The emergence and spread of multidrug-resistant bacteria are a global public health problem, with closely related resistant and/or virulent strains being isolated from humans and other animals, food, and the environment. In this context, methicillin-resistant Staphylococcus aureus (MRSA) has been classified as a high priority pathogen by the World Health Organization (WHO). The successful combination of virulence factors (virulome) and antimicrobial resistance genes (resistome) support the high prevalence and endemicity of MRSA in healthcare-associated infections (HAIs). However, clinically relevant genomic data in Brazil is scarce. In the present study, a microbiological and genomic investigation of MRSA isolated from clinical samples from different Brazilian cities was carried out. Initially, the isolates species was confirmed (MALDI-TOF-MS, Bruker), and antibiotic resistance profile (disk-diffusion) and presence of the mecA gene (PCR) were determined. Worryingly, 87.5% (76/87) of MRSA isolates were multidrug-resistant. To investigate the genetic mechanisms related to this phenotype and determine the clonal lineages of these isolates, complete genome sequencing of 37 MRSA strains was performed (Illumina NextSeq). Whole-genome analysis (prediction of resistome, virulome, mobilome; determination of the ST, Sequence Type; SCCmec and spa type) were performed using bioinformatics tools. In this regard, the prevalence (n = 21) of ST105 isolates harboring SCCmec type II was highlighted. Isolates from ST5 (SCCmec II, (n = 3; SCCmec IV, (n = 3), ST8 (SCCmec IV, (n = 5; SCCmec II, (n = 1); and single isolates of ST88 (SCCmec IV), ST239 (SCCmec III), ST5286 (SCCmec IVa), and ST398 (mecA positive, SCCmec negative) were also identified. In addition to the mecA gene, several non-β-lactam antibiotics resistance genes have been predicted [macrolides and/or lincosamides (ermA, mrsA, emrC, mphC); aminoglycosides (aph-(3')-III, ant(9)-Ia); chloramphenicol (cat(pC221)); fosfomycin (fosB); mutations related to fluoroquinolone resistance (gyrA (S84L, E88K); grlA (S80Y, E84F, S80F, E84K)); biocide tolerance genes [triclosan (sh-fabI); quaternary ammonium compounds (qacACJ)], oxidative stress [H₂O₂ (perR)], and heavy metals [arsenic (arsBCR); cadmium (cadADX); copper (copZ); mercury (merABRT)]. A broad virulome was predicted in all genomes, with the presence of genes to produce enterotoxins (egc cluster) in isolates from different STs; and Panton-Valentine Leukocidin (lukFS-PV), in ST8 and ST88 isolates. Phylogenetic analysis based on Core-gene Single Nucleotide Polymorphisms (cg-SNPs) showed that isolates from São Paulo, Santa Catarina and Paraná (ST5, ST105 or ST8) were related to genomes from Rio de Janeiro, United States and South America (Ecuador, Colombia and Chile); grouped in clusters with genomes from emerging lineages in Brazil (ST105-SCCmecII), and with virulent lineages spread internationally (USA100, ST5-SCCmecII; USA300/USA300-LV, ST8-SCCmecIV ). The microbiological, genomic, and epidemiological data obtained in this work were available on the OneBR platform (http://onehealthbr.com/). The results highlight the increased prevalence of multidrug-resistant MRSA from ST105 harboring SCCmec type II, and the dissemination of multidrug-resistant and potentially virulent strains, as well as the emergence of ST8 in Brazilian hospitals, reinforcing the importance of MRSA genomic surveillance in Brazil.