Advances in metagenomic sequencing for infectious disease management: From pathogen profiling to antibiotic resistance

Metagenomics has revolutionized the study of infectious diseases by enabling the analysis of microbial communities without the need for cultivation. This approach, powered by high-throughput sequencing technologies like 16S rRNA sequencing and shotgun metagenomics, allows the identification of both culturable and unculturable microbes, providing a comprehensive view of pathogens. Metagenomics offers critical insights into microbial diversity and interactions, particularly in polymicrobial infections, respiratory and gastrointestinal infections, and bloodstream infections. Advancements in bioinformatics, artificial intelligence (AI), and machine learning have enhanced the accuracy and speed of metagenomic data interpretation, aiding pathogen detection, antibiotic resistance surveillance, and personalized treatment strategies. Despite challenges such as sample complexity, host DNA interference, and data interpretation difficulties, metagenomics continues to evolve as a crucial tool for diagnostics and therapeutic development. Future research aims to address current gaps, including integrating AI into metagenomics for more precise pathogen profiling and developing targeted therapies based on microbial communities.