Role of molecular diagnostics in ocular microbiology

Rapid Pathogen Detection in Infectious Uveitis Using Nanopore Metagenomic Next-Generation Sequencing: A Preliminary Study

PURPOSE

We establish an accurate and rapid diagnostic method for pathogen detection in infectious uveitis using nanopore metagenomic next-generation sequencing (NGS).

METHODS

In eight patients with suspected infectious uveitis, we prospectively compared the accuracy and time taken for pathogen identification between conventional diagnostic methods, such as cultures and PCR, and nanopore metagenomic NGS.

RESULTS

All causative pathogens were identified using nanopore sequencing, while only five of the eight patients were confirmed positive for a specific pathogen using conventional methods. The overall sample-to-answer turnaround time of nanopore sequencing was much shorter than that of conventional methods in the bacterial and fungal infection (mean, 17 h vs. 4d, respectively; P = .028). The pathogens could be detected even when the quantity or quality of DNA was not optimal.

CONCLUSION

Nanopore metagenomic NGS is a promising diagnostic tool that can rapidly and accurately identify the causative pathogen in infectious uveitis.

Infectious Keratitis: Characterization of Microbial Diversity through Species Richness and Shannon Diversity Index

Purpose: To characterize microbial keratitis diversity utilizing species richness and Shannon Diversity Index. Methods: Corneal impression membrane was used to collect samples. All swabs were processed and analyzed by Biolab Laboratory (level V-SSN Excellence: ISO 9001:2015), Biolab Srl (Ascoli Piceno, Italy). DNA extraction, library preparation, and sequencing were performed in all samples. After sequencing, low-quality and polyclonal sequences were filtered out by the Ion software. At this point, we employed Kraken2 for microbial community analysis in keratitis samples. Nuclease-free water and all the reagents included in the experiment were used as a negative control. The primary outcome was the reduction in bacterial DNA (microbial load) at T1, expressed as a percentage of the baseline value (T0). Richness and Shannon alpha diversity metrics, along with Bray-Curtis beta diversity values, were calculated using the phyloseq package in R. Principal coordinate analysis was also conducted to interpret these metrics. Results: 19 samples were included in the study. The results exhibited a motley species richness, with the highest recorded value surpassing 800 species. Most of the samples displayed richness values ranging broadly from under 200 to around 600, indicating considerable variability in species count among the keratitis samples. Conclusions: A significant presence of both typical and atypical bacterial phyla in keratitis infections, underlining the complexity of the disease's microbial etiology.

Pseudomonas Keratitis: From Diagnosis to Successful Deep Anterior Lamellar Keratoplasty

Pseudomonas keratitis is an aggressive form of bacterial keratitis that can have devastating consequences, such as corneal perforation, if not promptly identified and appropriately managed. The aim of this case report is to highlight key clinical features of Pseudomonas keratitis and evaluate the initial and long-term management options for this condition. We report a case of a 32-year-old female who presented with a large corneal abscess and hypopyon following contact lens wear. Corneal cultures confirmed Pseudomonas as the causative organism and she was treated with topical levofloxacin and gentamycin. Following sterilisation of the corneal ulcer, the patient was left with deep stromal scarring, peripheral corneal thinning as well as four-quadrant deep corneal vascularisation. She was listed for deep anterior lamellar keratoplasty surgery to clear her visual axis. We highlight some of the challenges that were faced both intra-operatively and post-operatively and how they were managed.

Performance of Metagenomic Next-Generation Sequencing of Cell-Free DNA From Vitreous and Aqueous Humor for Diagnoses of Intraocular Infections

BACKGROUND

Delayed diagnosis and improper therapy for intraocular infections usually result in poor prognosis. Due to limitations of conventional culture and polymerase chain reaction methods, most causative pathogens cannot be identified from vitreous humor (VH) or aqueous humor (AH) samples with limited volume.

METHODS

Patients with suspected intraocular infections were enrolled from January 2019 to August 2021. Metagenomic next-generation sequencing (mNGS) was used to detected causative pathogens.

RESULTS

This multicenter prospective study enrolled 488 patients, from whom VH (152) and AH (336) samples were respectively collected and analyzed using mNGS of cell-free DNA (cfDNA). Taking final comprehensive clinical diagnosis as the gold standard, there were 39 patients with indefinite final diagnoses, whereas 288 and 161 patients were diagnosed as definite infectious and noninfectious diseases, respectively. Based on clinical adjudication, the sensitivity (92.2%) and total coincidence rate (81.3%) of mNGS using VH samples were slightly higher than those of mNGS using AH samples (85.4% and 75.4%, respectively).

CONCLUSIONS

Using mNGS of cfDNA, an era with clinical experience for more rapid, independent, and impartial diagnosis of bacterial and other intraocular infections can be expected.

Alterations to the bovine bacterial ocular surface microbiome in the context of infectious bovine keratoconjunctivitis

BACKGROUND

Infectious bovine keratoconjunctivitis (IBK) is a common cause of morbidity in cattle, resulting in significant economic losses. This study aimed to characterize the bovine bacterial ocular surface microbiome (OSM) through conjunctival swab samples from Normal eyes and eyes with naturally acquired, active IBK across populations of cattle using a three-part approach, including bacterial culture, relative abundance (RA, 16 S rRNA gene sequencing), and semi-quantitative random forest modeling (real-time polymerase chain reaction (RT-PCR)).

RESULTS

Conjunctival swab samples were obtained from eyes individually classified as Normal (n = 376) or IBK (n = 228) based on clinical signs. Cattle unaffected by IBK and the unaffected eye in cattle with contralateral IBK were used to obtain Normal eye samples. Moraxella bovis was cultured from similar proportions of IBK (7/228, 3.07%) and Normal eyes (1/159, 0.63%) (p = 0.1481). Moraxella bovoculi was cultured more frequently (p < 0.0001) in IBK (59/228, 25.88%) than Normal (7/159, 4.40%) eyes. RA (via 16 S rRNA gene sequencing) of Actinobacteriota was significantly higher in Normal eyes (p = 0.0045). Corynebacterium variabile and Corynebacterium stationis (Actinobacteriota) were detected at significantly higher RA (p = 0.0008, p = 0.0025 respectively) in Normal eyes. Rothia nasimurium (Actinobacteriota) was detected at significantly higher RA in IBK eyes (p < 0.0001). Alpha-diversity index was not significantly different between IBK and Normal eyes (p > 0.05). Alpha-diversity indices for geographic location (p < 0.001), age (p < 0.0001), sex (p < 0.05) and breed (p < 0.01) and beta-diversity indices for geographic location (p < 0.001), disease status (p < 0.01), age (p < 0.001), sex (p < 0.001) and breed (p < 0.001) were significantly different between groups. Modeling of RT-PCR values reliably categorized the microbiome of IBK and Normal eyes; primers for Moraxella bovoculi, Moraxella bovis, and Staphylococcus spp. were consistently the most significant canonical variables in these models.

CONCLUSIONS

The results provide further evidence that multiple elements of the bovine bacterial OSM are altered in the context of IBK, indicating the involvement of a variety of bacteria in addition to Moraxella bovis, including Moraxella bovoculi and R. nasimurium, among others. Actinobacteriota RA is altered in IBK, providing possible opportunities for novel therapeutic interventions. While RT-PCR modeling provided limited further support for the involvement of Moraxella bovis in IBK, this was not overtly reflected in culture or RA results. Results also highlight the influence of geographic location and breed type (dairy or beef) on the bovine bacterial OSM. RT-PCR modeling reliably categorized samples as IBK or Normal.

Evaluation of a commercial NGS service for detection of bacterial and fungal pathogens in infectious ulcerative keratitis

OBJECTIVES

To compare results from a commercial next-generation sequencing (NGS) service to corneal cytology and culture for identification of causative organisms in veterinary patients presenting for infectious ulcerative keratitis (IUK).

PROCEDURE

Swabs for corneal aerobic and fungal cultures and DNA swabs for NGS were submitted for canine and equine normal controls (n = 11 and n = 4, respectively) and IUK patients (n = 22 and n = 8, respectively) for which microbrush cytology specimens confirmed the presence of infectious organisms. The sensitivity of the NGS results was compared with bacterial and fungal culture results. Concordance between the NGS and culture results was determined.

RESULTS

The NGS results were positive for bacterial and fungal organisms in 5 and 1 normal and 18 and 1 IUK cases, respectively. Bacterial and fungal cultures were positive for 7 and 2 normal and 20 and 5 IUK cases, respectively. Sensitivity of NGS was 82.14% (95% confidence interval (CI), 63.11% to 93.94%) and specificity was 76.47% (95% CI, 50.10% to 93.19%). Concordance (complete and partial) between identified bacterial and fungal organisms was found in 79% and 100% of cases, respectively. NGS identified organisms in 3 culture-negative IUK samples.

CONCLUSION

A commercial NGS service may be useful in the identification of causative agents in IUK cases with a sensitivity greater than the sensitivity previously reported for aerobic culture. Further testing is needed to determine the clinical significance of additional organisms isolated by NGS from infected cases, as well as organisms isolated from normal corneas.

Laboratory Investigations in Infectious Uveitis

Laboratory investigations can play a significant role in the diagnosis and decision-making of infectious uveitis. Though direct demonstration of the infective organism remains the gold standard of diagnosis, it is not always possible with ocular tissues. Recent advancements in molecular techniques have made it possible to overcome these limitations and to identify the genomic DNA of pathogens associated with infectious uveitis. Techniques such as next-generation sequencing can analyze all DNA-based lifeforms, regardless of whether they are bacteria, fungi, viruses, or parasites and have been used in the laboratory diagnosis of intraocular inflammation. On the other hand, serological tests, though they dominate the diagnostic landscape of various infectious etiologies in uveitis in routine clinical practice, have varied specificities and sensitivities in different infectious uveitis. In this review, we focus on various methods of laboratory diagnosis of infectious uveitis and discuss the recent advances in molecular diagnosis and their role in various infectious clinical entities.

An All-in-One Highly Multiplexed Diagnostic Assay for Rapid, Sensitive, and Comprehensive Detection of Intraocular Pathogens

PURPOSE

Intraocular infections are sight-threatening conditions that can lead to vision loss. Rapid identification of the etiologies plays a key role in early initiation of effective therapy to save vision. However, current diagnostic modalities are time consuming and lack sensitivity and inclusiveness. We present here a newly developed comprehensive ocular panel designed to improve diagnostic yields and provide a tool for rapid and sensitive pathogen detection.

DESIGN

Experimental laboratory investigation.

METHODS

A panel containing 46 pathogens and 2 resistance/virulence markers that are commonly detected in intraocular infections was developed. Genomic targets were scrutinized for stretches predicted to be specific for a particular species while being conserved across different strains. A set of primers for sample enrichment, and two 50mer NanoString compatible probes were then designed for each target. Probe-target hybrids were detected and quantified using the NanoString nCounter SPRINT Profiler. Diagnostic feasibility was assessed in a pilot clinical study testing samples from infectious retinitis (n = 15) and endophthalmitis (n = 12) patients, for which the etiologies were confirmed by polymerase chain reaction (PCR) or culture.

RESULTS

Analytical studies demonstrated highly sensitive detection of a broad spectrum of pathogens, including bacteria, viruses, and parasites, with limits of detection being as low as 2.5 femtograms per reaction. We also found excellent target specificity, with minimal cross-reactivity detected. The custom-designed NanoString ocular panel correctly identified the causative agent from all clinical specimens positive for a variety of pathogens.

CONCLUSION

This highly multiplexed panel for pathogen detection offers a sensitive, comprehensive, and uniform assay run directly on ocular fluids that could significantly improve diagnostics of sight-threatening intraocular infections.

Cutibacterium (Formerly Propionibacterium ) acnes Keratitis: A Review

ABSTRACT

Infectious keratitis is a devastating cause of vision loss worldwide. Cutibacterium acnes ( C. acnes ), a commensal bacterium of the skin and ocular surface, is an underrecognized but important cause of bacterial keratitis. This review presents the most comprehensive and up-to-date information for clinicians regarding the risk factors, incidence, diagnosis, management, and prognosis of C. acnes keratitis (CAK). Risk factors are similar to those of general bacterial keratitis and include contact lens use, past ocular surgery, and trauma. The incidence of CAK may be approximately 10%, ranging from 5% to 25% in growth-positive cultures. Accurate diagnosis requires anaerobic blood agar and a long incubation period (≥7 days). Typical clinical presentation includes small (<2 mm) ulcerations with deep stromal infiltrate causing an anterior chamber cell reaction. Small, peripheral lesions are usually resolved, and patients recover a high visual acuity. Severe infections causing VA of 20/200 or worse are common and often do not significantly improve even after treatment. Vancomycin is considered the most potent antibiotic against CAK, although other antibiotics such as moxifloxacin and ceftazidime are more commonly used as first-line treatment.

Application of metagenomic next-generation sequencing in suspected intraocular infections

PURPOSE

To evaluate the efficacy of metagenomic next-generation sequencing (mNGS) and to explore its value in the diagnosis of intraocular infection.

METHODS

A retrospective case-series study of patients with suspected intraocular infection was performed. Intraocular fluid samples were collected from all the patients and sent for mNGS. Detailed clinical data, the results of mNGS and other laboratory examinations, the sequencing data of mNGS, and the final diagnosis were recorded.

RESULTS

Fifteen eyes of 15 patients were included in the study. Eight samples were identified as positive for different kinds of pathogens by mNGS, which were all confirmed by other laboratory examinations or effective diagnostic treatment. The mNGS results were negative in seven samples. The final diagnosis was still intraocular infection in four of the seven negative results. Of these, one patient was diagnosed with fungal endophthalmitis according to the clinical characteristics and good treatment response to the anti-fungal therapy, one patient underwent vitrectomy and the bacterial culture of the vitreous sample was positive for Brucella melitensis, and two patients were diagnosed with ocular tuberculosis according to the positive T-SPOT test and effective anti-tuberculous treatments.

CONCLUSIONS

mNGS could be helpful in determining pathogens in cases of suspected intraocular infection. The mNGS protocols should be optimized for the detection of intracellular bacterial and fungal pathogens.

Ocular Lesions in Brucella Infection: A Review of the Literature

Ocular lesions due to Brucella infection are uncommon and easily overlooked in clinical management, but must be differentiated from non-infectious eye diseases and treated promptly to protect the patient's vision. We reviewed the relevant literature and identified 47 patients with ocular complications of Brucella infection. Among them, 28 showed ocular neuropathy, 15 presented with uveitis, and four patients displayed other ocular symptoms. Ocular symptoms accompanying Brucella infection require prompt diagnosis and treatment. The main methods of diagnosis are intraocular fluid tests and blood tests. Early diagnosis and treatment with suitable antibiotics are central to protecting the patient's vision. Notably, in terms of mechanism of injury, Brucella infection is chronic and cannot be eliminated by phagocytes, and can cause damage to the eye by inducing autoimmune reactions, antigen-antibody complex production, release of endogenous and exogenous toxins, and bacterial production of septic thrombi in the tissues. In this review, we summarize the ocular symptoms, diagnosis, treatment and prognosis of Brucella infection, and discuss the mechanisms of Brucella in ocular lesions, providing a reference for the diagnosis and treatment of Brucella ocular lesions.

Occurrence of Chlamydia spp. in Conjunctival Samples of Stray Cats in Timișoara Municipality, Western Romania

Despite the widespread public health concern about stray cats serving as reservoirs for zoonotic agents, little is known about the effect of urban and peri-urban landscapes on exposure risk. We conducted this study to monitor the presence of Chlamydia spp. in stray cats, with or without conjunctivitis, living in Timișoara Municipality, Western Romania, using staining and PCR methods. A total of 95 cats were enrolled, and conjunctival samples were harvested from 68 clinically healthy cats and another 27 cats presenting with clinical signs of conjunctivitis. Overall, we found that 65.3% (62/95) of the cats tested positive for Chlamydia spp. by PCR. Chlamydia spp. were detected in 45/95 conjunctival samples using a standard Giemsa stain, compared with 62/95 using PCR (Cohen’s kappa index = 0.308; p = 0.0640). Of the cats that tested positive by PCR, 72.6% (45/62) were asymptomatic, and another 27.4% (17/62) expressed clinical signs of conjunctivitis. We found no significant difference between (p > 0.05) the distribution of infection and the recorded epidemiological data (sex, breed, age, territorial distribution, or sampling season). However, the Chlamydia spp. detection frequency was significantly higher in asymptomatic than in symptomatic cats (p = 0.0383). The obtained results increase the level of concern and awareness about the possible zoonotic potential of this pathogen and highlight that urban stray cats can be essential sources of feline chlamydiosis.

Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform

PURPOSE

To evaluate the utility of nanopore sequencing for identifying potential causative pathogens in endophthalmitis, comparing culture results against full-length 16S rRNA nanopore sequencing (16S Nanopore), whole genome nanopore sequencing (Nanopore WGS), and Illumina (Illumina WGS).

DESIGN

Cross-sectional diagnostic comparison.

METHODS

Patients with clinically suspected endophthalmitis underwent intraocular vitreous biopsy as per standard care. Clinical samples were cultured by conventional methods, together with full-length 16S rRNA and WGS using nanopore and Illumina sequencing platforms.

RESULTS

Of 23 patients (median age 68.5 years [range 47-88]; 14 males [61%]), 18 cases were culture-positive. Nanopore sequencing identified the same cultured organism in all of the culture-positive cases and identified potential pathogens in two culture-negative cases (40%). Nanopore WGS was able to additionally detect the presence of bacteriophages in three samples. The agreements at genus level between culture and 16S Nanopore, Nanopore WGS, and Illumina WGS were 75%, 100%, and 78%, respectively.

CONCLUSIONS

Whole genome sequencing has higher sensitivity and provides a viable alternative to culture and 16S sequencing for detecting potential pathogens in endophthalmitis. Moreover, WGS has the ability to detect other potential pathogens in culture-negative cases. Whilst Nanopore and Illumina WGS provide comparable data, nanopore sequencing provides potential for cost-effective point-of-care diagnostics.

Exploring the Healthy Eye Microbiota Niche in a Multicenter Study

Purpose: This study aims to explore and characterize healthy eye microbiota. Methods: Healthy subjects older than 18 years were selected for this descriptive cross-sectional study. Samples were collected with an eSwab with 1 mL of Liquid Amies Medium (Copan Brescia, Italy). Following DNA extraction, libraries preparation, and amplification, PCR products were purified and end-repaired for barcode ligation. Libraries were pooled to a final concentration of 26 pM. Template preparation was performed with Ion Chef according to Ion 510, Ion 520, and Ion 530 Kit-Chef protocol. Sequencing of the amplicon libraries was carried out on a 520 or 530 chip using the Ion Torrent S5 system (Thermo Fisher; Waltham, MA, USA). Raw reads were analyzed with GAIA (v 2.02). Results: Healthy eye microbiota is a low-diversity microbiome. The vast majority of the 137 analyzed samples were highly enriched with Staphylococcus, whereas only in a few of them, other genera such as Bacillus, Pseudomonas, and Corynebacterium predominate. We found an average of 88 genera with an average Shannon index of 0.65. Conclusion: We identified nine different ECSTs. A better understanding of healthy eye microbiota has the potential to improve disease diagnosis and personalized regimens to promote health.

Infectious keratitis: A review

Globally, infectious keratitis is the fifth leading cause of blindness. The main predisposing factors include contact lens wear, ocular injury and ocular surface disease. Staphylococcus species, Pseudomonas aeruginosa, Fusarium species, Candida species and Acanthamoeba species are the most common causal organisms. Culture of corneal scrapes is the preferred initial test to identify the culprit organism. Polymerase chain reaction (PCR) tests and in vivo confocal microscopy can complement the diagnosis. Empiric therapy is typically commenced with fluoroquinolones, or fortified antibiotics for bacterial keratitis; topical natamycin for fungal keratitis; and polyhexamethylene biguanide or chlorhexidine for acanthamoeba keratitis. Herpes simplex keratitis is mainly diagnosed clinically; however, PCR can also be used to confirm the initial diagnosis and in atypical cases. Antivirals and topical corticosteroids are indicated depending on the corneal layer infected. Vision impairment, blindness and even loss of the eye can occur with a delay in diagnosis and inappropriate antimicrobial therapy.

Metagenomic Next-Generation Sequencing to Investigate Infectious Endophthalmitis of Brucella: A Case Report

Introduction

Brucellosis is a systemic disease that exists prevalently in clinical manifestations. The symptoms present in organs such as the eyes (in ocular brucellosis) can lead to misdiagnosis or even failure to diagnose. Metagenomic Next-Generation Sequencing (mNGS), a high-throughput sequencing approach, could be applied for the detection of microorganisms.

