Microbial Keratitis in Nepal: Predicting the Microbial Aetiology from Clinical Features

Development and Clinical Evaluation of a CRISPR/Cas12a-Based Nucleic Acid Detection Platform for the Diagnosis of Keratomycoses

Objective

The objective of this study was to develop a rapid and accurate clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a-based molecular diagnostic assay (Rapid Identification of Mycoses using CRISPR, RID-MyC assay) to detect fungal nucleic acids and to compare it with existing conventional mycologic methods for the diagnosis of fungal keratitis (FK).

Design

This study was structured as a development and validation study focusing on the creation and assessment of the RID-MyC assay as a novel diagnostic modality for FK.

Subjects

Participants comprised 142 individuals presenting with suspected microbial keratitis at 3 tertiary care institutions in South India.

Methods

The RID-MyC assay utilized recombinase polymerase amplification targeting the 18S ribosomal RNA gene for isothermal amplification, followed by a CRISPR/Cas12a reaction. This was benchmarked against microscopy, culture, and polymerase chain reaction for the diagnosis of FK.

Main Outcome Measures

The primary outcome measures focused on the analytical sensitivity and specificity of the RID-MyC assay in detecting fungal nucleic acids. Secondary outcomes measured the assay's diagnostic sensitivity and specificity for FK, including its concordance with conventional diagnostic methods.

Results

The RID-MyC assay exhibited a detection limit ranging from 13.3 to 16.6 genomic copies across 4 common fungal species. In patients with microbial keratitis, the RID-MyC assay showed substantial agreement with microscopy (kappa = 0.714) and fair agreement with culture (kappa = 0.399). The assay demonstrated a sensitivity of 93.27% (95% confidence interval [CI], 86.62%-97.25%) and a specificity of 89.47% (95% CI, 66.86%-98.70%) for FK diagnosis, with a median diagnostic time of 50 minutes (range, 35-124 minutes).

Conclusions

The RID-MyC assay, utilizing CRISPR-Cas12a technology, offers high diagnostic accuracy for FK. Its potential for point-of-care use could expedite and enhance the precision of fungal diagnostics, presenting a promising solution to current diagnostic challenges.

Financial Disclosures

Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Microbial keratitis and its management at a rural centre: achieving success with limited resources

PURPOSE

Microbial keratitis is a sight-threatening condition with a higher incidence in agrarian populations. In countries with a high indigent population, due to financial and other constraints, patients prefer to seek therapy locally rather than travel to advanced centres. The aim of this study is to describe the epidemiology, clinical characteristics, and outcomes of 60 consecutive patients with microbial keratitis managed at a rural centre.

METHODS

Descriptive case series. All patients clinically diagnosed with infectious keratitis were included. Corneal scrapings were obtained and microbiological identification was done by Gram stain. Anti-microbial therapy was commenced based on smear findings and the patients were followed up till disease resolution.

RESULTS

Sixty eyes of 60 patients were diagnosed with microbial keratitis in the study period. The mean age was 47.43 ± 18.69 years. Male:female ratio was 47:53. Risk factors included ocular trauma in the majority of patients (46/60; 76.7%). Microorganisms were identified on 75.6% of smears, with fungal filaments (65.4%) being the most common. Ulcers were central in over half (32/60; 53.3%), and > 3 mm in diameter in over three-fourths (81.6%) of patients. Forty-four patients (73.3%) achieved treatment success whereas 16/60 (26.6%) required referral to our tertiary-eye care facility for management. The median time to resolution was 14 days (IQR 10-26 days).

CONCLUSION

Our series demonstrates the feasibility of microbiology-guided therapy in microbial keratitis by ophthalmologists at the secondary rural eye-care level. Two-thirds of the patients could be successfully managed at the rural centre and only severe cases needed a referral to tertiary centres.

Epidemiological and microbiological profiles of microbial keratitis in a tertiary eye center in Eastern India (Bihar)

Purpose

To determine the demography, risk factors, and causative organisms of microbial keratitis (MK) in Bihar, an eastern state of India.

Design

Retrospective study.

Methods

We reviewed the demographic, clinical, and microbiological data of 2303 patients with MK (non-viral) presenting between January 2019 and December 2022.

