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Zhao JY, He YX, Wu ML, Wang RQ. The application of high-throughput sequencing technology in corneal diseases. Int Ophthalmol 2024; 44:53. [PMID: 38340174 PMCID: PMC10858842 DOI: 10.1007/s10792-024-03049-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
High-throughput sequencing technology, also known as next-generation sequencing technology, can explore new biomarkers and specific gene mutations. It has a pivotal role in promoting the gene research, which can limit the detection area, lessen the time needed for sequencing. Also, it can quickly screen out the suspected pathogenic genes of patients, gain the necessary genetic data, and provide the basis for clinical diagnosis and genetic counseling. In the research of corneal diseases, through the DNA sequencing of patients' diseased cells, it can provide a deeper understanding of corneal diseases and improve the diagnosis, classification and treatment alternatives of various corneal diseases. This article will introduce the application progress of high-throughput sequencing technology in corneal diseases, which will help to understand the application of this technology in various corneal diseases.
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Affiliation(s)
- Jing Yi Zhao
- The Second Clinical Medical College of Jilin University, Changchun, 130012, Jilin, China
| | - Yu Xi He
- The Eye Center, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Mei Liang Wu
- The Eye Center, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Rui Qing Wang
- The Eye Center, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China.
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2
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Zhang J, Lu X, Cheng Z, Zou D, Shi W, Wang T. Alterations of conjunctival microbiota associated with orthokeratology lens wearing in myopic children. BMC Microbiol 2023; 23:397. [PMID: 38087200 PMCID: PMC10717905 DOI: 10.1186/s12866-023-03042-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 10/03/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Orthokeratology (OK) lens wear increases the risk of bacterial infection, but little is known about the microbiota of the conjunctival sac in myopic children wearing OK lenses. This study aimed to investigate the changes of conjunctival microbiota in children after treatment with OK lenses using 16 S rDNA sequencing. METHODS Twenty-eight myopic children who had been continuously wearing OK lenses for 12 to 13 months were enrolled in this prospective study. Twenty-two gender- and age-matched myopic children who had not worn OK lenses or discontinued OK lens wear at least 1 year ago were recruited as controls. Conjunctival swabs from each participant were collected for exploration of the microbiota profiles, targeting the V3-V4 regions of the 16 S rRNA gene by MiSeq sequencing. The differences in the microbial community structure and diversity were also compared between groups. RESULTS The bacterial alpha diversity indices in the OK lens group were not different from those in the non-wearer group (P > 0.05, Wilcoxon test), while beta diversity examined using principle coordinate analysis of unweighted UniFrac divided the two groups into different clusters. Proteobacteria, Bacteroidetes, and Firmicutes were the abundant phyla in the conjunctival sac microbiota in both groups (P < 0.05, Mann-Whitney U test). Among children in the OK lens group, the Linear discriminant analysis Effect Size identified the compositional changes in OK lens-associated bacteria. Key functional genera such as Blautia, Parasutterella, and Muribaculum were enriched, whereas Brevundimonas, Acinetobacter, Proteus, and Agathobacter decreased significantly (P < 0.05, Mann-Whitney U test). Phylogenetic investigation of communities by reconstruction of unobserved states also showed altered bacterial metabolic pathways in OK lens-associated microbiota. Moreover, using receiver operating characteristic curves, Brevundimonas, Acinetobacter, Proteus, and Agathobacter alone (the area under the curve was all > 0.7500) or in combination (the area under the curve was 0.9058) were revealed to discriminate OK lens wearers from controls. CONCLUSIONS The relative abundance of the microbial community in the conjunctival sac of myopic children can alter after OK lens wear. Brevundimonas, Acinetobacter, Proteus, and Agathobacter may be candidate biomarkers to distinguish between OK lens wearers and non-wearers.
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Affiliation(s)
- Ju Zhang
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Eye Hospital of Shandong First Medical University (Shandong Eye Hospital), 372 Jingsi Road, Jinan, 250021, China
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Qingdao, China
| | - Xiuhai Lu
- Eye Hospital of Shandong First Medical University (Shandong Eye Hospital), 372 Jingsi Road, Jinan, 250021, China
| | - Zhiwei Cheng
- Eye Hospital of Shandong First Medical University (Shandong Eye Hospital), 372 Jingsi Road, Jinan, 250021, China
| | - Dulei Zou
- Eye Hospital of Shandong First Medical University (Shandong Eye Hospital), 372 Jingsi Road, Jinan, 250021, China
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Qingdao, China
- Medical College, Qingdao University, Qingdao, China
| | - Weiyun Shi
- Eye Hospital of Shandong First Medical University (Shandong Eye Hospital), 372 Jingsi Road, Jinan, 250021, China.
