the vancomycin MIC increases from 1 to 8 g/ml) have been recovered from patients receiving prolonged courses of vancomycin (1-3). A number of abnormalities have been noted among VISA isolates, including reduced rate of growth, decreased cell wall cross-linking (6, 16), increased cell wall thickness (4, 10), decreased autolysis (17), changes in penicillin binding proteins (6, 9, 15), and alterations in glutamate amidation of the peptidoglycan stem peptide (5). No unifying molecular hypothesis has been proposed that explains the VISA phenotype, but the current hypothesis is that the thickened, poorly cross-linked cell wall provides more peripheral targets for vancomycin, trapping the antibiotic before it can reach its site of lethal action at the cell membrane (17). It is also assumed that because of the long clinical vancomycin exposure times required to generate resistance, multiple genes and, probably, multiple metabolic pathways have been altered.We sought to assess genomic changes in gene transcription (the transcriptome) by DNA microarray and took a number of approaches different from those taken by others in trying to understand genomic changes associated with the VISA phenotype. First, we used clinical VISA isolates as parents rather than vancomycin-susceptible laboratory strains. There is evidence that there is something unique about VISA isolates that allows them to become resistant to vancomycin more easily than other S. aureus isolates (13). Second, we sought to amplify the phenotype by continued exposure of VISA isolates to vancomycin in vitro, further increasing the vancomycin MIC. We hypothesized that in this way, we would create isogenic strain sets that exaggerate the changes present in clinical VISA isolates. Third, we compared stable mutants of VISA strains for which vancomycin MICs were increased and we did not grow strains in the presence of the antibiotic, removing any direct effect of the antibiotic on transcription.Generation of mutant...