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Clinical metagenomics

Nature Reviews Genetics volume 20, pages 341–355 (2019)Cite this article

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Abstract

Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing how physicians diagnose and treat infectious disease, with applications spanning a wide range of areas, including antimicrobial resistance, the microbiome, human host gene expression (transcriptomics) and oncology. Here, we focus on the challenges of implementing mNGS in the clinical laboratory and address potential solutions for maximizing its impact on patient care and public health.

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Fig. 1: Clinical applications of metagenomic sequencing.
Fig. 2: Targeted versus untargeted shotgun metagenomic next-generation sequencing approaches.
Fig. 3: Challenges to routine deployment of metagenomic sequencing in the clinical setting.
Fig. 4: A typical metagenomic next-generation sequencing bioinformatics pipeline.

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Nature Reviews Genetics thanks J. C. Lagier, A. Nitsche and J. Dekker for their contribution to the peer review of this work.

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Authors and Affiliations

  1. Department of Laboratory Medicine, University of California, San Francisco, CA, USA

    Charles Y. Chiu & Steven A. Miller

  2. Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA

    Charles Y. Chiu

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  1. Charles Y. Chiu
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  2. Steven A. Miller
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The authors contributed equally to all aspects of the article.

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Correspondence to Charles Y. Chiu.

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Competing interests

C.Y.C. is the director of the UCSF–Abbott Viral Diagnostics and Discovery Center (VDDC) and receives research support from Abbott Laboratories. C.Y.C. and S.A.M. are inventors on a patent application on algorithms related to SURPI+ software titled ‘Pathogen Detection using Next-Generation Sequencing’ (PCT/US/16/52912).

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Related links

External RNA Controls Consortium (ERCC): http://jimb.stanford.edu/ercc/

FDA-ARGOS: https://www.ncbi.nlm.nih.gov/bioproject/231221

FDA Reference Viral Database (RVDB): https://hive.biochemistry.gwu.edu/rvdb

National Center for Biotechnology Information (NCBI) Nucleotide database: https://www.ncbi.nlm.nih.gov/nucleotide/

Glossary

Microbiome

The entirety of organisms that colonize individual sites in the human body.

Microarrays

Commonly referred to as ‘chips’, these platforms consist of spots of DNA fragments, antibodies or proteins printed onto surfaces, enabling massive multiplexing of hundreds to thousands of targets.

Reads

In DNA sequencing, reads are inferred sequences of base pairs corresponding to part of or all of a single DNA fragment.

Metagenomic NGS

(mNGS). A shotgun sequencing approach in which all genomic content (DNA and/or RNA) of a clinical or environmental sample is sequenced.

Transmission network analysis

The integration of epidemiological, laboratory and genomic data to track patterns of transmission and to infer origin and dates of infection during an outbreak.

Precision medicine

An approach to medical care by which disease treatment and prevention take into account genetic information obtained by genomic or molecular profiling of clinical samples.

Reference standards

In laboratory test development, well-characterized, standardized and validated reference materials or databases that enable measurement of performance characteristics of an assay, including sensitivity, specificity and accuracy.

Latex agglutination

A clinical laboratory test for detection of a specific antibody in which the corresponding antigen is adsorbed on spherical polystyrene latex particles that undergo agglutination in the presence of the antibody.

Seroconversion

The development of detectable antibodies in the blood that are directed against an infectious agent, such as HIV-1, after which the infectious disease can be detected by serological testing for the antibody.

Library

In DNA sequencing, a collection of DNA fragments with known adapter sequences at one or both ends that is derived from a single clinical or environmental sample.

Sanger sequencing

A classical method of DNA sequencing based on selective incorporation of chain-terminating dideoxynucleotides developed by Frederick Sanger and colleagues in 1977; now largely supplanted by next-generation sequencing.

Subtyping

In microbiology, refers to the identification of a specific genetic variant or strain of a microorganism (for example, virus, bacterium or fungus), usually by sequencing all or part of the genome.

Liquid biopsy

The detection of molecular biomarkers from minimally invasive sampling of clinical body fluids, such as DNA sequences in blood, for the purpose of diagnosing disease.

Spike-in

In laboratory test development, refers to the use of a nucleic acid fragment or positive control microorganism that is added to a negative sample matrix (for example, plasma from blood donors) or clinical samples and that serves as an internal control for the assay.

No-template control

In PCR or sequencing reactions, a negative control sample in which the DNA or cDNA is left out, thus monitoring for contamination that could produce false-positive results.

Biorobots

The automated instrumentation in the clinical laboratory that enables parallel processing of many samples at a time.

Point-of-care

Refers to diagnostic testing or other medical procedures that are done near the time and place of patient care (for example, at the bedside, in an emergency department or in a developing-world field laboratory).

Cluster density

On Illumina sequencing systems, a quality control metric that refers to the density of the clonal clusters that are produced, with each cluster corresponding to a single read. An optimal cluster density is needed to maximize the number and accuracy of reads generated from a sequencing run.

Q-score

A quality control metric for DNA sequencing that is logarithmically related to the base calling error probabilities and serves as a measurement of read accuracy.

Proficiency testing

A method for evaluating the performance of individual laboratories for specific laboratory tests using a standard set of unknown samples that permits interlaboratory comparisons.

Nanopore sequencing

A sequencing method in which DNA or RNA molecules are transported through miniature pores by electrophoresis. Sequencing reads are generated by measurement of transient changes in ionic current as the molecule passes through the pore.

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Chiu, C.Y., Miller, S.A. Clinical metagenomics. Nat Rev Genet 20, 341–355 (2019). https://doi.org/10.1038/s41576-019-0113-7

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