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Qingdao, China.
| | - Ting Wang
- Eye Hospital of Shandong First Medical University (Shandong Eye Hospital), 372 Jingsi Road, Jinan, 250021, China.
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Qingdao, China.
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Zilliox MJ, Bouchard CS. The Microbiome, Ocular Surface, and Corneal Disorders. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:1648-1661. [PMID: 37236506 DOI: 10.1016/j.ajpath.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/25/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023]
Abstract
The ocular surface microbiome is an emerging field of study that seeks to understand how the community of microorganisms found on the ocular surface may help maintain homeostasis or can potentially lead to disease and dysbiosis. Initial questions include whether the organisms detected on the ocular surface inhabit that ecological niche and, if so, whether there exists a core microbiome found in most or all healthy eyes. Many questions have emerged around whether novel organisms and/or a redistribution of organisms play a role in disease pathogenesis, response to therapies, or convalescence. Although there is much enthusiasm about this topic, the ocular surface microbiome is a new field with many technical challenges. These challenges are discussed in this review as well as a need for standardization to adequately compare studies and advance the field. In addition, this review summarizes the current research on the microbiome of various ocular surface diseases and how these findings may impact treatments and clinical decision-making.
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Affiliation(s)
- Michael J Zilliox
- Department of Ophthalmology, Loyola University Medical Center, Maywood, Illinois
| | - Charles S Bouchard
- Department of Ophthalmology, Loyola University Medical Center, Maywood, Illinois.
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Cheng Y, An N, Ishaq HM, Xu J. Ocular microbial dysbiosis and its linkage with infectious keratitis patients in Northwest China: A cross-sectional study. Microb Pathog 2023; 184:106371. [PMID: 37741304 DOI: 10.1016/j.micpath.2023.106371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
OBJECTIVES To evaluate the alteration of ocular surface microbiome of patients with infectious keratitis in northwest of China. METHODS The corneal scrapings, eyelid margin and conjunctiva samples were collected from 57 participants, who were divided into bacterial keratitis, fungal keratitis, viral keratitis and control group. The V3-V4 region of bacterial 16S rDNA in each sample was amplified and sequenced on the Illumina HiSeq 2500 sequencing platform, and the differences among different groups were compared bioinformatically. RESULTS Significant alterations of the microbiome were observed in alpha-diversity and beta-diversity analysis between the keratitis groups and the control group (p < 0.05). There was no significant differences between eyelid margin and conjunctiva samples in Alpha-Diversity analysis, but a significant difference between eyelid margin and corneal scraping samples in the keratitis group (p < 0.05, independent t-test). The abundances of Bacillus, Megamonas, Acinetobacter, and Rhodococcu were significantly elevated, while the abundance of Staphylococcus was decreased in the keratitis group compared to the control group. CONCLUSIONS The abundance of the ocular microbiome in patients with bacterial keratitis, fungal keratitis, or viral keratitis was significantly higher than those in the control group. Keratitis patients may have ecological disorder on ocular surface microbiome compared with controls. We believe that the conjunctiva and eyelid margin microbiome combined analysis can more comprehensively reflect the composition and abundance of ocular surface microbiome.
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Affiliation(s)
- Yan Cheng
- Department of Microbiology and Immunology, Key Laboratory of Environment and Genes Related to Diseases of Chinese Ministry of Education, School of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Na An
- The Fist Affiliated Hospital of Northwestern University, Department of Ophthalmology, The Xi'an Fist Hospital, Shaanxi Institute of Ophthalmology, China
| | - Hafiz Muhammad Ishaq
- Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef University of Agriculture Multan, Pakistan
| | - Jiru Xu
- Department of Microbiology and Immunology, Key Laboratory of Environment and Genes Related to Diseases of Chinese Ministry of Education, School of Medicine, Xi'an Jiaotong University, Xi'an, China.