Results

This study revealed a predominance of males (65.0%) compared to females (34.9%), with a mean age of 48.4 ± 16.5 years. The majority of patients (63.1%) presented after 2 weeks from the onset of symptoms. The most common risk factor observed was corneal injury (58.1%), followed by ocular surface diseases (13.6%) and diabetes mellitus (13.3%). The majority of patients (73.16%) were involved in agriculture. Prior to presentation, almost all patients (92%) had received topical antibiotics. Unsupervised use of topical corticosteroids was observed in 29.2% of the patients for the median duration of 3 days (odds ratio, 0.17). At presentation, the median size of corneal ulcers was 5 mm, the best-corrected visual acuity was less than 20/400 in 51.4% of patients, and corneal perforation was in 14% of patients. The smear and culture positivity rate were 75.4% and 47.9%, respectively. The common causative organism was fungus (48.8%), followed by bacteria (17.4%). Aspergillus spp. and Staphylococcus spp. were the most commonly identified organisms; a quarter of the patients (24.5%) remained unidentified. All bacteria showed good sensitivity to vancomycin.

Conclusion

MK is a significant cause of ocular morbidity in Bihar. The knowledge of epidemiology, risk factors, and microbiological profiles of MK can provide a valuable approach to disease prevention, diagnosis, and management.

Positive Microbiological Culture among Patients with Infective Keratitis Visiting the Cornea Unit of a Tertiary Care Centre

Introduction

Keratitis is the infection and inflammation of the cornea. Microbial keratitis is a potentially sight-threatening corneal condition. The aim of this study was to find out the prevalence of positive microbiological culture among patients with infective keratitis visiting the Cornea Unit of a tertiary care centre.

Methods

A descriptive cross-sectional study was conducted among patients with a clinical diagnosis of infective keratitis presenting to the Cornea Unit of a tertiary eye care centre from 16 October 2020 to 16 March 2021 after obtaining ethical approval from the Ethical Review Board. After slit-lamp examination, corneal scrapings were performed under aseptic conditions which were subjected to Gram stain, potassium hydroxide preparation and culture for bacterial and fungal pathogens. A convenience sampling method was used. The point estimate was calculated at a 95% Confidence Interval.

Results

Among 428 patients, 337 (78.73%) (73.24-84.33, 95% Confidence Interval) had a positive microbiological culture. A total of 213 (49.76%) of enrolled samples had a prior history of ocular trauma. Aspergillus species 68 (20.17%) and Streptococcus species 33 (9.79%) were the most common organisms isolated from fungal and bacterial corneal ulcers respectively.

Conclusions

The prevalence of positive microbiological culture among patients with infective keratitis from this study is similar to the pattern reported from similar settings.

Keywords

corneal ulcer; keratitis; prevalence.

Diagnosis of Fungal Keratitis in Low-Income Countries: Evaluation of Smear Microscopy, Culture, and In Vivo Confocal Microscopy in Nepal

Clinically diagnosing fungal keratitis (FK) is challenging; diagnosis can be assisted by investigations including in vivo confocal microscopy (IVCM), smear microscopy, and culture. The aim of this study was to estimate the sensitivity in detecting fungal keratitis (FK) using IVCM, smear microscopy, and culture in a setting with a high prevalence of FK. In this cross-sectional study nested within a prospective cohort study, consecutive microbial keratitis (MK) patients attending a tertiary-referral eye hospital in south-eastern Nepal between June 2019 and November 2020 were recruited. IVCM and corneal scrapes for smear microscopy and culture were performed using a standardised protocol. Smear microscopy was performed using potassium hydroxide (KOH), Gram stain, and calcofluor white. The primary outcomes were sensitivities with 95% confidence intervals [95% CI] for IVCM, smear microscopy and culture, and for each different microscopy stain independently, to detect FK compared to a composite referent. We enrolled 642 patients with MK; 468/642 (72.9%) were filamentous FK, 32/642 (5.0%) were bacterial keratitis and 64/642 (10.0%) were mixed bacterial-filamentous FK, with one yeast infection (0.16%). No organism was identified in 77/642 (12.0%). Smear microscopy had the highest sensitivity (90.7% [87.9-93.1%]), followed by IVCM (89.8% [86.9-92.3%]) and culture (75.7% [71.8-79.3%]). Of the three smear microscopy stains, KOH had the highest sensitivity (85.3% [81.9-88.4%]), followed by Gram stain (83.2% [79.7-86.4%]) and calcofluor white (79.1% [75.4-82.5%]). Smear microscopy and IVCM were the most sensitive tools for identifying FK in our cohort. In low-resource settings we recommend clinicians perform corneal scrapes for microscopy using KOH and Gram staining. Culture remains an important tool to diagnose bacterial infection, identify causative fungi and enable antimicrobial susceptibility testing.

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.