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Chapter 24 : Evolution of Glycopeptide Resistance
Category: Fungi and Fungal Pathogenesis; Bacterial Pathogenesis
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This chapter briefly reviews the mode of action and the mechanism of bacterial resistance to glycopeptides, as exemplified by the VanB type, and discusses its diversity, regulation, evolution, origin, and recent dissemination to methicillin-resistant Staphylococcus aureus. Classification of glycopeptide resistance is based on the primary sequence of the structural genes for the resistance ligases. Although the six types of resistance involve related enzymic functions, they can be distinguished by the location of the corresponding genes and by the mode of regulation of gene expression. An interesting phenomenon that has developed in some VanB- and VanA-type enterococci is vancomycin dependence. These glycopeptide-dependent strains are also able to grow in the absence of glycopeptides if supplied with the dipeptide D-Ala-D-Ala, confirming that they are unable to produce the ligase encoded by the chromosomal ddl gene. The vanF operon is composed of five genes (vanYF, vanZF, vanHF, vanF, and vanXF) encoding homologues of VanY, VanZ, VanH, VanA, and VanX, and the genes essential for resistance (vanHF, vanF, and vanXF) are organized and oriented as in VanA-type strains. The evolutionary lineage of these groups of homologous genes is not clear, but they may have a common ancestor, or Paenibacillus could be a progenitor of the resistance operons acquired by enterococci. Conjugal transfer of plasmids that have acquired Tn1546-like elements by transposition appears to be responsible for the spread of glycopeptide resistance in enterococci.
VanB-type glycopeptide resistance. (Top) Synthesis of peptidoglycan precursors in a VanB-type resistant strain. Tri, L-Ala-γ-D-Glu-L-Lys; Tetra, L-Ala-γ-D-Glu-L-Lys-D-Ala; Penta, L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala; Pentadepsi, L-Ala-γ-D-Glu-LLys-D-Ala-D-Lac. (Bottom) organization of the vanB operon. Open arrows represent coding sequences and indicate the direction of transcription. The regulatory and resistance genes are cotranscribed from promoters Preg and Pres , respectively.
VanC-type glycopeptide resistance. (Top) Synthesis of peptidoglycan precursors in a VanC-type strain. Tri, L-Ala-γ-D-Glu-L-Lys; Tetra, L-Ala-γ-D-Glu-L-Lys-D-Ala. (Bottom) Organization of the vanC operon. Open arrows represent coding sequences and indicate the direction of transcription.
Comparison of the van gene clusters. Open arrows represent coding sequences and indicate the direction of transcription. The guanosine plus cytosine content (percent GC) is indicated in the arrows. The percentage of amino acid (aa) identity between the deduced proteins of reference strains BM4147 (VanA) (Arthur et al., 1993), V583 (VanB) (Evers and Courvalin, 1996), BM4339 (VanD) (Casadewall and Courvalin, 1999), BM4174 (VanC) (Arias et al., 2000), BM4405 (VanE) (Abadía et al., 2002), and BM4518 (VanG) (Depardieu et al., 2003a) is indicated under the arrows. NA, not applicable; IR, inverted repeat; L, left; R, right.
VanRBSB two-component regulatory system. (Top) Structure of VanSB and VanRB. Asp, aspartate; His, histidine; P, phosphate. (Bottom) Phosphorylation (left) and dephosphorylation (right) of VanRB by VanSB.
Synthesis of peptidoglycan precursors in a VanB-type vancomycin-dependent strain. Because of inactivation of the host chromosomal D-Ala:D-Ala ligase (Ddl), presence of vancomycin in the environment is required to induce expression of the resistance pathway required for cell wall synthesis. Tri, L-Ala-γ-D-Glu-L-Lys; Pentadepsi, L-Ala-γ-D-Glu-L-LysD-Ala-D-Lac.
VanB genetic tinkering. i, inducible; D, dependent; R, resistant; S, susceptible; Te, teicoplanin; Vm, vancomycin.
VanD-type glycopeptide resistance. (Top) Synthesis of peptidoglycan precursors in a VanD-type resistant strain. (Bottom) Organization of the vanD operon. Open arrows represent coding sequences and indicate the direction of transcription. The regulatory and resistance genes are cotranscribed from promoters PRD and PYD , respectively. X, mutated ddl and vanSD nonfunctional genes.
Schematic representation of the genes for D-Ala:D-Ala ligases of enterococci. The positions of the amino acids implicated in the binding of D-Ala1, D-Ala2, and ATP and conserved in E. faecium and E. faecalis are indicated by dotted, hatched, and black bars, respectively (McKessar et al., 2000; Stinear et al., 2001). In E. faecium strains BM4339(ddl[(::5bp37)]; vanSD [C517A]), BM4416(ddl[::IS19 at position 762]; vanSD [Δ1bp670]), A902(ddl[A38G]; vanSD [Δ1bp657]), and BM4538 (ddl[G956A]; vanRD [G419A]) the differences relative to ddl from E. faecium BM4147 are indicated in italics. In E. faecalis strains BM4539(ddl[::7bp870]; vanSD [::7bp753]) and BM4540(ddl[::7bp361]; vanSD [::7bp753]), a 7-bp insertion (italics) at the positions corresponding to amino acid 290 or 121, respectively, is responsible for a frameshift mutation leading to the synthesis of 297–and 128–amino acid peptides instead of the putative 348–amino acid Ddl.
Comparison of the vanD gene clusters. Arrows represent coding sequences and indicate direction of transcription. The two-component regulatory systems are represented by dotted arrows, the D,D-carboxypeptidases by hatched arrows, and the genes necessary for resistance by open arrows. The guanosine plus cytosine content (percent GC) is indicated in the arrows. The percentages of identity between the deduced proteins relative to those of BM4339 are indicated under the arrows. Insertion sequence ISEfa4 in 10/96A is indicated by a double headed arrow and horizontally hatched arrows corresponding to ORFA and ORFB. The asterisks indicate the positions of point mutations. The vertical bars in vanSD of BM4416, A902, and of BM4539/BM4540 and vanYD of 10/96A indicate the positions of the frameshift mutations leading to predicted truncated proteins.
Schematic representation of the VanSB sensor and location of the amino acid substitutions in teicoplanin-resistant mutants. H, N, G1, F, and G2 refer to the motifs conserved in histidine protein kinases. The putative membrane-associated sensor domain (dotted black) containing transmembrane segments (black) and the putative cytoplasmic kinase domain (white) are indicated. Het, heterogeneously resistant; R, resistant; S, susceptible; Te, teicoplanin; Vm, vancomycin.
Phylogenetic tree derived from the alignment of D-Ala:D-Ala ligases and related enzymes.
Proposed mechanism for van gene transfer from Enterococcus to Staphylococcus. Wavy lines represent resident DNA (chromosome or plasmid). pBHRT is a plasmid with a broad host range of transfer.
Glycopeptide resistance in gram-positive bacteria