Antimicrobial Resistance in the Modern Era: Advances in Laboratory Detection, Emerging Mechanisms, and Diagnostic Challenges

Abstract

Antimicrobial resistance (AMR) has emerged as a major global health challenge, reducing the effectiveness of antimicrobial therapies and complicating the management of bacterial infections. The rapid emergence and dissemination of resistant microorganisms are driven by genetic mutations, horizontal gene transfer, antimicrobial selection pressure, and inappropriate use of antimicrobial agents. Laboratory diagnosis plays a critical role in identifying resistant pathogens and guiding appropriate therapeutic decisions. Conventional antimicrobial susceptibility testing methods, including disk diffusion, broth microdilution, and automated systems, remain widely used; however, their limitations include prolonged turnaround times and difficulties in detecting certain resistance phenotypes. Recent advances in molecular diagnostics, multiplex polymerase chain reaction, whole-genome sequencing, and rapid phenotypic technologies have improved the detection of resistance-associated genes and mechanisms. Nevertheless, the increasing diversity of resistance determinants presents significant diagnostic challenges, particularly when genotypic resistance markers do not directly correspond with phenotypic susceptibility. Emerging mechanisms, including enzymatic drug inactivation, alteration of antimicrobial targets, reduced membrane permeability, and enhanced efflux activity, further complicate laboratory detection. In addition, biofilm formation and heteroresistance may contribute to treatment failure while remaining difficult to identify using routine diagnostic approaches. This review highlights recent advances in laboratory-based AMR detection, examines major and emerging mechanisms of antimicrobial resistance, and discusses diagnostic limitations affecting timely and accurate identification of resistant pathogens. Strengthening laboratory capacity, integrating rapid molecular and phenotypic methods, and implementing standardized diagnostic approaches are essential for improving antimicrobial stewardship and supporting effective clinical management of resistant infections.