The Need of Non-traditional Techniques to Screen for the Virus

BACKGROUND: At the present moment, the etiological diagnosis of SARS-CoV-2 is based on the polymerase chain reaction (PCR). False negative cases are increasingly reported in several studies using reverse transcription-PCR (RT-PCR). For example, the positive rate of RT-PCR for throat swabs was reported to be about 60% in early stage of COVID-19. AIM: We aimed to present metagenomic next-generation sequencing (mNGS) as a potential tool to detect pathogens. METHODS: In the recent year, mNGS is shown the potential to detect pathogens without the need of hypothesis guided approach and is proven to be highly effective. RESULTS: A recent prospective study in the United States compared the diagnostic performance of routine diagnostic tests with mNGS and showed that mNGS detected a bacteria or virus in the CSF of 13 of 58 patients presenting with meningoencephalitis who were negative for or not assessed with routine diagnostic test including PCR. NGS also has the advantage to cover entire viral genomes. CONCLUSION: As viral metagenomics has significantly improved in recent years and become more cost effective, we think that a change in the approach toward a shot-gun metagenomic testing should be explored and could potentially aid the diagnosis of COVID-19 cases and the management of this pandemic

Cooperative low-rank models for removing stripe noise from OCTA images

Optical coherence tomography angiography (OCTA) is an emerging non-invasive imaging technique for imaging the microvasculature of the eye based on phase variance or amplitude decorrelation derived from repeated OCT images of the same tissue area. Stripe noise occurs during the OCTA acquisition process due to the involuntary movement of the eye. To remove the stripe noise (or ‘destriping’) effectively, we propose two novel image decomposition models to simultaneously destripe all the OCTA images of the same eye cooperatively: cooperative uniformity destriping (CUD) model and cooperative similarity destriping (CSD) model. Both the models consider stripe noise by low-rank constraint but in different ways: the CUD model assumes that stripe noise is identical across all the layers while the CSD model assumes that the stripe noise at different layers are different and have to be considered in the model. Compared to the CUD model, CSD is a more general solution for real OCTA images. An efficient solution (CSD+) is developed for model CSD to reduce the computational complexity. The models were extensively evaluated against state-of-the-art methods on both synthesized and real OCTA datasets. The experiments demonstrated not only the effectiveness of the CSD and CSD+ models in terms of peak signal-to-noise ratio (PSNR) and structural similarity index (SSIM) and CSD+ is twice faster than CSD, but also their beneficiary effect on the vessel segmentation of OCTA images. We expect our models will become a powerful tool for clinical applications

Metagenome techniques to reduce diagnostic delay in Acanthamoeba keratitis

publishersversionPeer reviewe

Corneal Endothelial Cell Loss in Glaucoma and Glaucoma Surgery and the Utility of Management with Descemet Membrane Endothelial Keratoplasty (DMEK)

Publisher Copyright: © 2022 Neeru A Vallabh et al.The corneal endothelium has a crucial role in maintaining a clear and healthy cornea. Corneal endothelial cell loss occurs naturally with age; however, a diagnosis of glaucoma and surgical intervention for glaucoma can exacerbate a decline in cell number and impairment in morphology. In glaucoma, the mechanisms for this are not well understood and this accelerated cell loss can result in corneal decompensation. Given the high prevalence of glaucoma worldwide, this review aims to explore the abnormalities observed in the corneal endothelium in differing glaucoma phenotypes and glaucoma therapies (medical or surgical including with new generation microinvasive glaucoma surgeries). Descemet membrane endothelial keratoplasty (DMEK) is increasingly being used to manage corneal endothelial failure for glaucoma patients and we aim to review the recent literature evaluating the use of this technique in this clinical scenario.publishersversionPeer reviewe

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

Next-generation sequencing for the detection of microorganisms present in human donor corneal preservation medium.