Case Presentation

A 57-year-old female with acute right-eye vision loss, treated with clindamycin and dexamethasone sodium phosphate for 1.5 months, was difficult to diagnose using regular methods. mNGS was utilized for the aqueous fluid from the patient, and Brucella melitensis was identified. The inflammation was treated with 3 months of antibiotherapy. However, even with specific medicine and surgery, the vision remained poor because severe ocular conditions last for a long time.

Conclusion

It suggests that brucella should still be a probable pathogen in endophthalmitis despite its low incidence in non-epidemic areas. Moreover, mNGS can achieve early diagnosis and timely treatment for difficult-to-diagnose ocular infections.

GENERATION AND USE OF FUNCTIONALISED HYDROGELS THAT CAN RAPIDLY SAMPLE INFECTED SURFACES

This paper outlined our method for developing polymer-linked contact lens type materials for rapid detection and differentiation of Gram-positive, Gram-negative bacteria and fungi in infected corneas. It can be applied to both model synthetic or ex-vivo corneal models and has been successfully trialed in an initial efficacy tested animal study. First a hydrogel substrate for the swab material is selected, we have demonstrated selective swabs using a glycerol monomethacrylate hydrogel. Alternatively any commercial material with carboxylic acid functional groups is suitable but risks nonspecific adhesion. This is then functionalised via use of N-hydroxysuccinimide reaction with amine groups on the specified highly branched polymer ligand (either individually gram negative, gram positive or fungal binding polymers or a combination of all three can be employed for desired sensing application). The hydrogel is then cut into swabs suitable for sampling, used, and then the presence of gram positive, game negative and fungi are disclosed by the sequential addition of dyes (fluorescent vancomycin, fluorescein isothiocyanate and calcofluor white).

In summary this method presents:

Method to produce glycerol monomethacrylate hydrogels to minimize nonspecific binding

Methods of attaching pathogen binding highly branched polymers to produce selective hydrogel swabs

Method for disclosing bound pathogens to this swab using sequential dye addition

Practical Guidance for Clinical Microbiology Laboratories: Diagnosis of Ocular Infections

The variety and complexity of ocular infections have increased significantly in the last decade since the publication of Cumitech 13B, Laboratory Diagnosis of Ocular Infections (L. D. Gray, P. H. Gilligan, and W. C. Fowler, Cumitech 13B, Laboratory Diagnosis of Ocular Infections, 2010). The purpose of this practical guidance document is to review, for individuals working in clinical microbiology laboratories, current tools used in the laboratory diagnosis of ocular infections. This document begins by describing the complex, delicate anatomy of the eye, which often leads to limitations in specimen quantity, requiring a close working bond between laboratorians and ophthalmologists to ensure high-quality diagnostic care. Descriptions are provided of common ocular infections in developed nations and neglected ocular infections seen in developing nations. Subsequently, preanalytic, analytic, and postanalytic aspects of laboratory diagnosis and antimicrobial susceptibility testing are explored in depth.

Rational laboratory testing in uveitis: A Bayesian analysis

Uveitis encompasses a heterogeneous group of clinical entities with the common feature of intraocular inflammation. In addition to patient history and examination, a focused set of laboratory investigations is frequently necessary to establish a specific diagnosis. There is limited consensus among uveitis specialists regarding appropriate laboratory evaluation for many distinct patient presentations. The appropriateness of a laboratory test for a given case of uveitis will depend on patient-specific as well as epidemiologic factors. Bayesian analysis is a widely used framework for the interpretation of laboratory testing, but is seldom adhered to in clinical practice. Bayes theorem states that the predictive value of a particular laboratory test depends on the sensitivity and specificity of that test, as well as the prevalence of disease in the population being tested. In this review we will summarize the performance of commonly-utilized laboratory tests for uveitis, as well as the prevalence of uveitic diagnoses in different geographic practice settings. We will propose a logical framework for effective laboratory testing in uveitic disease through rigorous application of Bayesian analysis. Finally, we will demonstrate that while many highly sensitive laboratory tests offer an effective means to rule out associated systemic disease, limited test specificity and low pretest probability often preclude the diagnosis of systemic disease association with any high degree of certainty, even in the face of positive testing.

Uveitis for the non-ophthalmologist

The uveitides are a heterogeneous group of diseases characterized by inflammation inside the eye. The uveitides are classified as infectious or non-infectious. The non-infectious uveitides, which are presumed to be immune mediated, can be further divided into those that are associated with a known systemic disease and those that are eye limited,-ie, not associated with a systemic disease. The ophthalmologist identifies the specific uveitic entity by medical history, clinical examination, and ocular imaging, as well as supplemental laboratory testing, if indicated. Treatment of the infectious uveitides is tailored to the particular infectious organism and may include regional and/or systemic medication. First line treatment for non-infectious uveitides is corticosteroids that can be administered topically, as regional injections or surgical implants, or systemically. Systemic immunosuppressive therapy is used in patients with severe disease who cannot tolerate corticosteroids, require chronic corticosteroids at >7.5 mg/day prednisone, or in whom the disease is known to respond better to immunosuppression. Management of many of these diseases is optimized by coordination between the ophthalmologist and rheumatologist or internist.

Detecting Streptococcus suis by nanopore sequencing in endophthalmitis: A case report

Endophthalmitis is a rare and infectious disease caused by Streptococcus suis (S suis). Traditionally, S suis is detected by the pathogenic microorganism culture method, which has low positivity and high false negativity. Nanopore sequencing (NS), which is a third-generation sequencing technology, has several advantages over the traditional method; in particular, it is cost and time effective and has a high throughput. In this report, a case of infectious endophthalmitis caused by trauma is examined. The NS results suggest that the pathogen in question is a mixed infection caused by S suis and Clostridium perfringens. This case report provides evidence of the fact that NS can quickly identify pathogens, which is of great significance for clinical diagnosis and treatment.

The Next Generation of Ocular Pathogen Detection

ABSTRACT

Metagenomic next-generation sequencing is a powerful method for pathogen detection that combines advanced genome sequencing technology with cutting-edge bioinformatics to analyze microbial populations. Metagenomic next-generation sequencing has the potential to identify uncommon, unculturable, and even previously unidentified pathogens from a clinical isolate. Of particular interest to ophthalmology, this robust data extraction can occur from very small volume clinical samples. Here we discuss the opportunities and limitations of this technique and their current and future application to ophthalmic diagnostics.

Application of Metagenomic Sequencing in the Diagnosis of Infectious Uveitis

Purpose: to summarize the origin and very recent history of the use of metagenomic sequencing for the diagnosis of infectious uveitis, convey the technique as described by one of the primary institutions experimenting with the technology, and present recent successful applications of the technology as well as potential advantages and pitfalls compared to other current diagnostic tools.Methods: review of peer-reviewed literature concerning metagenomic sequencing for the diagnosis of infectious uveitis.Conclusion: compared to existing diagnostic methods, metagenomic deep sequencing is a sensitive, unbiased, and comprehensive technique with great potential for diagnosing the causative pathogens of cases of infectious uveitis. However, many issues remain to be addressed in the process of developing this technology, including but not limited to the potentially overwhelming amount of information generated, definition of diagnostic thresholds, demonstration of validity, contamination, and cost.

