ST-1 VISA/DAP-R CA-MRSA INTEGRATED OMICS: A FIRST REPORT OF HYPER-VIRULENCE AND MULTI-DRUG RESISTANT SUPERBUG

Methicillin Resistant Staphylococcus aureus (MRSA) represents a global human health problem for its rising multi-drug resistance phenotype, involvement in nosocomial infections and outbreaks worldwide, and for its capability to spread in both hospital (HA-MRSA) and community (CA-MRSA) environments. The aim of this study was to characterize a VISA/DAP-R CA-MRSA superbug strain for its Genomic and Transcriptomic traits by using Whole Genome Sequencing (WGS), RNA-sequencing (RNA-seq) and Bioinformatics, compared to its VSSA/DAP-S CA-MRSA parental strain. The WGS data were used for Genomic Single-Nucleotide Polymorphism call (SNP call) and to investigate the Virulome and Resistome. Briefly, 288 non-synonymous SNPs (nsSNPs) were found in the resistant strain, among these 21 nsSNPs were considered having a disruptive (high) impact in the encoded proteins (e.g. AgrA, TpiA, Spa); the remaining nsSNPs had a moderate impact in the protein effectiveness (e.g. AgrC, ClfA, ClfB, DnaJ, IcaB, MprF, MurC, MurE, RpoB, SdrD, SodA, SodM). Most of the amino-acid alterations described in this work have not previously been associated with the VISA/DAP-R phenotype, except for T345A in mprF and H481Y in rpoB related to rifampicin/vancomycin and daptomycin resistance, respectively. The Resistome of the strain-pair was characterized by the presence of genes involved in aminoglycosides, β-lactams, macrolides and tetracyclines resistance, reflecting a multi-drug resistant behaviour. While the Virulome underlined the presence of adhesins, capsular polysaccharides, clumping factors, endotoxins, haemolysins, and leukotoxins including genes encoding the Panton-Valentine leucocidin. The Transcriptome analysis evidenced 147 over-expressed and 53 under-expressed genes in the VISA/DAP-R CA-MRSA strain. Considering the SNP call analysis and the Transcriptomics, DAVID enrichment analyses were performed to better explore the role of genes having non-synonymous SNPs (nsSNPs) and to better understand the transcriptome traits characterizing the superbug phenotype, in VISA/DAP-R CA-MRSA strain. The results highlighted some important clusters involved in Cell wall, Cell membrane, Cellular response to stress, Oxidation and reduction processes, Pathogenesis, Response to antibiotic, Transcription regulation, Transport, and Two-component regulatory systems. Integrated omics data showed, for the first time, an overview of several important traits characterizing the VISA/DAP-R CA-MRSA superbug strain.