The Current State of Metagenomics in Infectious Disease

Key points

Significance

Metagenomics is the study of all genetic material (RNA and/or DNA) as it exists in a particular location or environment, such as a soil, seawater, or the human nasopharynx. Owing to the mixed nature of microbial communities, metagenomic studies historically were accomplished via amplification of conserved targets, cloning, and Sanger sequencing. Although meaningful clinical results could be derived from these approaches in humans [8], these methods were far too costly, laborious, and slow for

Strategies to overcome the abundance of human nucleic acids

Regardless of the sample type, human nucleic acids dominate the reads obtained by MDS for both DNAseq and RNAseq. This factor is most acute for highly human-cellular samples, such as tissues and sources with inflammatory responses in the setting of infection, but also presents a challenge for acellular sites such as plasma. In numerous clinical studies applying shotgun MDS to a variety of sample types, human reads typically constitute more than 99% of the data [1], [2], [4], [5], [6], [9], [10]

Regulatory aspects of metagenomic deep sequencing

Despite the tremendous enthusiasm for MDS in the clinical microbiology laboratory, this approach has primarily been applied in research studies, with very few clinically validated diagnostic MDS tests. As MDS grows in clinical diagnostics, standards and guidelines for assay design, validation, and interpretation are acutely needed for the appropriate clinical implementation of this complex methodology, expertly reviewed by Schlaberg and colleagues [39] and Gargis and colleagues [46]. Human

Present relevance and future avenues to consider or to investigate

The common theme between the clinical studies, methods considerations, and regulatory aspects discussed in this review is the lack of standardization for diagnostic MDS. Furthermore, the accuracy of MDS as a standalone assay is limited by the presence and quantity of pathogen nucleic acid and reference databases used. Indeed, MDS may never be sensitive enough if the pathogen quantity is too low to be detected over background contamination or if the pathogen nucleic acid present is not

Summary

Given the tremendous clinical promise, MDS will no doubt find its place in the future of infectious disease diagnostics. The technical and interpretive challenges outlined in this review require careful consideration by laboratories adopting this methodology. The standardization of wet bench and informatics approaches between laboratories and/or in collaboration with professional organizations and regulatory agencies may also ensure the best outcomes for patient care.