Prognostic Utility of Whole-Genome Sequencing and Polymerase Chain Reaction Tests of Ocular Fluids in Postprocedural Endophthalmitis

PURPOSE

To associate detection of potential pathogen DNA in endophthalmitis with clinical outcomes.

DESIGN

Prospective cohort study.

METHODS

Patients in whom endophthalmitis was diagnosed following an intraocular procedure were recruited. Clinical outcome data from baseline, week-1, month-1, and month-3 visits were collected. Intraocular biopsy samples were cultured by standard methods. Quantitative polymerase chain reaction (qPCR) was performed for specific pathogens and whole-genome sequencing (WGS).

RESULTS

A total of 50 patients (mean age 72 years old; 52% male) were enrolled. Twenty-four cases were culture-positive and 26 were culture-negative. WGS identified the cultured organism in 76% of culture-positive cases and identified potential pathogens in 33% of culture-negative cases. Month-1 and -3 visual acuities did not vary by pathogen-positive versus pathogen-negative cases as detected by either culture or WGS. Visual outcomes of Staphylococcus epidermidis endophthalmitis were no different than those of pathogen-negative cases, whereas the patients infected with other pathogens showed worse outcome. Higher baseline bacterial DNA loads of bacteria other than those of S epidermidis detected by WGS were associated with worse month-1 and -3 visual acuity, whereas the S epidermidis loads did not appear to influence outcomes. Torque teno virus (TTV) and Merkel cell polyomavirus (MCV) were detected by qPCR in 49% and 19% of cases, respectively. Presence of TTV at presentation was associated with a higher rate of secondary pars plana vitrectomy (P = .009) and retinal detachment (P = .022).

CONCLUSIONS

The presence and higher load of bacteria other than S epidermidis detected by WGS or DNA from TTV by qPCR in ocular fluids is associated with worse outcomes in post-procedure endophthalmitis.

Comparison of the Vitreous Fluid Bacterial Microbiomes between Individuals with Post Fever Retinitis and Healthy Controls

Ocular microbiome research has gained momentum in the recent past and has provided new insights into health and disease conditions. However, studies on sight threatening intraocular inflammatory diseases have remained untouched. In the present study, we attempted to identify the bacterial microbiome associated with post fever retinitis using a metagenomic sequencing approach. For this purpose, bacterial ocular microbiomes were generated from vitreous samples collected from control individuals (VC, n = 19) and individuals with post fever retinitis (PFR, n = 9), and analysed. The results revealed 18 discriminative genera in the microbiomes of the two cohorts out of which 16 genera were enriched in VC and the remaining two in PFR group. These discriminative genera were inferred to have antimicrobial, anti-inflammatory, and probiotic function. Only two pathogenic bacteria were differentially abundant in 20% of the PFR samples. PCoA and heatmap analysis showed that the vitreous microbiomes of VC and PFR formed two distinct clusters indicating dysbiosis in the vitreous bacterial microbiomes. Functional assignments and network analysis also revealed that the vitreous bacterial microbiomes in the control group exhibited more evenness in the bacterial diversity and several bacteria had antimicrobial function compared to the PFR group.

Toxoplasma gondii SAG2 type III in an atypical presentation of ocular toxoplasmosis in Indonesia

OBJECTIVE

This study aimed to perform genotyping of Toxoplasma gondii strain or variant causing atypical toxoplasmic uveitis in Indonesian patients.

METHODS

Ocular fluid samples originating from 46 uveitis patients with non-specific ocular manifestations were analysed for Toxoplasma infection by PCR of the B1 locus. The clonal type was determined by amplification, sequencing and phylogenetic analysis of SAG2 and GRA6 loci in B1-positive samples. Clinical data were obtained from the medical records.

RESULTS

Pan uveitis was the most frequent manifestation (65.2%) and mostly unilateral (76.1%). PCR of the B1 locus identified eight positive subjects (12.5%); six had panuveitis and two of these had diabetes mellitus. Phylogenetic analysis with maximum likelihood of the SAG2 locus in the B1-positive samples resulted in Toxoplasma gondii SAG2 type III allele. No positive result was obtained from the PCR of GRA6 locus.

CONCLUSION

Toxoplasma gondii SAG2-type III allele was identified in an atypical presentation of toxoplasmic uveitis in Indonesia.

The cereus matter of Bacillus endophthalmitis

Bacillus cereus (B. cereus) endophthalmitis is a devastating intraocular infection primarily associated with post-traumatic injuries. The majority of these infections result in substantial vision loss, if not loss of the eye itself, within 12-48 h. Multifactorial mechanisms that lead to the innate intraocular inflammatory response during this disease include the combination of robust bacterial replication, migration of the organism throughout the eye, and toxin production by the organism. Therefore, the window of therapeutic intervention in B. cereus endophthalmitis is quite narrow compared to that of other pathogens which cause this disease. Understanding the interaction of bacterial and host factors is critical in understanding the disease and formulating more rational therapeutics for salvaging vision. In this review, we will discuss clinical and research findings related to B. cereus endophthalmitis in terms of the organism's virulence and inflammogenic potential, and strategies for improving of current therapeutic regimens for this blinding disease.

Atypical herpes simplex keratitis: frequency, clinical presentations and treatment results

AIMS

To determine herpes simplex virus (HSV) DNA positivity in corneal scraping samples obtained from patients with microbial keratitis whose findings were not specific for HSV keratitis and to evaluate these particular cases with respect to clinical features and antiviral treatment results.

METHODS

Records of patients with microbial keratitis treated in a tertiary eye care hospital within the 3-year period were evaluated retrospectively. Real-time polymerase chain reaction (PCR) was used to identify HSV DNA. Smear slides were evaluated by light microscopy. Patients with typical presentations and histories of HSV keratitis were excluded.

RESULTS

Two hundred and seventy-six eyes of 276 patients were included in the study. HSV-1 DNA was detected in 25 eyes (9%). In these 25 eyes, the initial diagnosis was fungal or bacterial keratitis. The mean symptom duration was 20 ± 14 days (2-60 days). The risk factors were ocular surgery (20%), blepharitis (16%), trauma (8%) and contact lens wear (4%); however, the majority of patients did not have any specific cause for keratitis (52%). Clinical features were variable and not typical for any particular etiology. Culture and microscopic examinations revealed bacteria and/or fungi in 6 patients in addition to herpes infection. Antiviral treatment was successful in 72% of patients.

CONCLUSION

Herpetic corneal infections can present without typical dendritic or geographic ulcers and may be masked by other infections. Real-time PCR is a useful method for rapid and definitive diagnosis. HSV infection should be considered for microbial keratitis without specific risk factors, with negative culture results and poor response to antimicrobial agents.

