Within-Host Genotypic Concordance of Oral and Extraoral Staphylococcus aureus: A Scoping Review

Background/Objectives: The oral cavity is a potential Staphylococcus aureus reservoir, but whether oral strains are genetically related to S. aureus at other body sites of the same individual is unclear. This scoping review mapped the evidence on within-person genotypic concordance between oral and extraoral S. aureus and on the direction of dissemination. Methods: Following PRISMA-ScR, PubMed and Web of Science were searched (last update 28 September 2026), supplemented by citation and recent-literature searches, for human studies comparing S. aureus from a true oral specimen with isolates from at least one extraoral site of the same individual by a strain-level genotypic method (e.g., pulsed-field gel electrophoresis, multilocus sequence typing, whole-genome sequencing). Findings were synthesized descriptively. Results: Fifteen reports (2003–2026) were included, covering 16 oral–extraoral comparisons: oral–nasal (n = 7), oral–lower respiratory or endotracheal (n = 5), oral–skin/wound (n = 3), and oral–rectal (n = 1). Within-person concordance was frequent but not universal: in the largest paired oral–nasal whole-genome study, 23 of 34 dual-site carriers (67.6%) harbored the same clone, and among intubated patients, 13 of 22 oral–nasal and 16 of 26 oral–subglottic isolate pairs differed by ≤9 single-nucleotide polymorphisms. Directional evidence was sparse and bidirectional, ranging from an oral clone preceding tracheal colonization to patterns compatible with nasal-to-oral seeding. Conclusions: Genetically related S. aureus lineages are repeatedly shared between the oral cavity and extraoral sites, supporting the oral cavity as one component of a dynamic multisite reservoir that is not addressed by screening and decolonization strategies directed at the nares alone. Establishing whether it is an upstream source of extraoral colonization or infection requires longitudinal multisite studies with high-resolution genomics.