Evaluation of full-length nanopore 16S sequencing for detection of pathogens in microbial keratitis.

ABSTRACT:

Background

Microbial keratitis is a leading cause of preventable blindness worldwide. Conventional sampling and culture techniques are time-consuming, with over 40% of cases being culture-negative. Nanopore sequencing technology is portable and capable of generating long sequencing reads in real-time. The aim of this study is to evaluate the potential of nanopore sequencing directly from clinical samples for the diagnosis of bacterial microbial keratitis.

Methods

Using full-length 16S rRNA amplicon sequences from a defined mock microbial community, we evaluated and benchmarked our bioinformatics analysis pipeline for taxonomic assignment on three different 16S rRNA databases (NCBI 16S RefSeq, RDP and SILVA) with clustering at 97%, 99% and 100% similarities. Next, we optimise

SUBMITTER: Low L 

PROVIDER: S-EPMC7891086 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature