Diagnostic Approach to Ocular Infections Using Various Techniques From Conventional Culture to Next-Generation Sequencing Analysis

Abstract

Ocular infection is caused by both endogenous (resident) and exogenous (environmental) microbes. As the ocular surface interacts with both outer environment and its own resident microbiota, clinical ocular samples are predicted to contain a diverse set of microorganisms. Microscopy of sample smears is an important step in the diagnostic process of infectious diseases to interpret the culture results. Traditional culture techniques have several limitations in the detection and/or identification of uncharacterized bacteria of environmental origin. Molecular biological techniques, such as polymerase chain reaction of pathogen-specific virulence genes, 16S rRNA gene clone library analysis, and next-generation sequencing of 16S rDNA amplicons, compensate for diagnostic culture techniques in diagnosing infectious diseases. These techniques are expected to provide novel insights into the ocular microbiota and pathology of ocular infections. In this article, we describe various ocular infections, including contact lens-related keratitis, silicone buckle infection, and dacryocystitis, which were analyzed using molecular biological techniques. The advantages and disadvantages of these highly sensitive and inclusive microbiological detection systems for ocular infections are discussed.

Composition and Diversity of Bacterial Community on the Ocular Surface of Patients With Meibomian Gland Dysfunction

“…16,25 As the gold standard of microorganism detection in clinical laboratories, culture-based methods can be used to identify samples at the species level and measure the density of strains, but the results are generally affected by factors like culture conditions and culture duration. 26,27 16S Compared with the healthy control group and the mild MGD group, both the moderate MGD group and the severe MGD group had a significantly lower abundance of Corynebacterium; compared with the other three groups, the severe MGD group had a significantly higher abundance of Staphylococcus. And the relative abundance of Sphingomonas was significantly lower in control group.…”

Comparison of the ocular microbiome between chronic Stevens-Johnson syndrome patients and healthy subjects

“…Conventional culture method usually demonstrates the lower number of microorganisms due to the limitation of detecting slow-growing and uncultivable microorganisms 5 . Molecular biological methods, on the contrary, show higher rates of microbial detection 10,11 . Two commonly-used molecular methods are 16S rRNA gene sequencing by Sangen method and the modern sequencing technology, next-generation sequencing method (NGS).…”

Metagenomics in ophthalmology: Hypothesis or real prospective?

“…Results could also be biased due to the fast-growing microorganisms, which can be easily cultivated on a standard media [11]. Moreover, studies comparing conventional culture techniques and molecular analysis have shown very often, that results obtained by these methods are incomplete or biased by false-positive data, thus highlighting the limitations of traditional culture-based techniques in terms of sensitivity and reproducibility [21,[25], [26], [27], [28], [29]]. Graham et al studied the bacterial population of 91 subjects classified as normal or dry eye [30].…”