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Metagenomic DNA sequencing for the diagnosis of intraocular infections

By Thuy Doan, Nisha R Acharya, Benjamin A. Pinsky, Malaya K. Sahoo, Eric D. Chow, Niaz Banaei, Indre Budvytiene, Vicky Cevallos, Lina Zhong, Zhaoxia Zhou, Thomas M Lietman, Joseph DeRisi

Posted 18 Feb 2017
bioRxiv DOI: 10.1101/109686 (published DOI: 10.1016/j.ophtha.2017.03.045)

Purpose: To compare the performance of unbiased high-throughput sequencing with pathogen-directed PCR using DNA isolated from archived ocular fluid, approaches that are compatible with the current sample handling practice of ophthalmologists. Design: Retrospective molecular study of banked vitreous samples. Methods: We evaluated a metagenomic DNA sequencing-based approach (DNA-seq) using archived positive (n = 31) and negative (n=36) vitreous specimens as determined by reference pathogen-specific PCR assays (herpes simplex virus 1 and 2, cytomegalovirus, varicella-zoster virus, and Toxoplasma gondii). Pathogens were identified using a rapid computational pipeline to analyze the non-host sequences obtained from DNA-seq. Clinical samples were de-identified and laboratory personnel handling the samples and interpreting the data were masked. Results: Metagenomic DNA sequencing detected 87% of positive reference samples. In the presumed negative reference samples, DNA-seq detected an additional 6 different pathogens in 8 samples (22% of negative samples) that were either not detected or not targeted with pathogen-specific PCR assays. Infectious agents identified only with DNA-seq were Candida dubliniensis, Klebsiella pneumoniae, human herpesvirus 6 (HHV-6), and human T-cell leukemia virus type 1 (HTLV-1). Discordant samples were independently verified in CLIA-certified laboratories. CMV sequences were compared against the antiviral mutation database and 3 of the samples were found to have mutations conferring ganciclovir resistance. Conclusions: Metagenomic DNA sequencing was highly concordant with pathogen-directed PCRs. The unbiased nature of metagenomics DNA sequencing allowed an expanded scope of pathogen detection, including bacteria, fungal species, and viruses, resolving 22% of cases that had previously escaped detection by routine pathogen-specific PCRs. The detection of drug resistance mutations highlights the potential for unbiased sequencing to provide clinically actionable information beyond pathogen species detection.

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