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2020 OMIG Abstract

Assessment of the Impact of Sample Collection Order on the Diagnostic Performance of Metagenomic Deep Sequencing for Infectious Keratitis

Travis K Redd, MD, MPH1, Prajna Lalitha, MD2, N. Venkatesh Prajna, MD2, Misra Sikha, MD2, Rameshkumar Gunasekaran, MD2, Armin Hinterwirth, PhD1, Cindi Chen, MS2, Lina Zhong, BS2,
Zijun Liu, MS2, Thomas Lietman, MD1, Jeremy Keenan, MD, MPH2, Thuy Doan, MD, PhD2,
Gerami Seitzman, MD1

1Francis I. Proctor Foundation, University of California San Francisco, CA, USA; 2Aravind Eye Hospital, Madurai, Tamil Nadu, India

Purpose: To determine whether the diagnostic yield of metagenomic deep sequencing (MDS) for determining the causative pathogen in infectious keratitis is affected by the order of sample collection relative to other microbiologic specimens.

Methods: We performed a cross sectional evaluation of diagnostic test performance among subjects presenting with infectious corneal ulcers at Aravind Eye Hospital in Madurai, India. All subjects underwent corneal scrapings of the affected eye to obtain KOH smear, gram stain, bacterial culture, and fungal culture, in this order. MDS specimen collection was randomized to occur anywhere between the 1st and 5th specimen collected, which served as the primary predictor. Outcomes included the normalized copy number of pathogenic RNA detected by MDS, the proportion of MDS samples which were diagnostic, and agreement of MDS results with cultures.

Results: MDS samples from 46 subjects with corneal ulcers were evaluated. MDS was positive in 33 subjects (76%) and had 74% overall agreement with culture results. There was no association between order of MDS sample collection and normalized copy number of genetic material detected (P=0.62) or the likelihood of MDS positivity (P=0.46). However, the likelihood of agreement between MDS and cultures decreased when MDS samples were collected after other specimens (P=0.04). This was true regardless of bacterial or fungal etiology. Specifically, MDS samples collected later were more likely to be positive while cultures were negative (P=0.05).

Conclusion: The overall yield of MDS for detecting the cause of infectious keratitis was not affected by sample collection order. However, diagnostic agreement between MDS and cultures decreased when MDS samples were collected after other specimens. Additional investigation is warranted to determine whether this represents increased sensitivity of MDS compared to cultures or higher susceptibility to contaminants. These results may inform strategic specimen collection when suspicion for a particular pathogen is high.

Disclosure: N

Support: Supported by the Career Developmental Award and the unrestricted departmental funding provided by Research to Prevent Blindness and the K08EY026986.



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