RT Journal Article
SR Electronic
T1 Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 176529
DO 10.1101/176529
A1 Philipp Kirstahler
A1 Søren Solborg Bjerrum
A1 Alice Friis-Møller
A1 Morten la Cour
A1 Frank M. Aarestrup
A1 Henrik Westh
A1 Sünje Johanna Pamp
YR 2018
UL http://biorxiv.org/content/early/2018/01/31/176529.abstract
AB Advances in genomics have the potential to revolutionize clinical diagnostics. Here, we examine the microbiome of vitreous (intraocular body fluid) from patients who developed endophthalmitis following cataract surgery or intravitreal injection. Endophthalmitis is an inflammation of the intraocular cavity and can lead to a permanent loss of vision. As controls, we included vitreous from endophthalmitis-negative patients, balanced salt solution used during vitrectomy, and DNA extraction blanks. We compared two DNA isolation procedures and found that an ultraclean production of reagents appeared to reduce background DNA in these low microbial biomass samples. We created a curated microbial genome database (>5700 genomes) and designed a metagenomics workflow with filtering steps to reduce DNA sequences originating from: i) human hosts, ii) ambiguousness/contaminants in public microbial reference genomes, and iii) the environment. Our metagenomic read classification revealed in nearly all cases the same microorganism than was determined in cultivation‐ and mass spectrometry-based analyses. For some patients, we identified the sequence type of the microorganism and antibiotic resistance genes through analyses of whole genome sequence (WGS) assemblies of isolates and metagenomic assemblies. Together, we conclude that genomics-based analyses of human ocular body fluid specimens can provide actionable information relevant to infectious disease management.