title: Daptomycin resistance mechanisms in clinically derived Staphylococcus aureus strains assessed by a combined transcriptomics and proteomics approach.
abstract: OBJECTIVE
  The development of daptomycin resistance in Staphylococcus aureus is associated with clinical treatment failures. The mechanism(s) of such resistance have not been clearly defined.
  
  
  METHODS
  We studied an isogenic daptomycin-susceptible (DAP(S)) and daptomycin-resistant (DAP(R)) S. aureus strain pair (616; 701) from a patient with relapsing endocarditis during daptomycin treatment, using comparative transcriptomic and proteomic techniques.
  
  
  RESULTS
  Minor differences in the genome content were found between strains by DNA hybridization. Transcriptomic analyses identified a number of genes differentially expressed in important functional categories: cell division; metabolism of bacterial envelopes; and global regulation. Of note, the DAP(R) isolate exhibited reduced expression of the major cell wall autolysis gene coincident with the up-regulation of genes involved in cell wall teichoic acid production. Using quantitative (q)RT-PCR on the gene cadre putatively involved in cationic peptide resistance, we formulated a putative regulatory network compatible with microarray data sets, mainly implicating bacterial envelopes. Of interest, qRT-PCR of this same gene cadre from two distinct isogenic DAP(S)/DAP(R) clinical strain pairs revealed evidence of other strain-dependent networks operative in the DAP(R) phenotype. Comparative proteomics of 616 versus 701 revealed a differential abundance of proteins in various functional categories, including cell wall-associated targets and biofilm formation proteins. Phenotypically, strains 616 and 701 showed major differences in their ability to develop bacterial biofilms in the presence of the antibacterial lipid, oleic acid.
  
  
  CONCLUSIONS
  Compatible with previous in vitro observations, in vivo-acquired DAP(R) in S. aureus is a complex, multistep phenomenon involving: (i) strain-dependent phenotypes; (ii) transcriptome adaptation; and (iii) modification of the lipid and protein contents of cellular envelopes.
authors.affiliation: Genomic Research Laboratory, University Hospitals of Geneva and University of Geneva, Geneva, Switzerland. adrien.fischer@genomic.ch
authors.forename: Adrien
authors.initials: A
authors.lastname: Fischer
authors.forename: Soo-Jin
authors.initials: SJ
authors.lastname: Yang
authors.forename: Arnold S
authors.initials: AS
authors.lastname: Bayer
authors.forename: Ali R
authors.initials: AR
authors.lastname: Vaezzadeh
authors.forename: Sébastien
authors.initials: S
authors.lastname: Herzig
authors.forename: Ludwig
authors.initials: L
authors.lastname: Stenz
authors.forename: Myriam
authors.initials: M
authors.lastname: Girard
authors.forename: George
authors.initials: G
authors.lastname: Sakoulas
authors.forename: Alexander
authors.initials: A
authors.lastname: Scherl
authors.forename: Michael R
authors.initials: MR
authors.lastname: Yeaman
authors.forename: Richard A
authors.initials: RA
authors.lastname: Proctor
authors.forename: Jacques
authors.initials: J
authors.lastname: Schrenzel
authors.forename: Patrice
authors.initials: P
authors.lastname: François
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D017576:Daptomycin / Q000494:pharmacology*; D024881:Drug Resistance, Bacterial; D004697:Endocarditis, Bacterial / Q000382:microbiology; D020869:Gene Expression Profiling; D006801:Humans; D046228:Microarray Analysis; D009693:Nucleic Acid Hybridization; D020543:Proteome / Q000032:analysis*; D012008:Recurrence; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013203:Staphylococcal Infections / Q000382:microbiology*; D013211:Staphylococcus aureus / Q000187:drug effects* / Q000302:isolation & purification
chemical_list: D000900:Anti-Bacterial Agents; D020543:Proteome; D017576:Daptomycin