Daptomycin Resistant Staphylococcus aureus Clinical Strain With Novel Non-synonymous Mutations in the mprF and vraS Genes: A New Insight Into Daptomycin Resistance

Abstract

Objectives: Daptomycin (DAP) resistance in Staphylococcus aureus is uncommon but there are increasing reports of the emergence of resistance during DAP therapy. Most clinical DAP-resistant S. aureus isolates investigated carried mutations in the mprF gene. The aim of this study was to identify mutations between a clinical pair of methicillin-susceptible S. aureus (MSSA) isolates (DAP-susceptible and DAP-resistant). Additionally, the activity of genes previously associated with DAP resistance was assessed.Materials and Methods: Two MSSA isolates from patient with left-sided endocarditis were analyzed by whole genome sequencing (WGS) and reverse transcription-quantitative real-time PCR (RT-qPCR). The first isolate, DAP-susceptible, was obtained before initiation of treatment and the second isolate, DAP-resistant, was recovered after 4 weeks of DAP therapy.Results: Comparison of complete genomes of DAP-susceptible and its DAP-resistant variant identified two non-synonymous and one synonymous mutations. The non-synonymous mutations consisted of a S829L substitution in mprF and a T331I substitution in vraS. The RT-qPCR experiments revealed an increased expression of vraS, dltA, mprF, and sceD genes in DAP-resistant variant. Strikingly, the expression of dltA and mprF genes was significantly downregulated by DAP.Conclusion: The mprF and vraS genes were previously associated with DAP resistance, however, none of the mutations described in this study had been previously identified and linked to DAP resistance. Moreover, we provide a new insight into the DAP action on S. aureus, in which the expression of key genes in DAP resistance is decreased by the antibiotic.

Association of mprF mutations with cross-resistance to daptomycin and vancomycin in methicillin-resistant Staphylococcus aureus (MRSA)

“…Accordingly, cells lacking the mprF gene showed increased susceptibility toward many positively charged antibiotics, including CAMPs, DAP, or VCM 16,44 . Previous studies frequently attributed reduced DAP susceptibility to mprF mutation, but a few mentioned about its association with alteration of VCM susceptibility 25,45,46 . Our current study demonstrated that mprF mutations are major determinants of cross-reduced susceptibility to DAP and VCM in MRSA during DAP therapy but have only partial contribution during the course of VCM chemotherapy (Table 1 and 2).…”

Genomic and Long-Term Transcriptomic Imprints Related to the Daptomycin Mechanism of Action Occurring in Daptomycin- and Methicillin-Resistant Staphylococcus aureus Under Daptomycin Exposure

“…Briefly, S. aureus can adopt different strategies to resist DAP. The first is to alter the net cell-surface charge, preventing the positively charged DAP-calcium binding to the cell envelope by electrostatic repulsion, mainly due to dlt over-expression—increasing the alanylation rate of the wall teichoic acids ( Yang et al, 2009 ; Cafiso et al, 2014 )—and to mpr F mutations increasing the amount of the positively charged lysyl-phosphatidylglycerol on the outer membrane, conferring a “gain-of-function” and positively increasing the cell-envelope charge ( Rubio et al, 2011 ; Bayer et al, 2015 ; Ernst et al, 2018 ; Sabat et al, 2018 ; Ernst and Peschel, 2019 ). The second is the alteration of membrane phospholipid composition, with decreased phosphatidylglycerol amount, or changes in membrane fluidity interfering with DAP binding and oligomerization ( Jones et al, 2008 ; Kilelee et al, 2010 ; Mishra et al, 2011 ; Zhang et al, 2014 ).…”

“…A third mechanism is the involvement of global regulatory genes modulating cell-envelope stress and maintenance, affecting the expression of the cell-wall (CW) “stimulon” ( Utaida et al, 2003 ; Cafiso et al, 2012 ). Specifically, VraSR operon ( Muthaiyan et al, 2008 ; Mehta et al, 2012 ; Sabat et al, 2018 ; Taglialegna et al, 2019 ), orthologous to the Bacillus subtilis LiaSR ( Jordan et al, 2006 ), was involved and up-regulated by vancomycin and DAP exposure, and associated with CW biosynthesis via transcription of PBP2 (penicillin-binding protein 2), tag A (wall teichoic acids-synthesis), prs A (a-chaperone), and mur Z (UDP- N -acetylglucosamine-enolpyruvyl transferase) ( Kuroda et al, 2003 ; Mwangi et al, 2007 ). YycFG (also named WalKR), among the two-component regulatory systems (TCRSs), was implicated in the control of the peptidoglycan biosynthesis through the regulation of LytM and AtlA ( Dubrac and Msadek, 2004 ; Fukushima et al, 2011 ).…”

Verification of a Novel Approach to Predicting Effects of Antibiotic Combinations: In Vitro Dynamic Model Study with Daptomycin and Gentamicin against Staphylococcus aureus

“…The extensive use of daptomycin in clinical practice has led to decreased daptomycin effectiveness due to the emergence of bacterial resistance [ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 ]. Daptomycin treatment failures have been reported in patients with Staphylococcus aureus infections after prolonged daptomycin exposure [ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 ] and also following vancomycin administration that was associated with vancomycin-resistant S. aureus [ 9 , 10 , 11 , 12 , 13 , 14 , 15 ]. Similarly, infections caused by vancomycin-resistant enterococci with lowered susceptibility to daptomycin can be difficult to treat even at high dosing regimens of daptomycin [ 16 ].…”