TABLE 4.

Genes associated with VISAb

Gene, predicted mutationImpact of mutationDescriptionReference(s)
graR, nucleotide substitutionLed to a GraR aa substitution, N197S; expression of the mutant graR allele in hVISA strain Mu3 converted this strain to VISAComparative genomic study also with allele-swapping experiments using hVISA strain Mu3, VISA strain Mu50, and VSSA strain N315; looking at the contribution of individual genes to vancomycin susceptibility225
graRS, DNA deletionDeletion of graR led to increased susceptibility to vancomycinReverse genetics, using laboratory strains of S. aureus and VISA strain Mu50; this study shows that GraRS and VraFG are important mediators of VISA204
vraFG, DNA deletionDeletion of vraG led to increased susceptibility to vancomycin
SA1702,a nucleotide substitutionLed to a predicted aa substitution in SA1702, H164R; SA1702 is a protein of unknown function immediately upstream of vraS; this isolate was obtained when the vancomycin MIC increased from 1 to 4 μg per mlComparative genomic study of five sequential S. aureus bloodstream isolates obtained from a single patient during 3 mo of antibiotic treatment222
SA1249, frameshiftLed to a predicted loss-of-function in SA1249; the function of SA1249 is unknown, but its genomic location suggests that it might be part of the murG operon with a role in peptidoglycan synthesis; this isolate was obtained when the vancomycin MIC increased from 4 to 6 μg per ml
agrC, frameshiftLed to a predicted loss of function in agrC; this gene is part of the agr quorum-sensing locus; this is one of six mutations affecting protein-coding sequences, where the vancomycin MIC increased from 6 to 8 μg per ml
yycH, premature stop codonLed to a predicted loss of function in yycH (90% protein not translated); YycH is a hypothetical protein within an operon containing the two-component regulator that controls cell wall synthesis (WalKR/YycFG) by promoting expression of genes involved in autolysis; this is one of six mutations affecting protein-coding sequences, where the vancomycin MIC increased from 6 to 8 μg per ml
isdE, nucleotide substitutionLed to a predicted aa substitution in IsdE, A84V; involved in heme-iron transport; this is one of six mutations affecting protein-coding sequences, where the vancomycin MIC increased from 6 to 8 μg per ml
prsA, frameshiftLed to a possible loss of function in PrsA; PrsA is a putative membrane-linked ribose-phosphate pyrophosphokinase that can chaperone secreted proteins in Gram-positive bacteria; this is one of six mutations affecting protein-coding sequences, where the vancomycin MIC increased from 6 to 8 μg per ml
SA2094, nucleotide substitutionLed to a predicted aa substitution in SA2094, A94T; the function of SA2094 is unknown, but it is predicted to be membrane associated, and it shares similarity with an Na+/H+ antiporter from B. subtilis; this is one of six mutations affecting protein-coding sequences, where the vancomycin MIC increased from 6 to 8 μg per ml
graS, nucleotide substitutionLed to an aa substitution in GraS, T136I; this was one of six mutations detected in VISA strain JKD6008 compared to VSSA progenitor strain JKD6009; replacement of the mutant graS allele in VSSA strain JKD6009 resulted in an increase in the MET MIC from 2 to 6 μg per mlComparative genomic study with allele-swapping experiments with two S. aureus blood culture isolates (ST239) obtained from a patient before and after 42 days of vancomycin therapy; this study highlights the key role that GraRS plays in the formation of VISA among clinical isolates123
graRS, DNA deletionLed to a loss of GraRS function in VSSA JKD6009 and resulted in increased sensitivity of this strain to vancomycin, with a decrease in the MET MIC from 2 to 1 μg per ml
vraS, premature stop codonLed to a predicted loss of VraS function in VSSA strain Mu50Ω; replacement of this disrupted vraS allele with intact vraS from VISA strain Mu50 resulted in an increase in the vancomycin MIC from 0.5 to 3.5 μg per mlComparative genomic study also with allele-swapping experiments using VISA isolates Mu50 and Mu50Ω; the latter strain was isolated from the same patient 1.5 yr after Mu50 was isolated60
