Background: Accurate Methicillin-resistant Staphyloccus aureus (MRSA) colonization surveillance depends critically on anatomical site selection. Conventional protocols prioritize nasal swabbing, but evidence from immunocompetent populations may not apply to people living with HIV/AIDS (PLWH), who exhibit atypical cutaneous colonization patterns. Concurrently, the staphylococcal cassette chromosome mec (SCCmec) type — the principal molecular classifier distinguishing healthcare-associated from community-associated MRSA lineages — has not been characterised in any PLWH cohort from Edo State, Nigeria. This study evaluates the diagnostic yield of different anatomical swabbing strategies and characterizes the prevalence and co-carriage of SCCmec types II and V among MRSA isolates from PLWH at ISTH.

Methods: 230 MRSA isolates from nasal, axillary, and groin swabs of 176 PLWH were subjected to multiplex PCR for SCCmec types II and V (Zhang protocol). Site-specific MRSA positivity rates and incremental mecA-positive detection yields of all single-site and multi-site swabbing combinations were calculated. Chi-square, phi coefficient (φ = √χ²/n), Spearman rank correlation (continuous variables), and logistic regression assessed SCCmec associations.

Results: Groin had the highest specimen positivity rate (53.4%, 94/176), exceeding nasal (40.3%, 71/176) and axilla (36.9%, 65/176). A nasal-only protocol captured 31.7% of mecA+ isolates; nasal+groin captured 71.5%; all three sites captured 100%. SCCmec type II was detected in 105 isolates (45.7%) and type V in 108 (47.0%). Both co-occurred in 88 isolates (38.3%; φ=0.668, χ²=102.64, p<0.001, OR=27.2, 95%CI 13.4–55.1). SCCmec distribution was uniform across sites (all p>0.88). Underlying disease independently predicted SCCmec II positivity (aOR=0.35, p=0.017); hand covering while sneezing predicted SCCmec V positivity (aOR=2.18, p=0.022).

Conclusion: Groin is the highest-yield single MRSA site in PLWH. A nasal+groin two-site strategy captures 71.5% of mecA+ isolates; three-site swabbing achieves 100%. The near-equal co-predominance of SCCmec types II and V with large-magnitude phi concordance (φ=0.668) is consistent with a dual-cassette MRSA complex circulating in this ART clinic setting.