The inputs of metagenomics in the diagnostic of infectious diseases

Abstract

Summary Over the past decade, next-generation sequencing (NGS) has made tremendous progress, transforming genomic analysis and opening up for many new opportunities in infectious disease diagnosis. The ability of metagenomics to analyze microbial communities without culturing organisms has even enlarged the application potential in this ever growing field. Whether based on targeted or unbiased (shotgun) sequencing approaches, metagenomics still rely on complex laboratory workflow and computational tools. However, recent advancement in sequencing platforms, turnaround time, nucleic acid extraction, library preparation and bio informatics pipelines are now positioning metagenomics very attractively for routine application in clinical microbiology laboratories. Although the completeness and correctness of the genome reference database along with the ability to rapidly interpret the relevant information remain the key challenges for delivering actionable results. Many examples on how to use metagenomics in clinical laboratories can be found in the medical literature. While a single metagenomics analysis delivers the potential to detect rare and novel pathogens, it is however, still necessary to balance the scientific plausibility against the possibility of identifying a truly novel association pathogen–infection when interpreting results. Additionally, metagenomics has brought a revolution in the field of microbiome analysis by generating new insights into the host-microbe relationship and into the therapeutic potential of microbiota modification. Now, the fast evolution of metagenomics challenges the regulatory framework and mandates cooperation among the medical and research communities, industry and regulatory bodies to foster the development of innovative solutions aimed at integrating metagenomics into the infectious diseases diagnostic arsenal.