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Kara Marie Cavuoto, Anat Galor, Darlene Miller, Santanu Banerjee; Determining the Ideal Swab Material for Analyzing the Ocular Surface Microbiome. Invest. Ophthalmol. Vis. Sci. 2018;59(9):904. doi: https://doi.org/.
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© ARVO (1962-2015); The Authors (2016-present)
Many different types of swab materials have been used to evaluate the ocular surface microbiome, however no study has directly compared the materials. We sought to identify which collection material was optimal for recovering bacterial DNA from the paucibacterial ocular surface in both pediatric and adult populations.
Prospective, cross-sectional study using 16S sequencing to evaluate the ocular surface microbiome comparing bacterial yield and composition by swab type. 16S sequencing was performed using Illumina MiSeq 250 and analyzed using Qiime. Statistical analysis was performed using a two-sided student’s t-test and Monte Carlo permutations.
30 patients (15 children [mean 3.7 years], 15 adults [mean 60.4 years]) were sampled using cotton, calcium alginate and polyester swabs. Calcium alginate samples had the highest operational taxonomic unit (OTU) counts compared to cotton or polyester. Alpha diversity calculations showed that calcium alginate swabs exhibited significantly higher sequencing depth than cotton or polyester applicators (p=0.001). Shannon index measurements demonstrated the samples collected with calcium alginate showed compact diversity/evenness values for each sample in both age groups. In contrast, polyester samples exhibited a wide range of diversity in the pediatric samples and cotton showed a wide range for both age groups. In Faith’s PD analysis, both calcium alginate and polyester showed close diversity values among samples of each age group compared to cotton, in which the species richness values were inconsistent. Samples collected with calcium alginate swabs showed adult and pediatric samples formed significantly distinct clusters on a principal coordinate analysis plot, without any sub-clustering based on a specific eye, prior surgical intervention, or topical medication use.
Calcium alginate swabs were superior to cotton or polyester swabs for ocular surface microbiome specimen collection in both pediatric and adult populations.
This is an abstract that was submitted for the 2018 ARVO Annual Meeting, held in Honolulu, Hawaii, April 29 - May 3, 2018.
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