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5
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Barrera B, Bustamante A, Marín-Cornuy M, Aguila-Torres P. Contact lenses and ocular dysbiosis, from the transitory to the pathological. ARCHIVOS DE LA SOCIEDAD ESPANOLA DE OFTALMOLOGIA 2023; 98:586-594. [PMID: 37648207 DOI: 10.1016/j.oftale.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/19/2023] [Indexed: 09/01/2023]
Abstract
Normal ocular microbiota is composed of different Gram-negative and positive bacterial communities that act as commensals on the ocular surface. An imbalance in the homeostasis of the native species or dysbiosis triggers functional alterations that can eventually lead to ocular conditions, indicating the use of contact lenses as the most relevant predisposing factor. Through a bibliographic review that added scientific articles published between 2018 and 2022, the relationship between healthy ocular microbiota and dysbiosis associated with the use of contact lenses that trigger ocular conditions was analyzed. The ocular microbiota in healthy individuals is mainly composed of bacteria from the phyla: Proteobacteria, Actinobacteria and Firmicutes. These bacterial communities associated with the use of contact lenses develop dysbiosis, observing an increase in certain genera such as Staphylococcus spp. and Pseudomonas spp., which under normal conditions are commensals of the ocular surface, but as their abundance is increased, they condition the appearance of various ocular conditions such as corneal infiltrative events, bacterial keratitis and corneal ulcer. These pathologies tend to evolve rapidly, which, added to late detection and treatment, can lead to a poor visual prognosis. It is suggested that professionals in the ophthalmology area learn about the composition of the communities of microorganisms that make up this ocular microbiota, in order to correctly distinguish and identify the causative agent, thereby providing a adequate and effective treatment to the user.
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Affiliation(s)
- B Barrera
- Laboratorio de Microbiología Molecular, Escuela de Tecnología Médica, Universidad Austral de Chile, Puerto Montt, Chile
| | - A Bustamante
- Laboratorio de Microbiología Molecular, Escuela de Tecnología Médica, Universidad Austral de Chile, Puerto Montt, Chile
| | - M Marín-Cornuy
- Laboratorio de Microbiología Molecular, Escuela de Tecnología Médica, Universidad Austral de Chile, Puerto Montt, Chile
| | - P Aguila-Torres
- Laboratorio de Microbiología Molecular, Escuela de Tecnología Médica, Universidad Austral de Chile, Puerto Montt, Chile.
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Evaluation of Serratia marcescens Adherence to Contact Lens Materials. Microorganisms 2023; 11:microorganisms11010217. [PMID: 36677509 PMCID: PMC9861737 DOI: 10.3390/microorganisms11010217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/07/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Bacterial keratitis is a risk associated with the use of contact lenses for cosmetic purposes or vision correction. In this in vitro experimental study, we examined the ability of the ocular pathogen Serratia marcescens to adhere to monthly or biweekly replacement contact lenses. We performed quantitative adhesion assays to evaluate the adherence of S. marcescens to seven contact lens materials: comfilcon A, senofilcon A, omafilcon B, fanfilcon A, balafilcon A, senofilcon C, and lehfilcon A. Lehfilcon A is a newly marketed silicon hydrogel contact lens with a surface modification of poly-(2-methacryloyloxyethyl phosphorylcholine) (PMPC). PMPC has previously been demonstrated to be an effective anti-biofouling treatment for numerous surfaces. We observed low S. marcescens adherence to lehfilcon A compared to other materials. We demonstrate the use of the fluorescent dye 5(6)-Carboxytetramethylrhodamine succinimidyl ester to covalently stain live cells prior to material adhesion studies.