Objective:To detect the presence of microorganisms in the storage media of human donor corneas using next-generation sequencing method. Methods:Seven samples from organ culture (OC) group (Cornea Max, Eurobio, Les Ulis, France) with one control (sterile media without any cornea) and seven samples from hypothermic storage group (Cornea Cold, Eurobio) with one control were used for this study. The corneas were placed in the respective storage media for 14 days before collecting the samples. Storage media (2 mL) from each sample were collected in RNAase-free tubes and shipped for ribosomal RNA sequencing of 16 S and 18 S. Simultaneously, another 1 mL of media sample was used for conventional diagnostic method (CDM) using Bactec instruments. Results:In both, OC and hypothermic storage and control samples, the most abundant genera were Pseudomonas, Comamonas, Stenotrophomonas, Alcanivorax, Brevundimonas and Nitrobacter. Acidovorax, Acetobacter and Hydrogenophilus were detected mostly in the hypothermic storage group. The most abundant fungal pathogen detected belonged to the genus Malassezia, which was found in both the storage conditions. CDM was negative for microorganisms in all the samples. Conclusion:Metagenomics provides full taxonomic profiling of the detected genomic material of the organisms and thus has the potential to deliver a much wider microbiological diagnostic approach than CDM. The costs and turn-around time need to be reduced, and; the detection of viable organisms would help this technology to be introduced into routine clinical practice

Selective transepithelial ablation with simultaneous accelerated corneal crosslinking for corneal regularization of keratoconus : STARE-X protocol

Publisher Copyright: Copyright © 2021 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of ASCRS and ESCRS.PURPOSE: To evaluate the changes in refractive outcomes and corneal aberrations in central and paracentral keratoconus after selective transepithelial topography-guided photorefractive keratectomy combined with accelerated corneal crosslinking (STARE-X). SETTINGS: Centro Polispecialistico Mediterraneo, Siena Crosslinking Center, and University of Messina, Italy. DESIGN: Prospective, interventional, multicentric study. METHODS: Patients were subdivided into 2 groups: Group 1 with cone located within the central 3 mm zone (50 eyes) and Group 2 (50 eyes) with cone located outside the central 3 mm zone. Follow-up was 2 years at least for all eyes. Outcome parameters included uncorrected distance visual acuity (UDVA) and corrected distance visual acuity (CDVA). Corneal tomography and corneal wavefront aberrations were assessed and compared before and 2 years after the treatment. RESULTS: 100 eyes of 100 patients underwent STARE-X protocol. At 2 years, UDVA and CDVA improved, and sphere, cylinder, and Kmax reduced after treatment in both groups (P < .001, respectively). Moreover, a statistically significant reduction was observed of total higher-order aberrations root main square (RMS), coma RMS, and spherical aberration RMS in both groups (P < .001, respectively). However, CDVA improved more in Group 1 than in Group 2 (P < .02). CONCLUSIONS: The STARE-X protocol demonstrated effective results in halting keratoconus progression and improving corneal regularity with a safe and effective profile. STARE-X improved both visual acuity and corneal aberration at 2 years. Longer follow-up studies are warranted to observe further long-term CXL flattening effect on the cone.Peer reviewe

Solar retinopathy: a new setting of red, green, and blue channels

Purpose: To introduce a new color imaging technique using improved settings of red, green, and blue channels for improved delineation of retinal damage in patients with solar retinopathy. Method: A retrospective case series of patients with poor vision secondary to solar retinopathy were analyzed. All patients underwent visual acuity, refraction, and dilated fundus examination. A spectral domain–optical coherence tomography of the macula and color fundus imaging using optimized red, green, and blue color setting was performed. Patients were reviewed over a 6-month period. The data were analyzed for statistical significance using an independent t test and a receiver operating characteristic curve. Results: In total, 20 eyes of 10 patients were included between 2009 and 2017. The mean age was 24.9 ± 18.1 years. Best corrected visual acuity at first consultation was 0.78 ± 0.11 and after 6 months was 0.83 ± 0.09. Spectral domain–optical coherence tomography demonstrated retinal abnormalities at the myoid zone, ellipsoid zone, and the outer segment of photoreceptors. Receiver operating characteristic curve analysis showed an improving effect (area under the curve = 0.62; 95% confidence interval = 0.42–0.79). The color channels parameters, which improve visualization of the lesions were found to be 67-0.98-255 for the R-guided setting, 19-0.63-121 for the B-guided setting, and 7-1.00-129 for the G-guided setting. The ideal red, green, and blue setting was in 24-0.82-229. Conclusion: The use of a new setting of red, green, and blue channels could improve the diagnosis and monitoring of solar retinopathy, hence improving patient care