A Genomic Approach to Investigating Ocular Surface Microorganisms: Monitoring Core Microbiota on Eyelid Margin with a Dot hybridization Assay

Characterization and Comparison of Ocular Surface Microbiome in Newborns

The ocular microbiome is of fundamental importance for immune eye homeostasis, and its alteration would lead to an impairment of ocular functionality. Little evidence is reported on the composition of the ocular microbiota of term infants and on the impact of antibiotic prophylaxis. Methods: A total of 20 conjunctival swabs were collected from newborns at birth and after antibiotic treatment. Samples were subjected to 16S rRNA sequencing via system MiSeq Illumina. The data were processed with the MicrobAT software and statistical analysis were performed using two-way ANOVA. Results: Antibiotic prophylaxis with gentamicin altered the composition of the microbiota. In detail, a 1.5- and 2.01-fold reduction was recorded for Cutibacterium acnes (C. acnes) and Massilia timonae (M. timonae), respectively, whereas an increase in Staphylococcus spp. of 6.5 times occurred after antibiotic exposure. Conclusions: Antibiotic prophylaxis altered the ocular microbiota whose understanding could avoid adverse effects on eye health.

Application Progress of High-Throughput Sequencing in Ocular Diseases

Ocular diseases affect multiple eye parts and can be caused by pathogenic infections, complications of systemic diseases, genetics, environment, and old age. Understanding the etiology and pathogenesis of eye diseases and improving their diagnosis and treatment are critical for preventing any adverse consequences of these diseases. Recently, the advancement of high-throughput sequencing (HTS) technology has paved wide prospects for identifying the pathogenesis, signaling pathways, and biomarkers involved in eye diseases. Due to the advantages of HTS in nucleic acid sequence recognition, HTS has not only identified several normal ocular surface microorganisms but has also discovered many pathogenic bacteria, fungi, parasites, and viruses associated with eye diseases, including rare pathogens that were previously difficult to identify. At present, HTS can directly sequence RNA, which will promote research on the occurrence, development, and underlying mechanism of eye diseases. Although HTS has certain limitations, including low effectiveness, contamination, and high cost, it is still superior to traditional diagnostic methods for its efficient and comprehensive diagnosis of ocular diseases. This review summarizes the progress of the application of HTS in ocular diseases, intending to explore the pathogenesis of eye diseases and improve their diagnosis.

Temporal impacts of topical ceftazidime and tobramycin-vancomycin mixtures on the ocular surface microbiota in rabbits

Antibiotics are one of the important factors that can alter the diversity and composition of ocular surface microbiota. At present, there are a few studies about the antibiotic effect on ocular surface microbiota, including its time-dependent changes. However, these limited studies have revealed various results, and more experiments are required. In this study, we used 16 S rRNA sequencing method to investigate the effects of topical ceftazidime and tobramycin-vancomycin mixtures on the ocular surface microbiota and the temporal changes of the microbiota after discontinuing antibiotic treatment in rabbits. Seventeen healthy rabbits were treated with 5% ceftazidime and a mixture of 0.3% tobramycin-5% vancomycin (CTV) eye drops on one eye four times a day for 7 days. Swab samples of conjunctiva sacs were collected before antibiotic treatment (D0), 12 h after the last antibiotic treatment (D8) and two further time points on Day 15 (D15) and Day 30 (D30). We found that the species diversity of the ocular surface microbiota increased significantly at D8 and was restored at D15, namely, one week after antibiotic cessation. The community structure of the ocular surface microbiota changed after treatment with CTV but recovered at D30. At D8, the relative abundances of 13 bacterial phyla of the initial top 20 phyla and 11 bacterial genera of the initial top 20 genera were significantly different from the relative abundances of the phyla and genera at D0. Furthermore, the relative abundance of the dominant phylum Epsilonbacteraeota obviously decreased, while Proteobacteria and Bacteroidetes markedly increased. For dominant genera, the relative abundance of Helicobacter notably decreased, while Acinetobacter and Pasteurella greatly increased. Thirteen altered bacterial phyla and 7 of 11 altered bacterial genera recovered to preantibiotic levels at D30. In addition, there was a group of nondominant and rare bacteria enriched at D8, and most of them were restored at D30. In conclusion, the species diversity, community structure and composition of the ocular surface microbiota changed greatly after exposure to CTV, but they tended to be restored within weeks after discontinuing antibiotic treatment.

Comparison of 16S rDNA Amplicon Sequencing With the Culture Method for Diagnosing Causative Pathogens in Bacterial Corneal Infections

Purpose

The purpose of this study was to explore if 16S rDNA amplicon sequencing can improve the conventional diagnosis of causative pathogens for bacterial corneal infection.

Methods

Corneal scraping and conjunctiva and eyelid margin swab samples from infected eyes of patients diagnosed with "bacterial corneal infection" and conjunctiva and eyelid margin swab samples from a random eye of healthy participants were collected. Each swab was used for both aerobic and anaerobic cultures and 16S rDNA amplicon sequencing. The V3 to V4 region of the 16S rDNA was amplified using polymerase chain reaction (PCR) and sequenced on the Illumina HiSeq 2500 Sequencing Platform.

Results

The overall culture positivity rate for all 72 samples was 69% (72% in the bacterial keratitis group and 67% in the healthy control group), whereas 1719 operational taxonomic units in total were generated using 16S rDNA amplicon sequencing with each sample showing 123 to 337 different genera. Staphylococcus, Corynebacterium, Propionibacterium, and Micrococcus most frequently appeared in culture, whereas Streptococcus, Acinetobacter, and Lactobacillus were the most common genera, with large ratios in 16S rDNA amplicon sequencing. The causative pathogens detected by the two methods were inconsistent for most samples, except for several corneal samples.

Conclusions

We suggest that a combination of different techniques, such as clinical observation, microscopic analysis, culture, and next-generation sequencing techniques including 16S rDNA amplicon sequencing, should be used to comprehensively analyze pathogens in corneal and external ocular infections.

Translational Relevance

This paper uses a basic research methodology for studying the microbiome in ocular samples to help improve the diagnostic accuracy of corneal and external ocular infections.