The First Case of Trypanosoma cruzi-Associated Retinitis in an Immunocompromised Host Diagnosed With Pan-Organism Polymerase Chain Reaction

We report the first case of Trypanosoma cruzi-associated retinitis diagnosed using 28s ribosomal DNA sequencing. The case highlights the utility of broad-range molecular diagnostics for detecting rare and unsuspected ocular pathogens. Ocular involvement in Chagas disease is also discussed.

Metagenomics in ophthalmology: Hypothesis or real prospective?

Metagenomic analysis was originally associated with the studies of genetic material from environmental samples. But, with the advent of the Human Microbiome Project, it has now been applied in clinical practices. The ocular surface (OS) is the most exposed part of the eye, colonized by several microbial communities (both, OS and environmental) that contribute to the maintenance of the physiological state. Limited knowledge has been acquired on these microbes due to the limitations of conventional diagnostic methods. Emerging fields of research are focusing on Next Generation Sequencing (NGS) technologies to obtain reliable information on the OS microbiome. Currently only pre-specified pathogens can be detected by conventional culture-based techniques or Polymerase Chain Reaction (PCR), but there are conditions to state whether metagenomics could revolutionize the diagnosis of ocular diseases. The aim of this review is to provide an updated overview of the studies involving NGS technology for OS microbiome.

A Review of Next-Generation Sequencing (NGS): Applications to the Diagnosis of Ocular Infectious Diseases

Purpose: To review the value of next-generation sequencing (NGS) in identifying the pathogens which cause ocular infections, thereby facilitating prompt initiation of treatment with an optimal anti-microbial regimen. Both contemporary and futuristic approaches to identifying pathogens in ocular infections are covered in this brief overview. Methods: Review of the peer reviewed literature on conventional and advanced methods as applied to the diagnosis of infectious diseases of the eye. Conclusion: NGS is a novel technology for identifying the pathogens responsible for ocular infections with the potential to improve the accuracy and speed of diagnosis and hastening the selection of the best therapy.

Metagenomics in ophthalmology: current findings and future prospectives

Less than 1% of all microorganisms of the available environmental microbiota can be cultured with the currently available techniques. Metagenomics is a new methodology of high-throughput DNA sequencing, able to provide taxonomic and functional profiles of microbial communities without the necessity to culture microbes in the laboratory. Metagenomics opens to a ‘hypothesis-free’ approach, giving important details for future research and treatment of ocular diseases in ophthalmology, such as ocular infection and ocular surface diseases.

Reclassifying Idiopathic Uveitis: Lessons From a Tertiary Uveitis Center

PURPOSE

Idiopathic uveitis is frequently the most common diagnosis in series from uveitis clinics. This study sought to determine the percentage of patients initially diagnosed as idiopathic, noninfectious uveitis referred to a tertiary uveitis center who were subsequently found to have an identifiable cause of uveitis.

DESIGN

Retrospective case series.

METHODS

We performed a computerized database analysis of 179 consecutive patients who were referred to our practice with the diagnosis of idiopathic, noninfectious uveitis between 2008 and 2016. Patients were evaluated by a thorough history and ophthalmic examination with selected laboratory testing targeted by clues from the history and examination. Standardization of Uveitis Nomenclature (SUN) criteria were used to better assess different types of uveitis.

RESULTS

Fifty-two out of 179 (29.0%) patients initially diagnosed with idiopathic uveitis were subsequently diagnosed with an underlying condition. Among patients referred with a diagnosis of idiopathic disease, female patients were most commonly affected (121/179; 67.6%). Among subsequent diagnoses, sarcoidosis was the most common (19/52 or 36.5%), followed by HLA-B27-associated uveitis (11/52, 21.1%), infectious uveitis (6/52, 11.5%), tubulointerstitial nephritis with uveitis (6/52, 11.5%), and juvenile idiopathic uveitis (4/52, 7.7%). Other diagnosable conditions included Behçet disease, multifocal choroiditis, panuveitis, Crohn disease, multiple sclerosis, and relapsing polychondritis. An underlying condition was not found in 127 of 179 (70.9%) patients.

CONCLUSIONS

We report that 29% of patients referred to our tertiary uveitis center diagnosed as "idiopathic" had an associated identifiable cause. Identifying an underlying condition associated with uveitis could be potentially lifesaving for some illnesses (eg, sarcoidosis with cardiac involvement) and is critical to management (eg, infection). Although we were able to use limited testing to classify many patients who had been previously incorrectly labeled with idiopathic uveitis, idiopathic uveitis remains the most common diagnosis in our uveitis clinic.

Coinfections and differential diagnosis in immunocompetent patients with uveitis of infectious origin

BACKGROUND

Making a definite diagnosis of infectious uveitis is a challenging task because many other infectious, and non-infectious uveitis, may have similar non-specific symptoms and overlapping clinical appearances. Co-infections in immunocompetent patients are not frequently proved with traditional serologic-diagnostic tools.

METHODS

Descriptive transversal study, in a Uveitis Service of an Ophthalmology Reference Center, in Bogotá, Colombia, from July 2014 to February 2016. Aqueous humor (AH) and/or vitreous fluid, blood and serum samples were collected from consecutive patients suspected of having infectious uveitis. The diagnosis of ocular toxoplasmosis (OT) was confirmed by the Goldmann-Witmer coefficient (GWC) and by polymerase chain reaction (PCR). Differential diagnosis by PCR in AH was done for viral origin such as Cytomegalovirus (CMV), Herpes simplex virus type 1 (HSV1), Herpes simplex virus type 2 (HSV2), Varicella zoster virus (VZV), Epstein-Barr virus (EBV) and Mycobacterium tuberculosis.

RESULTS

In 66 Colombian patients with uveitis of presumed infectious origin: 22 (33.3%) were confirmed as OT, 16 (24.2%) as undetermined OT, five (7.5%) as co-infections and 23 (34.8%) as other uveitis. Toxoplasma coinfection with M. tuberculosis was identified in one case by PCR and in four cases with HSV by GWC. The initial clinical diagnosis changed, after laboratory examination, in 21 cases (31.8%).

CONCLUSIONS

Clinical diagnosis can be changed by laboratory examination in a significant proportion of cases of uveitis. Diagnosis of OT should combine the use of PCR and GWC to reach the maximum of confirmation of cases. The use of multiple laboratory methods is necessary to identify co-infections and viral infections that can mimic OT in immunocompetent patients.

Molecular Bioburden of the Lens Storage Case for Contact Lens-Related Keratitis

PURPOSE

To elucidate the bioburden of a lens care system in patients with contact lens (CL)-related keratitis.

METHODS

In this prospective case-control study, the CL storage case was used as the target of bioburden assessment. Participants were CL wearers with (n = 26) or without (n = 24) keratitis in southern Taiwan. The case fluid sample was consecutively collected and assessed using a dot hybridization assay (DHA) for bioburden assessment. The DHA was composed of 3 universal bacterial probes for detecting all bacteria, genus-specific probes for Pseudomonas and Acinetobacter, and 1 probe for Acanthamoeba. The receiver operating characteristic curve was used to analyze the differentiating performance of a probe.

