Comparative phylogenomic and long-read genomic characterization of an Egyptian ST6-MRSA-IVa clinical isolate within a globally conserved multidrug-resistant lineage

Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) remains a major global public health concern due to its multidrug resistance, extensive genome plasticity, and rapid evolutionary adaptability. In this study, 50 clinical MRSA isolates were screened using antimicrobial susceptibility testing and the VITEK® 2 system to identify multidrug-resistant phenotypes. One isolate (SAMN57098905; MRSA21-2025) exhibiting the broadest multidrug-resistant profile among the analyzed isolates was selected for integrated long-read genomic and comparative phylogenomic characterization. Whole-genome sequencing was performed using Oxford Nanopore Technologies followed by Medaka polishing, genome annotation, antimicrobial resistance profiling, virulence characterization, SCCmec typing, insertion-sequence analysis, prophage identification, multilocus sequence typing (MLST), and comparative phylogenomics against 50 publicly available ST6 genomes. Core-genome maximum-likelihood phylogeny together with Panaroo-based pan-genome reconstruction was applied to investigate evolutionary relatedness and genomic diversification. The near-complete genome assembly (~2.85 Mb; 33.14% GC content) was reconstructed into three contigs with high sequencing depth and assigned to ST6, spa type t304, and SCCmec type IVa (2B). Resistome analysis revealed a predominantly chromosomally encoded multidrug-resistant architecture centered on <i>mecA</i> and SCCmec-associated determinants together with multiple efflux-associated and regulatory-associated resistance loci including <i>norA</i>, <i>norC, sdrM, mgrA, arlS</i>, and <i>mepA</i>. Comparative phylogenomic analyses demonstrated that the Egyptian isolate clustered within a geographically distributed ST6-IVa lineage closely related to European and Asian clinical strains, supporting phylogenetic conservation within this clonal background. Pan-genome analysis identified 2,495 core genes within a total pan-genome of 2,680 genes, indicating substantial lineage conservation with accessory genome variability. Mobilome analysis identified 19 insertion-sequence elements distributed across eight IS families, highlighting extensive genome plasticity and potential genome remodeling activity. Two chromosomally integrated prophages were additionally detected, including a Sa3int-like immune evasion prophage carrying the IEC-associated genes <i>sak</i> and scn integrated within the <i>β</i>-hemolysin locus. Virulence profiling revealed a broad toxin-associated repertoire including <i>sea</i>, <i>hlgABC</i>, <i>lukDE</i>, splA/B/E, and aur, whereas canonical Panton-Valentine leukocidin genes were not fully detected. Collectively, this study provides a high-resolution long-read comparative genomic framework linking multidrug resistance, mobilome composition, prophage-associated virulence, and phylogenetic structure in an Egyptian ST6-MRSA-IVa isolate, highlighting the value of integrated comparative genomics for genomic surveillance and evolutionary tracking of clinically relevant MRSA lineages.