Methicillin-resistant Staphylococcus aureus (MRSA) is a notorious superbug which poses serious health threats to humanity. The severity of the infections depends on the prevalence of virulence factors and antibiotic resistance. In this study, attempts have been made to nominate the two most virulent and multidrug-resistant MRSA isolates demonstrating the preliminary features of intestinal adhesion for the futuristic applications of probiotics and postbiotics as antagonists to combat MRSA infections. In this context, six clinical isolates of MRSA were polyphasically characterized for their identity, multidrug resistance, and few selected virulence determinates such as hemolytic activity and production of coagulase, nuclease, and capsule. The gut colonizing ability of MRSA isolates was assessed by mucoadhesion, auto-aggregation, and cell surface hydrophobicity. An antibiogram of MRSA isolates suggested the resistance towards several antibiotics with multiple antibiotic resistance (MAR) index >0.5 (12/241, 12/206, and 5/255) as well as their genome portraying mecA mediated methicillin resistance. Besides exhibiting strong biofilm formation ability, all the isolates exhibited positive responses towards tested virulence assays coupled with their genome displaying Coa, NucA, and CapE genes. On the other hand, isolates exhibited different levels of auto-aggregation (37.90 ± 1.8 to 51.53 ± 3.1%) and mucin adhesion ability (68.93 ± 0.61% to 86.62 ± 1.96%) with a significant (P ≤ 0.05) variation in adhesion to different hydrocarbons. Finally, multivariate Principal Component Analysis and Hierarchical Cluster Analysis (HCA) heatmap using Euclidean distance measurement indicated MRSA 12/206 and 5/255 as most resistant and virulent isolates with the potential to adhere to the hydrophobic gut niche.