Phenotypic–Genotypic Discordance in Antimicrobial Susceptibility Testing of Staphylococcus aureus: Microbiological Mechanisms and Diagnostic Implications

Abstract

Antimicrobial susceptibility testing (AST) is central to the management of Staphylococcus aureus infections because therapeutic efficacy depends on the selection of agents that effectively target this highly adaptable pathogen. Conventional phenotypic AST techniques, including broth microdilution, disk diffusion, and automated systems, directly measure bacterial growth inhibition and are considered laboratory reference values. However, the increasing use of rapid genotypic methods, such as PCR-based resistance gene detection and whole-genome sequencing (WGS), has introduced additional complexity. Although molecular techniques provide faster turnaround times and high sensitivity for detecting known resistance determinants, they do not always correlate with phenotypic susceptibility. This phenomenon represents a major challenge in clinical microbiology and antimicrobial stewardship. Discordance may arise from silent resistance genes, mutations conferring insignificant, conditional resistance, and phenotypic resistance mechanisms involving novel or poorly defined pathways that are not detected by genotypic testing. Conversely, phenotypic susceptibility may not reflect the genetic potential for resistance activation under selective pressure. These discrepancies can generate clinical uncertainty, potentially leading to inappropriate antibiotic selection, delays in therapeutic adjustment, and unnecessary use of broad-spectrum agents. These outcomes emphasize the need to understand the factors underlying discordance and their clinical implications. This review examines the microbiological and molecular mechanisms responsible for phenotypic–genotypic discordance in S. aureus, with particular emphasis on the limitations of diagnostic assays and the interpretation challenges associated with current AST techniques. Understanding these mechanisms is essential for improving laboratory reporting strategies and enhancing the reliability of antimicrobial susceptibility assessments.