Custom-designed gene chips (Affymetrix) were used to determine genetic relatedness and gene expression profiles in Staphylococcus aureus isolates with increasing MICs of vancomycin that were recovered over a period of several weeks from the blood and heart valve of a patient undergoing extensive vancomycin therapy. The isolates were found to be isogenic as determined by the GeneChip based genotyping approach and thus represented a unique opportunity to study changes in gene expression that may contribute to the vancomycin resistance phenotype. No differences in gene expression were detected between the parent strain, JH1, and JH15, isolated from the nares of a patient contact. Few expression changes were observed between blood and heart valve isolates with identical vancomycin MICs. A large number of genes had altered expression in the late stage JH9 isolate (MIC ؍ 8 g/ml) compared to JH1 (MIC ؍ 1 g/ml). Most genes with altered expression were involved in housekeeping functions or cell wall biosynthesis and regulation. The sortase-encoding genes, srtA and srtB, as well as several surface protein-encoding genes were downregulated in JH9. Two hypothetical protein-encoding genes, SAS016 and SA2343, were dramatically overexpressed in JH9. Interestingly, 27 of the genes with altered expression in JH9 grown in drug-free medium were found to be also overexpressed when the parental strain JH1 was briefly exposed to inhibitory concentrations of vancomycin, and more than half (17 of 27) of the genes with altered expression belonged to determinants that were proposed to form part of a general cell wall stress stimulon (S. Utaida et al., Microbiology 149:2719-2732, 2003).
Staphylococcus aureus strains with decreased susceptibility to vancomycin (so-called vancomycin-intermediate S. aureus[VISA] strains) have been identified in clinical specimens in several countries during the past decade (10,11,25). Although several abnormal physiological properties have been described in VISA isolates, the mechanisms of resistance and whether or not it involves acquisition of genes has remained unclear. A major problem in mechanistic studies has been the lack of availability of isogenic vancomycin-susceptible strains that could be considered the parental strains of the VISA isolates. Even when a VISA isolate shared a common multilocus sequence type with a fully sequenced vancomycin-susceptible strain, the clinical origins and times of isolation were far apart, excluding the possibility of attributing genetic and phenotypic differences to the antibiotic susceptibility phenotype.A recently described series of methicillin-resistant S. aureus (MRSA) isolates (JH1 through JH15) were recovered from a single patient during extensive chemotherapy with vancomycin (24). Bacterial isolates recovered at various times during therapy showed increasing vancomycin MICs which in isolates JH9 and JH14 eventually reached 8 g/ml, a value typical of many clinical VISA isolates. The first isolate chronologically, JH1, and all of the subsequent isolates sha...