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2011 OMIG Abstract 8

Application of biome representational in silico karyotyping to characterization of
the contact lens microbiome

R.N. Van Gelder, L. Akileswaran, J. Shendure, K. Pepple                             
Departments of Ophthalmology and Genome Sciences, University of Washington, Seattle, WA

Purpose: Contact lens wear remains a leading risk factor for microbial keratitis in the US.  While contact lenses are known to form support substrates for development of biofilms, the full microbiome of normal contact lenses is not well established.

Methods: Biome representational in silico karyotyping (BRISK) is a method for generating a defined representation of all genomic DNA in a sample, and determining which sequences are derived from human, known microbial, and unknown microbial sources. 

Results: We have generated pilot data using BRISK for the analysis of the microbiome of two daily wear soft Acuvue contact lenses from one individual.  From the right lens, 1,039,332 33 bp tags were derived and 673,081 33 bp tags were derived from the left lens (for a total of ~56.5 million base pairs of sequenced DNA).  98% of sequences were of human origin, and a linear karyotype was obtained demonstrating quantitative recovery of tags.

A total of 878 tags matching known microbes were identified.  There was high concordance between lenses.  The three most commonly identified genera were Ralstonia, Propionibacteria, and Staphylococcus.  Multiple tags were identified for Cupriavidus, Streptococcus, Delftia, and Bradyrhizobium.  High levels of Propionibacterial phage were identified, along with rarer human papilloma virus-matching tags. 

25,890 tags matched neither human DNA nor known microbial DNA.  These sequences are presently being extended by chromosome walking to identify their source species.     

Conclusions: These data suggest that soft contact lenses harbor a rich and varied microbiome, which may include novel organisms, phage, and viruses.

Disclosures: S RVG: Alcon Research Labs, National Institutes of Health, Research to Prevent Blindness

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