RESULTS

The storage case bioburden was significantly higher in those with CL-related keratitis than in control subjects; patients with CL-related keratitis had stronger standardized signals in all universal bacterial probes. Moreover, in the cases of these patients, the bioburden was significantly heavier in confirmed infectious keratitis than in presumed noninfectious keratitis. Receiver operating characteristic analysis showed that stronger signals in all 3 universal bacterial probes and the Pseudomonas probe might suggest that the wearers have infectious keratitis. Only the storage case of the Acanthamoeba keratitis case showed positive detection by the Acanthamoeba probe.

CONCLUSIONS

A heavier bioburden in the lens storage case was associated with a higher risk of CL-related keratitis and infectious keratitis. Inappropriate maintenance of the CL will lead to microbial contamination and transfer the pathogen onto the ocular surface causing keratitis accordingly. The DHA assessment for the lens storage case might provide an alternative way to differentiate infectious from noninfectious CL-related keratitis.

Visions of Eye Commensals: The Known and the Unknown About How the Microbiome Affects Eye Disease

Until recently, the ocular surface is thought by many to be sterile and devoid of living microbes. It is now becoming clear that this may not be the case. Recent and sophisticated PCR analyses have shown that microbial DNA-based "signatures" are present within various ethnic, geographic, and contact lens wearing communities. Furthermore, using a mouse model of ocular surface disease, we have shown that the microbe, Corynebacterium mastitidis (C. mast), can stably colonize the ocular mucosa and that a causal relationship exists between ocular C. mast colonization and beneficial local immunity. While this constitutes proof-of-concept that a bona fide ocular microbiome that tunes immunity can exist at the ocular surface, there remain numerous unanswered questions to be addressed before microbiome-modulating therapies may be successfully developed. Here, the authors will briefly outline what is currently known about the local ocular microbiome as well as microbiomes associated with other sites, and how those sites may play a role in ocular surface immunity. Understanding how commensal microbes affect the ocular surface immune homeostasis has the potential revolutionize how we think about treating ocular surface disease.

Metagenomic deep sequencing of aqueous fluid detects intraocular lymphomas

Introduction

Currently, the detection of pathogens or mutations associated with intraocular lymphomas heavily relies on prespecified, directed PCRs. With metagenomic deep sequencing (MDS), an unbiased high-throughput sequencing approach, all pathogens as well as all mutations present in the host’s genome can be detected in the same small amount of ocular fluid.

Methods

In this cross-sectional case series, aqueous fluid samples from two patients were submitted to MDS to identify pathogens as well as common and rare cancer mutations.

Results

MDS of aqueous fluid from the first patient with vitreal lymphoma revealed the presence of both Epstein-Barr virus (HHV-4/EBV) and human herpes virus 8 (HHV-8) RNA. Aqueous fluid from the second patient with intraocular B-cell lymphoma demonstrated a less common mutation in the MYD88 gene associated with B-cell lymphoma.

Conclusion

MDS detects pathogens that, in some instances, may drive the development of intraocular lymphomas. Moreover, MDS is able to identify both common and rare mutations associated with lymphomas.

Updates in ophthalmic pathology

Ophthalmic pathology has a long history and rich heritage in the field of ophthalmology. This review article highlights updates in ophthalmic pathology that have developed significantly through the years because of the efforts of committed individuals and the confluence of technology such as molecular biology and digital pathology. This is an exciting period in the history of ocular pathology, with cutting-edge techniques paving the way for new developments in diagnostics, therapeutics, and research. Collaborations between ocular oncologists and pathologists allow for improved and comprehensive patient care. Ophthalmic pathology continues to be a relevant specialty that is important in the understanding and clinical management of ocular disease, education of eye care providers, and overall advancement of the field.

Update on the Epidemiology and Antibiotic Resistance of Ocular Infections

PURPOSE:

The purpose of this review is to provide an update on the epidemiology and current antibiotic-resistant threats in ophthalmology.

METHODS:

Trends in frequency and antibiotic-nonsusceptible profiles during an 11 year-period (2005–2015) were evaluated and compared with the 5-year Antibiotic Resistance Monitoring in Ocular Microorganism (ARMOR) study.

RESULTS:

Trends in the current review confirmed the continued high rates of fluoroquinolone nonsusceptbility circulating among ocular methicillin-susceptible Staphylococcus aureus, methicillin-susceptible Staphylococcus epidermidis, methicillin-resistant S. aureus, and methicillin-resistant S. epidermidis isolates as well as the detection of uncommon, but emerging resistance (<5%) for Streptococcus pneumoniae, Streptococcus viridans group, Haemophilus influenzae, and Pseudomonas aeruginosa. We documented significant differences in empirical fluoroquinolone and aminoglycoside coverage for the top three ocular pathogens (coagulase-negative staphylococci, S. aureus, and P. aeruginosa) in general and for corneal isolates between the Miami and the ARMOR studies. Collectively, the coverage for Miami was 74% versus 65.9% for ARMOR (P < 0.0001, 5.3674–10.8042) for ciprofloxacin and 95.9% versus 84.2% for aminoglycosides (gentamicin/tobramycin) (P < 0.0001, 9.9925–13.3974). Monotherapy coverage for ciprofloxacin and levofloxacin for the most recent 5 years (2011–2015) was 76.6% and 77.1%, respectively. Combination therapy with a fluoroquinolone and vancomycin and/or vancomycin and an aminoglycoside provided coverage for 99% and 98% of the isolates, respectively.

CONCLUSION:

The etiology of ocular pathogens is patient, source, and geography specific. The true incidence and/or prevalence are unknown. Fluoroquinolone monotherapy as standard therapy for common ocular infections needs to be reassessed. Ophthalmologists must become proactive and join the crusade to develop practical and prudent strategies for the administration of topical antibiotics.

A comparison of culture and PCR methods for identifying Propionibacterium acnes in lesions isolated from patients with acne

BACKGROUND/AIM

One of the factors that affect the occurrence of acne is the presence of Propionibacterium acnes. The present study was conducted to compare the culture and polymerase chain reaction (PCR) methods for identifying P. acnes in lesions isolated from patients with acne.

MATERIALS AND METHODS

To examine the presence of P. acnes, 70 samples of acne lesions were collected. Microbial culture and the PCR molecular technique were used to identify P. acnes.

RESULTS

Of the total of 70 samples, 14 cases (20%) were identified as P. acnes positive using microbial culture and 58 cases (82.85%) using PCR. The results obtained showed the lack of a relationship between the frequency of P. acnes and factors such as sex, family history of acne, and history of treatment with either of the techniques examined (i.e. the microbial culture and PCR). In contrast, a significant relationship was observed between the frequency of P. acnes and age with the culture method.

CONCLUSION

Given the limitations in the identification of P. acnes using microbial culture, PCR is proposed as a better method with a higher efficiency.

Paucibacterial Microbiome and Resident DNA Virome of the Healthy Conjunctiva

Purpose

To characterize the ocular surface microbiome of healthy volunteers using a combination of microbial culture and high-throughput DNA sequencing techniques.

