Molecular diagnostics in clinical microbiology: Advances, applications, and future directions

Abstract

Molecular diagnostics have transformed clinical microbiology by enabling rapid, accurate, and highly sensitive detection of infectious agents, significantly improving patient outcomes and public health response. Over the past decade, advances in polymerase chain reaction (PCR), next-generation sequencing (NGS), digital PCR, isothermal amplification, and CRISPR-based assays have enhanced pathogen identification, antimicrobial resistance profiling, and outbreak investigation. These technologies have been instrumental in detecting and monitoring emerging and re-emerging viral pathogens such as SARS-CoV-2, Nipah, Zika, H5N1 avian influenza, Mpox, Ebola, Marburg, and MERS-CoV. Molecular diagnostics also play a critical role in antimicrobial resistance surveillance and hospital infection control by enabling high-resolution tracking of resistance genes and pathogen transmission dynamics. Despite these achievements, challenges remain regarding implementation costs, technical expertise, infrastructure, and the need for global standardization. Future directions focus on developing cost-effective, point-of-care molecular platforms, integrating artificial intelligence and bioinformatics for enhanced interpretation, and applying these technologies within One Health and environmental surveillance frameworks. These innovations will be pivotal for early outbreak detection, real-time data-driven decision-making, and equitable access to advanced diagnostics worldwide. Ultimately, molecular diagnostics are poised to remain the cornerstone of precision medicine and infectious disease control in the era of global health challenges.