graR, no change compared with other VSSA isolatesReplacement of this graR allele in strain Mu50Ω with both vraS and graR from VISA strain Mu50 resulted in an increase in the vancomycin MIC for Mu50Ω from 0.5 to 6.0 μg per ml; these experiments show that point mutations in vraSR and graRS together are sufficient to induce VISA
yycFG, IS256 upstream insertionInsertion of IS256 led to upregulation of yycFG (walKR); overexpression in trans of yycFG led to increase in vancomycin resistanceComparative transcriptome study with overexpression experiments using hVISA strain SA137/93A and laboratory derivative SA137/93G141
mgrA and sarA, DNA deletionLed to a loss of SarA and MgrA function; SarA and MgrA are negative regulators of murein hydrolases (or autolysins); these enzymes (both dimeric, winged-helix proteins) are required for cell wall turnover; the double mutant showed increased Triton X-100-induced autolysis and increased sensitivity to killing by vancomycin and oxacillinUsed laboratory strains COL, MW2, and derivatives353
spoVG, deletedDeletion of spoVG decreases resistance to oxacillin and teicoplanin, with less impact on vancomycin resistance; loss of spoVG also led to a loss of capsule production; the yabJ/spoVG operon is under the control of the alternative sigma factor (SigB); the SigB regulon has been implicated in glycopeptide resistanceUsed laboratory strains COL, Newman, and derivatives305
vraS, nucleotide substitutionLed to a predicted aa substitution in VraS, I5N; this mutation was present only in Mu3 and Mu50 and not in other VSSA isolatesComparative genomic VISA strain, Mu50, hVISA strain Mu3, and VSSA strain N315; no experimental data provided234
mprF/fmtC, Tn917 insertionInsertion of Tn917 led to MprF loss of function and decreased vancomycin resistance; MprF (FmtC) is involved in synthesis of lysyl-phosphatidylglycerol (a major cell wall component), changing the content of the cell wall and increasing the net negative chargeMutagenesis study using S. aureus RN4220286
mprF/fmtC, Tn551 insertionInsertion of Tn551 led to MprF loss of function and decreased vancomycin resistance in VISA strains but slightly increased vancomycin resistance in VSSA strainsMutagenesis study using S. aureus COL and vancomycin-resistant laboratory derivatives228
trfA/trfB, insertional inactivation (antibiotic resistance marker)Loss of this locus led to an increase in susceptibility to teicoplanin, oxacillin, and vancomycin; function of TrfAB not knownConducted genetic studies with S. aureus RN4220, laboratory-derived teicoplanin-resistant mutants, and clinical strain NRS3270
ccpA, insertional inactivation (antibiotic resistance marker)Loss of CcpA (carbon catabolite protein A) impacts S. aureus in many ways (reduces growth, carbon metabolism, RNAIII expression, and capsule synthesis); loss of CcpA also reduced resistance to teicoplanin; the effect of this mutation on vancomycin resistance was not reportedConducted genetic studies with S. aureus strains COL, Newman, RN4220, and laboratory-derived mutants307
agr, insertional inactivation (antibiotic resistance marker)Loss of Agr led to increased probability of hVISA when population was exposed to 1 μg/ml vancomycinConducted genetic studies with S. aureus strains RN6390, RN6607, and RN4580294, 296
rsbU, DNA deletionRsbU is an anti-anti-sigma factor; selection for teicoplanin resistance in an rsbU mutant resulted in GISA, suggesting that a gene(s) (e.g., spoVG) within the SigB regulon can mediates glycopeptide resistance (refer to reference 305)Used S. aureus strain MRGR3, a teicoplanin-resistant mutant obtained from animal studies of wound infection23
pbp4, DNA deletionLoss of Pbp4 led to increased vancomycin resistance in VSSA, while overexpression of Pbp4 reduced vancomycin resistance in VISA; Pbp4 may be involved in transpeptidation, i.e., formation of peptidoglycan cross-linkingConducted genetic studies using S. aureus strains COL, RN450M, N315, and their laboratory-derived VISA mutants81
  • a Gene identifier according to S. aureus N315 locus tags.

  • b aa, amino acids.