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Ocul Surf. 2019 Oct 25. pii: S1542-0124(19)30396-9. doi: 10.1016/j.jtos.2019.10.007. [Epub ahead of print]

Clinical metagenomics for infectious corneal ulcers: Rags to riches?

Author information

1
Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA.
2
Francis I. Proctor Foundation, Department of Ophthalmology, University of California, San Francisco, CA, USA.
3
Department of Ophthalmology, University of Washington, Seattle, WA, USA.
4
Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in Saint Louis, Saint Louis, USA.
5
Department of Surgery (Ophthalmology), and Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA.
6
Department of Ophthalmology, University of Washington, Seattle, WA, USA. Electronic address: leecs2@uw.edu.
7
Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA. Electronic address: james_chodosh@meei.harvard.edu.

Abstract

The emergence of clinical metagenomics as an unbiased, hypothesis-free approach to diagnostic testing is set to fundamentally alter the way infectious diseases are detected. Long envisioned as the solution to the limitations of culture-based conventional microbiology, next generation sequencing methods will soon mature, and our attention will inevitably turn to how they can be applied to areas of medicine which need it most urgently. In ophthalmology, the demand for this technology is particularly pressing for the care of infectious corneal ulcers, where current diagnostic tests may fail to identify a causative organism in over half of cases. However, the optimism found in the budding discourse surrounding clinical metagenomics belies the reality that clinicians and scientists will soon be inundated by oppressive volumes of sequencing data, much of which will be foreign and unfamiliar. Therefore, our success in translating clinical metagenomics is likely to hinge on how we make sense of these data, and understanding its implications for the interpretation and implementation of sequencing into routine clinical care. In this consortium-led review, we provide an outline of these data-related issues and how they may be used to inform technical workflows, with the hope that we may edge closer to realizing the potential of clinical metagenomics for this important unmet need.

KEYWORDS:

Clinical metagenomics; Infectious corneal ulcers; Microbial keratitis; Next generation sequencing

PMID:
31669750
DOI:
10.1016/j.jtos.2019.10.007

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