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Cavuoto KM, Zhu AY. The Role of the Ocular Surface Microbiome (OSM) in Diseases of the Anterior Segment and Ocular Surface. CURRENT OPHTHALMOLOGY REPORTS 2022. [DOI: 10.1007/s40135-022-00294-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Dong K, Pu J, Yang J, Zhou G, Ji X, Kang Z, Li J, Yuan M, Ning X, Zhang Z, Ma X, Cheng Y, Li H, Ma Q, Li H, Zhao L, Lei W, Sun B, Xu J. The species-level microbiota of healthy eyes revealed by the integration of metataxonomics with culturomics and genome analysis. Front Microbiol 2022; 13:950591. [PMID: 36124162 PMCID: PMC9481467 DOI: 10.3389/fmicb.2022.950591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/09/2022] [Indexed: 11/21/2022] Open
Abstract
Objectives To characterize the healthy ocular surface microbiota at the species level, including cultured and uncultured taxa. Methods We integrated the metataxonomic method with culturomics and genome sequencing analysis of selected isolated strains to better illustrate the taxonomic structure of the ocular surface microbiota. The metataxonomics used the full-length 16S rRNA gene sequences and the operational phylogenetic unit strategy, which can precisely identify the cultured and uncultured or potentially new taxa to species level based on the phylogenetic tree constructed. Results We detected 1,731 operational phylogenetic units (OPUs) in 196 healthy eyes from 128 people, affiliated to 796 cultured species, 784 potentially new species, and 151 potentially new higher taxa. The microbiota for each eye had 49.17 ± 35.66 OPUs. Of the 796 cultured species, 170 (21.36%) had previously caused clinical infections. Based on where they were initially isolated, the ocular surface microbiota mainly came from human body sites (34.55%), the environment (36.93%), plants (9.05%), animals (4.90%), and others; 428 strains were isolated from 20 eyes, affiliated to 42 species, and had come from the environment (33.33%) and the skin (16.67%). Of these, 47.62% had previously caused clinical infections. Genome analysis of 73 isolators revealed that 68.5% of them carried antibiotic resistance genes. The most frequently isolated genera, namely Staphylococcus, Streptococcus, and Moraxella, had an average of 5.30, four, and three resistance genes per strain, respectively. Discussion The study found that the ocular surface microbiota mainly came from the environment, plants, animals, food, and human body sites such as the skin, oral cavity, upper respiratory tract, etc. No core member of ocular surface microbiota was detected at the species level. The human eyes were invaded and colonized by bacteria from the exposed environment, some of which were capable of causing infections in humans and carried antibiotic resistance genes. Preventive measures should be developed to protect our eyes from danger.
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Affiliation(s)
- Kui Dong
- Shanxi Eye Hospital, Shanxi Province Key Laboratory of Ophthalmology, Taiyuan, China
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guohong Zhou
- Shanxi Eye Hospital, Shanxi Province Key Laboratory of Ophthalmology, Taiyuan, China
| | - Xuan Ji
- Shanxi Eye Hospital, Shanxi Province Key Laboratory of Ophthalmology, Taiyuan, China
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Zhiming Kang
- Shanxi Eye Hospital, Shanxi Province Key Laboratory of Ophthalmology, Taiyuan, China
| | - Juan Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Min Yuan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaoling Ning
- Shanxi Eye Hospital, Shanxi Province Key Laboratory of Ophthalmology, Taiyuan, China
| | - Zhaoxia Zhang
- Shanxi Eye Hospital, Shanxi Province Key Laboratory of Ophthalmology, Taiyuan, China
| | - XingYu Ma
- Shanxi Eye Hospital, Shanxi Province Key Laboratory of Ophthalmology, Taiyuan, China
| | - Yanpeng Cheng
- School of Public Health, Shanxi Medical University, Taiyuan, China
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Hong Li
- Shanxi Eye Hospital, Shanxi Province Key Laboratory of Ophthalmology, Taiyuan, China
| | - Qin Ma
- Shanxi Eye Hospital, Shanxi Province Key Laboratory of Ophthalmology, Taiyuan, China
| | - Hong Li
- Shanxi Eye Hospital, Shanxi Province Key Laboratory of Ophthalmology, Taiyuan, China
| | - Lijun Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenjing Lei
- Shanxi Eye Hospital, Shanxi Province Key Laboratory of Ophthalmology, Taiyuan, China
| | - Bin Sun
- Shanxi Eye Hospital, Shanxi Province Key Laboratory of Ophthalmology, Taiyuan, China
- Bin Sun
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Institute of Public Heath, Nankai University, Tianjin, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Jianguo Xu
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Jeang L, Tuli SS. Therapy for contact lens-related ulcers. Curr Opin Ophthalmol 2022; 33:282-289. [PMID: 35779052 DOI: 10.1097/icu.0000000000000861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW The current review covers the current literature and practice patterns of antimicrobial therapy for contact lens-related microbial keratitis (CLMK). Although the majority of corneal ulcers are bacterial, fungus and acanthamoeba are substantial contributors in CLMK and are harder to treat due to the lack of commercially available topical medications and low efficacy of available topical therapy. RECENT FINDINGS Topical antimicrobials remain the mainstay of therapy for corneal ulcers. Fluoroquinolones may be used as monotherapy for small, peripheral bacterial ulcers. Antibiotic resistance is a persistent problem. Fungal ulcers are less responsive to topical medications and adjunct oral or intrastromal antifungal medications may be helpful. Acanthamoeba keratitis continues to remain a therapeutic challenge but newer antifungal and antiparasitic agents may be helpful adjuncts. Other novel and innovative therapies are being studied currently and show promise. SUMMARY Contact lens-associated microbial keratitis is a significant health issue that can cause vision loss. Treatment remains a challenge but many promising diagnostics and procedures are in the pipeline and offer hope.
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Affiliation(s)
- Lauren Jeang
- Department of Ophthalmology, University of Florida, Gainesville, Florida, USA
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Liang C, Wang N. Subretinal Drusenoid Deposits and Lower Serum High-Density Lipoprotein Cholesterol Levels Possess Latent Relation to Cardiovascular Disease and Can Be a Feasible Predictor. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:3135100. [PMID: 35813439 PMCID: PMC9270125 DOI: 10.1155/2022/3135100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/30/2022] [Accepted: 06/03/2022] [Indexed: 11/17/2022]
Abstract
Objective To ascertain whether lipid-related subretinal drusenoid deposits (SDD) are correlated with coexisting cardiovascular disease (CVD), as well as to reveal latent serum markers of CVD. Methods Patients older than 50 years and plagued by age-related macular degeneration (AMD) were included. Subjects with other retinal degenerations and vascular diseases, any recent treatment at other medical care institutions, and any previous oculopathy or ophthalmic surgery were excluded. All subjects were examined to ascertain whether they possess SDD, to analyze serum cholesterols, including low-density lipoprotein cholesterol (LDL), triglycerides (TG), high-density lipoprotein cholesterol (HDL), and total cholesterol (TC). Subjects were divided into SDD and non-SDD groups and further divided into subgroups by assessment of pump defect, valve defect, and carotid defect. Finally, logistic model trees and random forest algorithm analysis were performed. Results A total of 85 AMD patients including 43 with and 42 without SDD were involved. The 42 AMD (97.67%, 42/43) patients with SDD showed CVD, including 3 subjects presenting valve defect, 3 subjects presenting carotid defect, 8 subjects presenting pump defect, 14 subjects presenting both pump and valve defects, and 14 subjects presenting pump, valve, and carotid defects. By contrast, 5 AMD (11.90%, 5/42) patients without SDD showed CVD. Cholesterol level of SDD subjects presented significant higher TC (5.66 ± 1.01 vs. 5.58 ± 0.72, p = 0.032, Wilcoxon test) and lower HDL cholesterol (61 ± 17 vs. 70 ± 21, p = 0.031, Wilcoxon test) than that of non-SDD. The cases with HDL < 62 mg/dL were significantly related to CVD (p = 0.013, Wilcoxon test), and the cases with HDL < 40 mg/dL were not (p = 0.659, Wilcoxon test). Through machine learning based on the image from color fundus photography, the accuracy of predicting CVD was 95%. Conclusions The presence of SDD of AMD and lower serum HDL cholesterol level can predict certain CVD for AMD patients. The machine learning based on the SDD image and serum HDL cholesterol may open new avenue for the detection of CVD as a noninvasive approach.
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Affiliation(s)
- Changsen Liang
- Department of Ophthalmology, Jinan Seventh People's Hospital, Jinan 250132, China
| | - Ning Wang
- Department of Cardiovascularology, Jinan Seventh People's Hospital, Jinan 250132, China
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11
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Ren Z, Li W, Liu Q, Dong Y, Huang Y. Profiling of the Conjunctival Bacterial Microbiota Reveals the Feasibility of Utilizing a Microbiome-Based Machine Learning Model to Differentially Diagnose Microbial Keratitis and the Core Components of the Conjunctival Bacterial Interaction Network. Front Cell Infect Microbiol 2022; 12:860370. [PMID: 35558101 PMCID: PMC9086711 DOI: 10.3389/fcimb.2022.860370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/28/2022] [Indexed: 12/29/2022] Open
Abstract
Both healthy and diseased human ocular surfaces possess their own microbiota. If allowed, opportunistic pathogens within the ocular microbiota may cause microbial keratitis (MK). However, the nonpathogenic component of the ocular microbiota has been proven to undermine the performance of culture, the gold standard of the etiological diagnosis for MK. As the conjunctival bacterial microbiota generates unique alterations with various oculopathies, this study aimed to evaluate the feasibility of distinguishing MK using machine learning based on the characteristics of the conjunctival bacterial microbiome associated with various types of MK. This study also aimed to reveal which bacterial genera constitute the core of the interaction network of the conjunctival bacterial microbiome. Conjunctival swabs collected from the diseased eyes of MK patients and the randomly chosen normal eyes of healthy volunteers were subjected for high-throughput 16S rDNA sequencing. The relative content of each bacterial genus and the composition of bacterial gene functions in every sample were used to establish identification models with the random forest algorithm. Tenfold cross validation was adopted. Accuracy was 96.25% using the bacterial microbiota structure and 93.75% using the bacterial gene functional composition. Therefore, machine learning with the conjunctival bacterial microbiome characteristics might be used for differentiation of MKs as a noninvasive supplementary approach. In addition, this study found that Actinobacteria, Lactobacillus, Clostridium, Helicobacter, and Sphingomonas constitute the core of the interaction network of the conjunctival bacterial microbiome.
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Affiliation(s)
- Zhichao Ren
- Qingdao University Medical College, Qingdao, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
| | - Wenfeng Li
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qing Liu
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
| | - Yanling Dong
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
| | - Yusen Huang
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
- *Correspondence: Yusen Huang,
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12
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Tuft S, Somerville TF, Li JPO, Neal T, De S, Horsburgh MJ, Fothergill JL, Foulkes D, Kaye S. Bacterial keratitis: identifying the areas of clinical uncertainty. Prog Retin Eye Res 2021; 89:101031. [PMID: 34915112 DOI: 10.1016/j.preteyeres.2021.101031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022]
Abstract
Bacterial keratitis is a common corneal infection that is treated with topical antimicrobials. By the time of presentation there may already be severe visual loss from corneal ulceration and opacity, which may persist despite treatment. There are significant differences in the associated risk factors and the bacterial isolates between high income and low- or middle-income countries, so that general management guidelines may not be appropriate. Although the diagnosis of bacterial keratitis may seem intuitive there are multiple uncertainties about the criteria that are used, which impacts the interpretation of investigations and recruitment to clinical studies. Importantly, the concept that bacterial keratitis can only be confirmed by culture ignores the approximately 50% of cases clinically consistent with bacterial keratitis in which investigations are negative. The aetiology of these culture-negative cases is unknown. Currently, the estimation of bacterial susceptibility to antimicrobials is based on data from systemic administration and achievable serum or tissue concentrations, rather than relevant corneal concentrations and biological activity in the cornea. The provision to the clinician of minimum inhibitory concentrations of the antimicrobials for the isolated bacteria would be an important step forward. An increase in the prevalence of antimicrobial resistance is a concern, but the effect this has on disease outcomes is yet unclear. Virulence factors are not routinely assessed although they may affect the pathogenicity of bacteria within species and affect outcomes. New technologies have been developed to detect and kill bacteria, and their application to bacterial keratitis is discussed. In this review we present the multiple areas of clinical uncertainty that hamper research and the clinical management of bacterial keratitis, and we address some of the assumptions and dogma that have become established in the literature.
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Affiliation(s)
- Stephen Tuft
- Moorfields Eye Hospital NHS Foundation Trust, 162 City Road, London, EC1V 2PD, UK.
| | - Tobi F Somerville
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Ji-Peng Olivia Li
- Moorfields Eye Hospital NHS Foundation Trust, 162 City Road, London, EC1V 2PD, UK.
| | - Timothy Neal
- Department of Clinical Microbiology, Liverpool Clinical Laboratories, Liverpool University Hospital NHS Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK.
| | - Surjo De
- Department of Clinical Microbiology, University College London Hospitals NHS Foundation Trust, 250 Euston Road, London, NW1 2PG, UK.
| | - Malcolm J Horsburgh
- Department of Infection and Microbiomes, University of Liverpool, Crown Street, Liverpool, L69 7BX, UK.
| | - Joanne L Fothergill
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Daniel Foulkes
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Stephen Kaye
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
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