Abstarct:

Metagenomics next-generation sequencing (mNGS) has become a revolutionary tool in clinical infectious disease diagnostics, offering remarkable abilities for unbiased pathogen detection. This thorough review explores the development of mNGS from research settings to clinical use, evaluating its applications across various infectious diseases such as central nervous system infections, respiratory tract issues, bloodstream infections, and detection of emerging pathogens. We assess the main sequencing platforms, including Illumina, Oxford Nanopore Technologies, and MGI sequencing systems, discussing their benefits and drawbacks in clinical environments. The review critically examines the current obstacles in implementing mNGS clinically, such as complexities in sample processing, bottlenecks in bioinformatics analysis, lack of standardization, and cost factors. By analyzing clinical performance data in depth, we compare the diagnostic accuracy of mNGS with traditional methods across different infection types, emphasizing its improved detection rates for hard-to-culture organisms and its limitations in samples with high host background. The review also investigates emerging solutions to these technical challenges, like enhanced sample preparation techniques, automated bioinformatics pipelines, and standardized quality control practices. We address the economic impact of mNGS adoption, regulatory issues, and the technology's potential role in antimicrobial stewardship and outbreak investigations. Finally, we offer insights into the future of clinical metagenomics, including its integration with artificial intelligence, the creation of rapid sequencing protocols, and its expansion into personalized medicine. This review provides a comprehensive resource for clinicians, lab professionals, and researchers interested in the current status and future possibilities of clinical metagenomics in infectious disease diagnostics.