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Next generation sequencing for pathogen discovery, ready for prime time?

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AuthorBlock: Cecilia S. Lee1, James Chodosh2, Russell N. Van Gelder1, Paulo Bispo2, Regis P. Kowalski3, Todd Margolis4, Michael Zegans5, Tom Lietman6, Thuy Doan6, Lucia Sobrin2
1University of Washington, Seattle, Washington, United States; 2Massachusetts Eye and Ear, Massachusetts, United States; 3University of Pittsburgh, Pennsylvania, United States; 4Washington University in St. Louis, Missouri, United States; 5Dartmouth-Hitchcock Medical Center, New Hampshire, United States; 6Francis I. Proctor Foundation, California, United States;

DisclosureBlock: Cecilia S. Lee, None; James Chodosh, Shire Code C (Consultant) , Russell N. Van Gelder, None; Paulo Bispo, None; Regis P. Kowalski, None; Todd Margolis, CellScope retina Code P (Patent) , Rational Vaccines Code I (Personal Financial Interest) , Michael Zegans, None; Tom Lietman, None; Thuy Doan, None; Lucia Sobrin, None;

SIG Description (Limit 1200 Characters)
The causative pathogens of many sight-threatening ocular infections are often undetected by traditional culture techniques. The landmark trial Endophthalmitis Vitrectomy Study (EVS) revealed that only 291 out of 420 (69.3%) endophthalmitis cases were culture-positive, leaving more than 30% of the cases without an etiologic diagnosis. Even more problematic is the culture-positivity rate following intravitreal injections. A recent review of 27,735 consecutive intravitreal injections showed that among 23 cases of endophthalmitis, 16 (70%) were culture-negative, demonstrating the need for a more sensitive modality for pathogen detection.

Recent advances in molecular techniques have allowed more sensitive and specific diagnostic tools available for clinical use. In particular, next generation sequencing (NGS) allows massive parallel sequencing from a limited amount of sample and is being increasingly used for pathogen detections. However, no standard method of analyzing exists and its imitations are poorly understood. We will review the basics of NGS techniques and address the advantages and challenges of using NGS technology for pathogen detection in various presumed infectious cases.