Mechanisms of drug resistance: daptomycin resistance

Abstract

Daptomycin (DAP) is a cyclic lipopeptide with in vitro activity against a variety of Gram-positive pathogens, including multidrug-resistant organisms. Since its introduction into clinical practice in 2003, DAP has become an important key frontline antibiotic for severe or deep-seated infections caused by Gram-positive organisms. Unfortunately, DAP resistance (DAP-R) has been extensively documented in clinically important organisms such as Staphylococcus aureus, Enterococcus spp., and Streptococcus spp. Studies on the mechanisms of DAP-R in Bacillus subtilis and other Gram-positive bacteria indicate that the genetic pathways of DAP-R are diverse and complex. However, a common phenomenon emerging from these mechanistic studies is that DAP-R is associated with important adaptive changes in cell wall and cell membrane homeostasis with critical changes in cell physiology. Findings related to these adaptive changes have provided novel insights into the genetics and molecular mechanisms of bacterial cell envelope stress response and the manner in which Gram-positive bacteria cope with the antimicrobial peptide attack and protect vital structures of the cell envelope, such as the cell membrane. In this review, we will examine the most recent findings related to the molecular mechanisms of resistance to DAP in relevant Gram-positive pathogens and discuss the clinical implications for therapy against these important bacteria.

Keywords: Bacillus subtilis; Enterococcus; Staphylococcus aureus; daptomycin resistance.

Figure 1

Structure of daptomycin (A) and proposed mechanism of action (B). See text for details

Figure 2. The lia genes in some Gram-positive bacteria with low G + C content

The loci are drawn to scale. Gene names follow NCBI entries of the published genome sequences.

Figure 3. Proposed mechanisms of daptomycin resistance in Gram-positive organisms

Two main mechanisms of resistance have been postulated in enterococci. The first is diversion (Enterococcus faecalis only) of the antibiotic from the preferential binding site of DAP at the septum (black arrow) resulting in ineffective binding of DAP (panel a). Images of cells treated with BODIPY-labeled DAP (a fluorescent derivative of DAP) demonstrate binding of the antibiotic to the septum in DAP-S. When exposed to the same concentration, DAP binding does not appear to occur at the septum in a DAP-R isolate (panel b). Panel c evaluates the amount of DAP bound to cell membrane of enterococci by measurement of fluorescence intensity normalized to protein content. As shown, no change in fluorescence intensities were noted between DAP-S and -R, indicating similar binding of the antibiotic molecules to the cell membrane. The second mechanism, seen in Bacillus subtilis, Staphylococcus aureus, and Enterococcus faecium, is electrostatic repulsion of the positively charged DAP-Ca²⁺ complex from the cell membrane (panel d). Binding of BODIPY-labeled DAP is decreased in DAP-R isolate compared to its –S counterpart (panel e), demonstrated by E. faecium. Lower fluorescence intensity is also noted in DAP-R versus DAP-S (panel f) as described in E. faecium. DAP – daptomycin; R –resistant; rfu – relative fluorescence unit; S – susceptible. Bar – 1 μm.

Figure 4. Schematic representation of cardiolipin synthase Cls

Predicted N-terminal transmembrane (TM) domains and phospholipase (PLD) domains are indicated. Lines refer to positions of amino acid changes associated with daptomycin resistance in Enterococcus spp. (blue) and Staphylococcus aureus (red).

Figure 5

Crystal structure of the DNA binding domain LiaR of Enterococcus faecalis bound to DNA sequence upstream of its target genes. The α4 helices form part of the molecular recognition surface responsible for formation of the functional dimer required for DNA binding. The α3 DNA-recognition helices in the dimer are positioned to create a large electropositive DNA-binding surface. The LiaR-DNA complex structure shows a strong bend in the DNA, as shown by its helical axis (gray). Adapted from Davlieva M, et al. 2015. Nucleic Acids Res; 43(9):4758-73.