World Journal of
Pharmaceutical and Life Sciences

MOLECULAR PROFILING OF EMERGING ANTIMICROBIAL RESISTANCE GENES IN CLINICAL PATHOGENS: IMPLICATIONS FOR RAPID DIAGNOSTIC STRATEGIES

Bader S. Bin Owimer*, Khaled A. Alzahrani, Nasser A. Al-Homaid, Muna Alkhair, Atheer Y. Althagafi, Rahaf Algrafi, Refan Almowalad

ABSTRACT

The relentless dissemination of novel antimicrobial resistance (AMR) determinants among clinically salient Gram-negative and Gram-positive bacterial pathogens represents a profound threat to contemporary healthcare systems worldwide. Traditional culture-based phenotypic antimicrobial susceptibility testing (AST), while remaining a functional gold standard, suffers from inherent diagnostic latency, often requiring 48 to 72 hours from specimen acquisition to definitive actionable reporting. This investigation presents a comprehensive molecular profiling of emerging resistance genes—encompassing carbapenemases (blaNDM-1, blaKPC-2, blaOXA-48-like, blaVIM-2), plasmid-mediated colistin resistance determinants (mcr-1 through mcr-10), extended-spectrum β-lactamases (blaCTX-M-15, blaSHV, blaTEM), and novel aminoglycoside modifying enzymes (armA, rmtB) isolated from a high-density cohort of multidrug-resistant (MDR) clinical isolates. Utilizing target-capture Next-Generation Sequencing (NGS), quantitative real-time PCR (qPCR) multiplex arrays, and digital droplet PCR (ddPCR), we evaluated gene copy number variation, plasmid replicon architecture, and expression dynamics under sub-inhibitory antibiotic pressure. Our empirical findings demonstrate that molecular profiling yields diagnostic concordance exceeding 98.4% with phenotypic resistance profiles, while reducing turnaround time (TAT) from 54 hours to 4.2 hours. Furthermore, integrated bioinformatic modeling revealed horizontal gene transfer (HGT) hot-spots mediated by insertion sequences (IS26, ISCR1) and conjugative IncHI2/IncFII plasmids. Incorporating these molecular markers into point-of-care rapid diagnostic platforms provides a paradigm shift for clinical decision-making, enabling early targeted antibiotic therapy, optimizing stewardship programs, and curtailing nosocomial transmission chains.

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