TY - JOUR
T1 - Clinical metagenomics for infectious corneal ulcers
T2 - Rags to riches?
AU - Ung, Lawson
AU - Bispo, Paulo J.M.
AU - Doan, Thuy
AU - Van Gelder, Russell N.
AU - Gilmore, Michael S.
AU - Lietman, Thomas
AU - Margolis, Todd P.
AU - Zegans, Michael E.
AU - Lee, Cecilia S.
AU - Chodosh, James
N1 - Funding Information:
This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. The authors acknowledge funding to their respective Departments of Ophthalmology by Research to Prevent Blindness, NY, NY.Lawson Ung, MD ? None to disclose Paulo J.M. Bispo, PhD ? None to disclose Thuy Doan, MD, PhD ? Research supported by NEI-NIH K08EY026986, Research to Prevent Blindness Russell N. Van Gelder, MD, PhD ? NEI-NIH R21EY027453, Research to Prevent Blindness, and the Mark J. Daily, MD Research Fund Michael S. Gilmore, PhD ? NEI-NIH R01EY024285, Research to Prevent Blindness Thomas Lietman, MD ? NEI-NIH 5U10EY022880, Research to Prevent Blindness Todd P. Margolis, MD, PhD ? Unrestricted grant from Research to Prevent Blindness; scientific advisory board and equity (stock options) in Rational Vaccines; and intellectual property in Retinal Cellscope. Michael E. Zegans, MD ? NEI-NIH R21EY02877-01; investigator-initiated research grant from MedImmune; and intramural Dartmouth funding as the Francis A. L'Esperance, Jr., MD, Visual Sciences Scholar at Dartmouth. Cecilia S. Lee, MD, MS ? NEI-NIH K23EY029246, Research to Prevent Blindness James Chodosh, MD, MPH ? NEI-NIH EY013124, EY021558, and EY014104, Research to Prevent Blindness, Massachusetts Lions Eye Research Fund; scientific advisory board for Shire; co-Editor-in-Chief, British Journal of Ophthalmology.
Funding Information:
Lawson Ung, MD – None to disclose Paulo J.M. Bispo, PhD – None to disclose Thuy Doan, MD, PhD – Research supported by NEI- NIH K08EY026986, Research to Prevent Blindness Russell N. Van Gelder, MD, PhD – NEI-NIH R21EY027453, Research to Prevent Blindness, and the Mark J. Daily, MD Research Fund Michael S. Gilmore, PhD – NEI-NIH R01EY024285, Research to Prevent Blindness Thomas Lietman, MD – NEI-NIH 5U10EY022880, Research to Prevent Blindness Todd P. Margolis, MD, PhD – Unrestricted grant from Research to Prevent Blindness; scientific advisory board and equity (stock options) in Rational Vaccines; and intellectual property in Retinal Cellscope. Michael E. Zegans, MD – NEI- NIH R21EY02877-01; investigator-initiated research grant from MedImmune; and intramural Dartmouth funding as the Francis A. L'Esperance, Jr., MD, Visual Sciences Scholar at Dartmouth. Cecilia S. Lee, MD, MS – NEI-NIH K23EY029246, Research to Prevent Blindness James Chodosh, MD, MPH – NEI- NIH EY013124, EY021558, and EY014104, Research to Prevent Blindness , Massachusetts Lions Eye Research Fund; scientific advisory board for Shire; co-Editor-in-Chief, British Journal of Ophthalmology.
Publisher Copyright:
© 2019 Elsevier Inc.
PY - 2020/1
Y1 - 2020/1
N2 - 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.
AB - 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.
KW - Clinical metagenomics
KW - Infectious corneal ulcers
KW - Microbial keratitis
KW - Next generation sequencing
UR - http://www.scopus.com/inward/record.url?scp=85078917767&partnerID=8YFLogxK
U2 - 10.1016/j.jtos.2019.10.007
DO - 10.1016/j.jtos.2019.10.007
M3 - Editorial
C2 - 31669750
AN - SCOPUS:85078917767
VL - 18
SP - 1
EP - 12
JO - Ocular Surface
JF - Ocular Surface
SN - 1542-0124
IS - 1
ER -