Evaluation of the bacterial ocular surface microbiome in ophthalmologically normal dogs prior to and following treatment with topical neomycin-polymyxin-bacitracin

Abstract

The ocular surface microbiome of veterinary species has not been thoroughly characterized using molecular-based techniques, such as next generation sequencing (NGS), as the vast majority of studies have utilized traditional culture-based techniques. To date, there is one pilot study evaluating the ocular surface of healthy dogs using NGS. Furthermore, alterations in the ocular surface microbiome over time and after topical antibiotic treatment are unknown. The objectives of this study were to describe the bacterial composition of the ocular surface microbiome in clinically normal dogs, and to determine if microbial community changes occur over time or following topical antibiotic therapy. Topical neomycin-polymyxin-bacitracin ophthalmic ointment was applied to one eye each of 13 adult dogs three times daily for seven days, while contralateral eyes served as untreated controls. The inferior conjunctival fornix of both eyes was sampled via swabbing at baseline prior to antibiotic therapy (day 0), after 1 week of treatment (day 7), and 4 weeks after discontinuing treatment (day 35). Genomic DNA was extracted from the conjunctival swabs and primers targeting the V4 region of bacterial 16S rRNA genes were used to generate amplicon libraries, which were then sequenced on an Illumina platform. Data were analyzed using Quantitative Insights Into Molecular Ecology (QIIME 2.0). At baseline, the most relatively abundant phyla sequenced were Proteobacteria (49.7%), Actinobacteria (25.5%), Firmicutes (12%), Bacteroidetes (7.5%), and Fusobacteria (1.4%). The most common families detected were Pseudomonadaceae (13.2%), Micrococcaceae (12%), Pasteurellaceae (6.9%), Microbacteriaceae (5.2%), Enterobacteriaceae (3.9%), Neisseriaceae (3.5%), and Corynebacteriaceae (3.3%). Alpha and beta diversity measurements did not differ in both control and treatment eyes over time. This report examines the temporal stability of the canine ocular surface microbiome. The major bacterial taxa on the canine ocular surface remained consistent over time and following topical antibiotic therapy.

Prevalence and Antibiotic Susceptibility of Bacterial Isolates From Dogs With Ulcerative Keratitis in Midwestern United States

“…In fact, diagnostic tests other than culture-based methods will soon become the gold standard for microbial species identification as the field of clinical microbiology is rapidly evolving. Unlike culture-based methods, technologies such as mass spectrometry and nucleic acid sequencing provide rapid and sensitive tools to probe the microbiome in clinical patients ( 39 )—as recently described for the ocular surface of veterinary species ( 40 , 41 )—enabling clinicians to optimize the antibiotic treatment sooner and thereby improve clinical outcomes ( 42 ).…”

Prevalence of Antimicrobial Resistant Bacteria from Conjunctival Flora in an Eye Infection Prone Breed (Saint Bernard)

“…Among different species of the genus, the most predominantly involved in ocular diseases seems to be S. intermedius , followed by S. aureus and less coagulase negative staphylococci [ 18 ]. Although the second-most detected genus in this study was Trueperella , other studies have suggested a minor involvement in the pathogenesis of ocular diseases [ 19 , 20 ]. Conversely, the genus Micrococcus seems to be detected from both normal and pathogenic flora [ 20 , 21 , 22 ].…”

Case Report: Successful Management of Refractory Keratomycosis in an Alpaca Using Penetrating Keratoplasty and Combination Antifungal Therapy (Caspofungin 0.5% and Terbinafine 1%)

“…However, a decrease in positive fungal cultures were found after 2 weeks of NPB in normal horses ( 13 ). Additionally, in both normal dogs and horses, 1 week of NPB treatment did not significantly disrupt major bacterial taxa as measured by next generation sequencing ( 30 , 31 ). Conversely, in dogs, topical ofloxacin for 3 weeks after cataract surgery has been shown to lead to a decrease in positive bacterial cultures during treatment, an increase in positive bacterial cultures 3 weeks after stopping treatment, and an alteration in bacterial sensitivity ( 32 ).…”