Methods

Conjunctival swab samples from 107 healthy volunteers were analyzed by bacterial culture, 16S rDNA gene deep sequencing (n = 89), and biome representational in silico karyotyping (BRiSK; n = 80). Swab samples of the facial skin (n = 42), buccal mucosa (n = 50), and environmental controls (n = 27) were processed in parallel. 16S rDNA gene quantitative PCR was used to calculate the bacterial load in each site. Bacteria were characterized by site using principal coordinate analysis of metagenomics data. BRiSK data were analyzed for presence of fungi and viruses.

Results

Corynebacteria, Propionibacteria, and coagulase-negative Staphylococci were the predominant organisms identified by all three techniques. Quantitative 16S PCR demonstrated approximately 0.1 bacterial 16S rDNA/human actin copy on the ocular surface compared with greater than 10 16S rDNA/human actin copy for facial skin or the buccal mucosa. The conjunctival bacterial community structure is distinct compared with the facial skin (R = 0.474, analysis of similarities P = 0.0001), the buccal mucosa (R = 0.893, P = 0.0001), and environmental control samples (R = 0.536, P = 0.0001). 16S metagenomics revealed substantially more bacterial diversity on the ocular surface than other techniques, which appears to be artifactual. BRiSK revealed presence of torque teno virus (TTV) on the healthy ocular surface, which was confirmed by direct PCR to be present in 65% of all conjunctiva samples tested.

Conclusions

Relative to adjacent skin or other mucosa, healthy ocular surface microbiome is paucibacterial. Its flora are distinct from adjacent skin. Torque teno virus is a frequent constituent of the ocular surface microbiome. (ClinicalTrials.gov number, NCT02298881.)

A dot hybridization assay for the diagnosis of bacterial keratitis

Purpose

To evaluate a bacterial dot hybridization (BDH) assay for the diagnosis of bacterial keratitis (BK).

Methods

Sixty-one qualified corneal scrapings from 61 patients with suspected microbial keratitis were collected consecutively and prospectively. Among the 61 patients, 16 cases were BK and 45 cases were non-BK, including fungal keratitis, viral keratitis, parasitic keratitis, and non-microbial keratitis. Molecular diagnosis of BK in these corneal scrapes was performed using the BDH assay with three universal bacterial probes (PB1, PB2, and PB3) and three genus-specific probes (Aci, Klb, and Psu) to detect Acinetobacter, Klebsiella, and Pseudomonas, respectively. Signals were standardized after grayscale image transformation for objective validation using receiver operating characteristic (ROC) curves.

Results

The standardized intensities for the three universal probes differed statistically significantly between the BK group and the non-BK group. Based on the ROC curves, the sensitivities of PB1, PB2, and PB3 were 81.3%, 81.3%, and 93.8%, and the specificities were 71.1%, 88.9%, and 91.1%, respectively. The sensitivity and specificity of the Psu probe were 92% and 100%, respectively, while those of the Aci and Klb probes could not be estimated because there were no BK cases caused by Acinetobacter spp. or Klebsiella spp.

Conclusions

The BDH assay is an effective molecular approach to improve the diagnosis of BK. Because the bias from bacterial contamination on the ocular surface can be minimized with signal standardization, the assay has the potential to be adopted for routine clinical practice.

[Diagnostic and therapeutic contribution of microbiological analysis in severe microbial keratitis at Reims University Hospital between 2012 and 2014]

PURPOSE

To investigate the contribution of microbial analysis in the diagnosis and management of severe microbial keratitis.

MATERIAL AND METHOD

This is a monocentric retrospective study at the University Hospital of Reims from January 2012 to December 2014. Corneal scrapings with infectious keratitis were subjected to routine bacterial and fungal culture. PCR was also performed to detect various viral DNA (VZV, CMV, EBV, HSV 1 & 2, adenovirus) and Acanthamoeba sp. DNA. All contact lens cases were analyzed if available.

RESULTS

One hundred and six patients were hospitalized, including 30 contact lens wearers (28.3%). Sixty-four bacterial cultures were positive (68%). Twenty-five different bacterial species were identified with a majority of gram-positive bacteria (67.92%). Among contact lens wearers, the initial VA was better than non-wearers (P=0.0004) and 37% of bacteria identified (a plurality) were gram positive. Of 11 contact lens case analyzed, in only one case (3.3%) did the result correlate with the corneal culture. Only 9 samples from the 323 viral DNA extractions and real time PCR were positive (2.8%); 7 were HSV1. No prior antiviral therapy had been started. Fungal culture was positive in 2 of the 97 corneal samples taken and 63.6% of the contact lens cases (7/11 cases). Only one of the 40 Acanthamoeba sp. PCR's was positive.

CONCLUSION

The systematic performance of microbiological investigations is a good diagnostic approach given the polymorphism of clinical presentations of corneal ulcers, which can sometimes be extremely misleading. Culture of contact lens cases appears ineffective for the detection and determination of the causative microorganism. The high incidence of Staphylococcus in bacterial keratitis and the prevalence of infections with gram-positive bacteria in contact lens wearers were noted.

Review of clinical and basic approaches of fungal keratitis

Fungal keratitis (FK) is a serious disease which can cause blindness. This review has current information about the pathogenesis, limitations of traditional diagnosis and therapeutic strategies, immune recognition and the diagnosis and therapy of FK. The information of this summary was reviewed regularly and updated as what we need in the diagnosis and therapy of FK nowadays.

Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens

BACKGROUND

Ocular infections remain a major cause of blindness and morbidity worldwide. While prognosis is dependent on the timing and accuracy of diagnosis, the etiology remains elusive in ~50 % of presumed infectious uveitis cases. The objective of this study is to determine if unbiased metagenomic deep sequencing (MDS) can accurately detect pathogens in intraocular fluid samples of patients with uveitis.

METHODS

This is a proof-of-concept study, in which intraocular fluid samples were obtained from five subjects with known diagnoses, and one subject with bilateral chronic uveitis without a known etiology. Samples were subjected to MDS, and results were compared with those from conventional diagnostic tests. Pathogens were identified using a rapid computational pipeline to analyze the non-host sequences obtained from MDS.

RESULTS

Unbiased MDS of intraocular fluid produced results concordant with known diagnoses in subjects with (n = 4) and without (n = 1) uveitis. Samples positive for Cryptococcus neoformans, Toxoplasma gondii, and herpes simplex virus 1 as tested by a Clinical Laboratory Improvement Amendments-certified laboratory were correctly identified with MDS. Rubella virus was identified in one case of chronic bilateral idiopathic uveitis. The subject's strain was most closely related to a German rubella virus strain isolated in 1992, one year before he developed a fever and rash while living in Germany. The pattern and the number of viral identified mutations present in the patient's strain were consistent with long-term viral replication in the eye.

CONCLUSIONS

MDS can identify fungi, parasites, and DNA and RNA viruses in minute volumes of intraocular fluid samples. The identification of chronic intraocular rubella virus infection highlights the eye's role as a long-term pathogen reservoir, which has implications for virus eradication and emerging global epidemics.