Molecular Characterization and Comparative Genomics of Two <i>Staphylococcus pseudintermedius</i> Strains from Humans in Egypt

<i>Staphylococcus pseudintermedius</i> is an opportunistic bacterium previously associated with dogs but has recently been found in human infections, raising zoonotic concerns. Genomic characterization of human <i>S. pseudintermedius</i> isolates can provide preliminary information on antibiotic resistance, pathogenicity, and genomic features relevant to host range. Two <i>S. pseudintermedius</i> isolates (hereafter referred to as <i>S. pseudintermedius</i> EGH1 and <i>S. pseudintermedius</i> EGH2) from human clinical samples in Egypt were sequenced using the Illumina NovaSeq X Plus platform. To assess genetic relatedness to human <i>S. pseudintermedius</i> isolates worldwide, multilocus sequence typing (MLST), pangenome analysis, and antimicrobial resistance gene profiling were performed. The sequencing produced a total of 9,499,989 reads for <i>S. pseudintermedius</i> EGH1 and 9,567,531 reads for <i>S. pseudintermedius</i> EGH2. Sequences were assembled with Geneious Prime^® 2025 and annotated using NCBI Prokaryotic Genome Annotation Pipeline v6.10. Pangenome analysis identified 9574 genes, comprising 1681 core genes (17.56%), 180 soft-core genes (1.88%), 837 shell genes (8.74%), and 6876 cloud genes (71.82%). MLST was conducted on human <i>S. pseudintermedius</i> genome assemblies using MLST v2.23.0. The analysis revealed both isolates as novel sequence types: <i>S. pseudintermedius</i> EGH1 was assigned ST-3037 with a new allele (<i>purA</i>-107), and <i>S. pseudintermedius</i> EGH2 was assigned ST-2874. Clonal relationships among <i>S. pseudintermedius</i> isolates were evaluated using the eBURST algorithm. This study presents the first next-generation genome sequencing and comparative genomic analysis of <i>S. pseudintermedius</i> isolates from humans in Egypt. Future studies integrating genomic, epidemiological, and phenotypic data are required.