Genotypic and Phenotypic Divergence of MRSA in Northwestern Nigeria: Strengthening Actionable Surveillance and Clinical Diagnostics

<title>Abstract</title> <p> Background Methicillin-resistant <italic>Staphylococcus aureus</italic> (MRSA) remains a High Priority Pathogen on the World Health Organization (WHO) Bacterial Priority Pathogens List. However, phenotypic disc diffusion screening frequently overestimates <italic>mecA</italic> -mediated resistance in sub-Saharan Africa, creating significant diagnostic and therapeutic challenges. This study evaluated the phenotypic resistance profiles, <italic>mecA</italic> gene carriage, structural <italic>SCCmec</italic> cassette architectures, <italic>spa</italic> clonal diversity, and phylogenetic relationships of clinical <italic>S. aureus</italic> isolates across Northwestern Nigeria. Methods An 18-month (October 2019-July to 2021) multi-center cross-sectional surveillance study was executed across nine tertiary and specialist hospitals in Kano, Kaduna, Katsina, and Jigawa states. A total of 800 paired wound and nasal swab specimens were collected from 400 patients presenting with suppurative septic wounds. Phenotypic methicillin resistance was screened using 30µg cefoxitin disc diffusion per CLSI guidelines. Molecular confirmation of <italic>mecA</italic> and <italic>SCCmec</italic> structural types (I–V) was performed via multiplex PCR. Polymorphic X-region mapping of the <italic>spa</italic> gene was resolved through bidirectional Sanger chain-termination sequencing. Evolutionary relationships and ancestral distances were reconstructed using the Neighbor-Joining method in MEGA11. Results Phenotypic screening provisionally classified 144 clinical isolates (34.9%) as MRSA. Polymerase Chain Reaction (PCR) amplification confirmed the canonical <italic>mecA</italic> determinant in only 9 isolates (6.25%), leaving 135 phenotypic MRSA isolates (93.75%) as <italic>mecA</italic> -negative. Confirmed <italic>mecA</italic> -positive strains were restricted to urban tertiary centers in Kano and Kaduna states. <italic>SCCmec</italic> structural typing revealed Type III in 3 isolates (33.3%), Type II in 1 isolate (11.1%), and non-typeable (NT) elements in 5 isolates (55.6%). High-resolution <italic>spa</italic> typing identified four distinct clonal lineages: t037, t425, t1123, and t1223. Neighbor-Joining phylogenetic analysis demonstrated complete evolutionary separation of local Nigerian isolates from global NCBI reference genomes, forming distinct regional sub-clusters at ancestral nodes 47, 64, and 74. Conclusions A profound diagnostic divergence (93.75%) exists between phenotypic cefoxitin screening and <italic>mecA</italic> gene carriage in Northwestern Nigeria. Relying solely on disc diffusion over-diagnoses classical MRSA, driving inappropriate glycopeptide escalation and selection pressure for vancomycin resistance. Regional surveillance networks must integrate secondary target screening ( <italic>blaZ</italic> hyper-expression, <italic>pbp</italic> point mutations, <italic>mecC</italic> ) alongside genomic surveillance to accurately characterize non- <italic>mecA</italic> -mediated resistance phenotypes. </p>