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

Abstract

Daptomycin (DAP) is one of the last-resort treatments for heterogeneous vancomycinintermediate Staphylococcus aureus (hVISA) and vancomycin-intermediate S. aureus (VISA) infections. DAP resistance (DAP-R) is multifactorial and mainly related to cellenvelope modifications caused by single-nucleotide polymorphisms and/or modulation mechanisms of transcription emerging as result of a self-defense process in response to DAP exposure. Nevertheless, the role of these adaptations remains unclear. We aim to investigate the comparative genomics and late post-exponential growthphase transcriptomics of two DAP-resistant/DAP-susceptible (DAP R/S) methicillinresistant S. aureus (MRSA) clinical strain pairs to focalize the genomic and longterm transcriptomic fingerprinting and adaptations related to the DAP mechanism of action acquired in vivo under DAP pressure using Illumina whole-genome sequencing (WGS), RNA-seq, bioinformatics, and real-time qPCR validation. Comparative genomics revealed that membrane protein and transcriptional regulator coding genes emerged as shared functional coding-gene clusters harboring mutational events related to the DAP-R onset in a strain-dependent manner. Pairwise transcriptomic enrichment analysis highlighted common and strain pair-dependent Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, whereas DAP R/S double-pair cross-filtering returned 53 differentially expressed genes (DEGs). A multifactorial long-term transcriptomic-network characterized DAP R MRSA includes alterations in (i) peptidoglycan biosynthesis, cell division, and cell-membrane (CM) organization genes, as well as a cidB/lytS autolysin genes; (ii) ldh2 involved in fermentative metabolism; (iii) CM-potential perturbation genes; and (iv) oxidative and heat/cold stress response-related genes. Moreover, a D-alanyl-D-alanine decrease in cell-wall muropeptide characterized DAP/glycopeptide

Genomic Characterization of a New Biofilm-Forming and Adhesive ST398 Human-Adapted MSSA Lineage Causing Septic Knee Arthritis Following Surgical Reconstruction

“…Raw reads were processed using FastQC (v.0.11.7) to assess data quality. The Cutadapter tool (v.1.16) implemented in Python (v.3.5.2) was used to remove residual PCR primers and to filter low-quality bases (Q_score < 30) and short reads (<150 bp) [ 20 ]. The filtered trimmed reads were included in the downstream analysis.…”

“…SNP calls were carried out from the PE library raw reads as previously published [ 20 ]. The CSI Phylogeny tool (v1.4) [ 21 ] was used to identify the closest relationships between the strains and the different S. aureus Reference Genomes (RefGen) deposited in GenBank.…”

Escaping mechanisms of ESKAPE pathogens from antibiotics and their targeting by natural compounds

“…Daptomycin is used as an alternative therapeutic agent to vancomycin for invasive MRSA or MSSA infections in patients who are allergic to β-lactams. It has been considered as a last-resort treatment for heterogeneous vancomycin-intermediate S. aureus (hVISA) and vancomycin-intermediate S. aureus (VISA) infections [62] . Although the precise mechanism of action of daptomycin is yet to be understood, a model proposes that daptomycin interacts with the plasma membrane resulting in its permeabilization and depolarization caused by a loss of cytoplasmic potassium ions [62] .…”

“…It has been considered as a last-resort treatment for heterogeneous vancomycin-intermediate S. aureus (hVISA) and vancomycin-intermediate S. aureus (VISA) infections [62] . Although the precise mechanism of action of daptomycin is yet to be understood, a model proposes that daptomycin interacts with the plasma membrane resulting in its permeabilization and depolarization caused by a loss of cytoplasmic potassium ions [62] . Although daptomycin resistance is uncommon, failure of treatment up to 33% may be observed in invasive infections including bacteremia or osteomyelitis [63] .…”

Nisin activity against methicillin-resistant and methicillin-sensitive Staphylococcus aureus and risk of resistance acquisition

“…Unfortunately, as evidenced by current scenarios, methicillin-resistant strains emerged quickly (Hiramatsu et al, 1990;Lozano et al, 2020). One of the major concerns today is the emergence of vancomycin and daptomycin-resistant S. aureus (Cafiso et al, 2020;Kang et al, 2015;Pader & Edwards, 2017).…”