Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing.

ABSTRACT:

Purpose

We test the ability of next-generation sequencing, combined with computational analysis, to identify a range of organisms causing infectious keratitis.

Methods

This retrospective study evaluated 16 cases of infectious keratitis and four control corneas in formalin-fixed tissues from the pathology laboratory. Infectious cases also were analyzed in the microbiology laboratory using culture, polymerase chain reaction, and direct staining. Classified sequence reads were analyzed with two different metagenomics classification engines, Kraken and Centrifuge, and visualized using the Pavian software tool.

Results

Sequencing generated 20 to 46 million reads per sample. On average, 96% of the reads were classified as human, 0.3% corresponded to known vectors or contami

SUBMITTER: Li Z 

PROVIDER: S-EPMC5770184 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature