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Naqvi M, Fineide F, Utheim TP, Charnock C. Culture- and non-culture-based approaches reveal unique features of the ocular microbiome in dry eye patients. Ocul Surf 2024; 32:123-129. [PMID: 38354907 DOI: 10.1016/j.jtos.2024.02.002] [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: 10/30/2023] [Revised: 01/24/2024] [Accepted: 02/11/2024] [Indexed: 02/16/2024]
Abstract
PURPOSE The purpose of this study was to investigate the ocular microbiome in individuals with dry eye disease and to identify features of their ocular microbiome of possible health and diagnostic significance. METHODS Conjunctival samples were collected from both eyes in duplicate from 91 individuals (61 dry eye, 30 healthy) and used for both culture-dependent and culture-independent analyses. Samples were either analysed using next generation sequencing (V3-V4 16S rDNA) or inoculated on a wide range of agar types and grown under a broad range of conditions to maximize recovery. Isolates were identified by partial sequencing of the 16S rDNA and rpoB genes and tested for antibiotic susceptibility. We applied a L2-regularized logistic regression model on the next generation sequencing data to investigate any potential association between severe dry eye disease and the ocular microbiome. RESULTS Culture-dependent analysis showed the highest number of colony forming units in healthy individuals. The majority of isolates recovered from the samples were Corynebacterium, Micrococcus sp., Staphylococcus epidermidis, and Cutibacterium acnes. Culture independent analysis revealed 24 phyla, of which Actinobacteria, Firmicutes and Proteobacteria were the most abundant. Over 405 genera were detected of which Corynebacterium was the most dominant, followed by Staphylococcus and Cutibacterium. The L2-regularized logistic regression model indicated that Blautia and Corynebacterium sp. may be associated with severe DED. CONCLUSIONS Our study indicates that the ocular microbiome has characteristic features in severe DED patients. Certain Corynebacterium species and Blautia are of particular interest for future studies.
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Affiliation(s)
- Maria Naqvi
- Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, Postbox 4, St. Olavs Plass, 0130, Oslo, Norway.
| | - Fredrik Fineide
- Department of Computer Science, Oslo Metropolitan University, Norway; Department of Medical Biochemistry, Oslo University Hospital, Norway; The Norwegian Dry Eye Clinic, Ole Vigs Gate 32 E, 0366, Oslo, Norway
| | - Tor Paaske Utheim
- Department of Medical Biochemistry, Oslo University Hospital, Norway; The Norwegian Dry Eye Clinic, Ole Vigs Gate 32 E, 0366, Oslo, Norway
| | - Colin Charnock
- Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, Postbox 4, St. Olavs Plass, 0130, Oslo, Norway
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Zhang X, Zhang L, Li Y, Wang N, Zhang Y. Clinical performance of metagenomic next-generation sequencing for diagnosis of invasive fungal disease after hematopoietic cell transplant. Front Cell Infect Microbiol 2024; 14:1210857. [PMID: 38590441 PMCID: PMC11000502 DOI: 10.3389/fcimb.2024.1210857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 03/04/2024] [Indexed: 04/10/2024] Open
Abstract
Background Timely diagnosis and appropriate antifungal therapy are critical for improving the prognosis of patients with invasive fungal disease (IFD) after hematopoietic stem cell transplantation (HSCT). We evaluated the performance of metagenomic next-generation sequencing (mNGS) and conventional microbiological testing (CMT), as well as the diagnosis, therapeutic management, and outcomes of IFD after HSCT. Methods We retrospectively studied 189 patients who underwent HSCT and were considered at risk for IFD. In total, 46 patients with IFD were enrolled in this study. The IFD consensus was followed for classifying IFD incidents. Results Forty-six patients were diagnosed with proven/probable (n = 12), possible (n = 27), and undefined (n = 7) IFD. Aspergillus was the most commonly detected fungal genus. Mucormycosis was found in 15 patients; two had Aspergillus, and one had Candida infections. Compared to CMT, mNGS significantly reduced the time required to identify pathogens (P = 0.0016). mNGS had a much higher sensitivity than CMT (84.78% vs. 36.96%; P < 0.0001). A total of 76.09% of patients received antifungal prophylaxis during fungal infections. All Pneumocystis infections occurred later than 100 days after transplantation. Among patients with Pneumocystis infection, 71.43% occurred following sulfonamide withdrawal, and subsequent treatment with sulfonamide alone or in combination with other drugs was effective. Based on the empirical antifungal treatment, the dosages, modes of administration, frequency of administration, or antifungal of 55.26% of the patients were changed according to the mNGS results. The 4-year overall survival rate of patients diagnosed with IFD after transplantation was 71.55% (95% CI, 55.18%-85.82%). Hypoproteinemia and corticosteroid use are independent risk factors for IFD. Conclusion mNGS, which has a high sensitivity and a short detection time, aids in the diagnosis and prognosis of pathogenic fungi. As a powerful technology, mNGS can influence treatment decisions in patients with IFD following HSCT.
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Affiliation(s)
- Xiaoying Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lingfeng Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yun Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Na Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yicheng Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
- Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
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Li F, Yang S, Ma J, Zhao X, Chen M, Wang Y. High-throughput sequencing reveals differences in microbial community structure and diversity in the conjunctival tissue of healthy and type 2 diabetic mice. BMC Microbiol 2024; 24:90. [PMID: 38493114 PMCID: PMC10943819 DOI: 10.1186/s12866-024-03247-y] [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: 08/19/2023] [Accepted: 03/03/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND To investigate the differences in bacterial and fungal community structure and diversity in conjunctival tissue of healthy and diabetic mice. METHODS RNA-seq assays and high-throughput sequencing of bacterial 16 S rDNA and fungal internal transcribed spacer (ITS) gene sequences were used to identify differentially expressed host genes and fungal composition profiles in conjunctival tissues of diabetic BKS-db/db mice and BKS (control) mice. Functional enrichment analysis of differentially expressed genes and the correlation between the relative abundance of bacterial and fungal taxa in the intestinal mucosa were also performed. RESULTS Totally, 449 differential up-regulated genes and 1,006 down-regulated genes were identified in the conjunctival tissues of diabetic mice. The differentially expressed genes were mainly enriched in metabolism-related functions and pathways. A decrease in conjunctival bacterial species diversity and abundance in diabetic mice compared to control mice. In contrast, fungal species richness and diversity were not affected by diabetes. The microbial colonies were mainly associated with cellular process pathways regulating carbohydrate and lipid metabolism, as well as cell growth and death. Additionally, some interactions between bacteria and fungi at different taxonomic levels were also observed. CONCLUSION The present study revealed significant differences in the abundance and composition of bacterial and fungal communities in the conjunctival tissue of diabetic mice compared to control mice. The study also highlighted interactions between bacteria and fungi at different taxonomic levels. These findings may have implications for the diagnosis and treatment of diabetes.
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Affiliation(s)
- Fengjiao Li
- Department of Opthalmology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Shuo Yang
- Eye Center, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
| | - Ji Ma
- Core Laboratory, The Affiliated Qingdao Central Hospital of Qingdao University, Qingdao, 266042, Shandong, China
| | - Xiaowen Zhao
- Core Laboratory, The Affiliated Qingdao Central Hospital of Qingdao University, Qingdao, 266042, Shandong, China
| | - Meng Chen
- Department of Opthalmology, Qingdao municipal hospital, Qingdao Municipal Hospital, No. 5 Donghai Middle Road, Shinan District, Qingdao, 266000, China.
| | - Ye Wang
- Core Laboratory, The Affiliated Qingdao Central Hospital of Qingdao University, Qingdao, 266042, Shandong, 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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Gunasekaran R, Chandrasekaran A, Rajarathinam K, Duncan S, Dhaliwal K, Lalitha P, Prajna NV, Mills B. Rapid Point-of-Care Identification of Aspergillus Species in Microbial Keratitis. JAMA Ophthalmol 2023; 141:966-973. [PMID: 37768674 PMCID: PMC10540059 DOI: 10.1001/jamaophthalmol.2023.4214] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/30/2023] [Indexed: 09/29/2023]
Abstract
Importance Microbial keratitis (MK) is a common cause of unilateral visual impairment, blindness, and eye loss in low-income and middle-income countries. There is an urgent need to develop and implement rapid and simple point-of-care diagnostics for MK to increase the likelihood of good outcomes. Objective To evaluate the diagnostic performance of the Aspergillus-specific lateral-flow device (AspLFD) to identify Aspergillus species causing MK in corneal scrape and corneal swab samples of patients presenting with microbial keratitis. Design, Setting, and Participants This diagnostic study was conducted between May 2022 and January 2023 at the corneal clinic of Aravind Eye Hospital in Madurai, Tamil Nadu, India. All study participants were recruited during their first presentation to the clinic. Patients aged 15 years or older met the eligibility criteria if they were attending their first appointment, had a corneal ulcer that was suggestive of a bacterial or fungal infection, and were about to undergo diagnostic scrape and culture. Main Outcomes and Measures Sensitivity and specificity of the AspLFD with corneal samples collected from patients with MK. During routine diagnostic scraping, a minimally invasive corneal swab and an additional corneal scrape were collected and transferred to aliquots of sample buffer and analyzed by lateral-flow device (LFD) if the patient met the inclusion criteria. Photographs of devices were taken with a smartphone and analyzed using a ratiometric approach, which was developed for this study. The AspLFD results were compared with culture reports. Results The 198 participants who met the inclusion criteria had a mean (range) age of 51 (15-85) years and included 126 males (63.6%). Overall, 35 of 198 participants with corneal scrape (17.7%) and 17 of 40 participants with swab samples (42.5%) had positive culture results for Aspergillus species. Ratiometric analysis results for the scrape samples found that the AspLFD achieved high sensitivity (0.89; 95% CI, 0.74-0.95), high negative predictive value (0.97; 95% CI, 0.94-0.99), low negative likelihood ratio (0.12; 95% CI, 0.05-0.30), and an accuracy of 0.94 (95% CI, 0.90-0.97). Ratiometric analysis results for the swab samples showed that the AspLFD had high sensitivity (0.94; 95% CI, 0.73-1.00), high negative predictive value (0.95; 95% CI, 0.76-1.00), low negative likelihood ratio (0.07; 95% CI, 0.01-0.48), and an accuracy of 0.88 (95% CI, 0.73-0.96). Conclusions and Relevance Results of this diagnostic study suggest that AspLFD along with the ratiometric analysis of LFDs developed for this study has high diagnostic accuracy in identifying Aspergillus species from corneal scrapes and swabs. This technology is an important step toward the provision of point-of-care diagnostics for MK and could inform the clinical management strategy.
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Affiliation(s)
- Rameshkumar Gunasekaran
- Department of Ocular Microbiology, Aravind Eye Hospital and Postgraduate Institute of Ophthalmology, Madurai, Tamil Nadu, India
| | - Abinaya Chandrasekaran
- Department of Cornea and Refractive Surgery Services, Aravind Eye Hospital and Postgraduate Institute of Ophthalmology, Madurai, Tamil Nadu, India
| | - Karpagam Rajarathinam
- Department of Ocular Microbiology, Aravind Eye Hospital and Postgraduate Institute of Ophthalmology, Madurai, Tamil Nadu, India
| | - Sheelagh Duncan
- Translational Healthcare Technologies Group, Centre for Inflammation Research, University of Edinburgh, United Kingdom
| | - Kevin Dhaliwal
- Translational Healthcare Technologies Group, Centre for Inflammation Research, University of Edinburgh, United Kingdom
| | - Prajna Lalitha
- Department of Ocular Microbiology, Aravind Eye Hospital and Postgraduate Institute of Ophthalmology, Madurai, Tamil Nadu, India
| | - N. Venkatesh Prajna
- Department of Cornea and Refractive Surgery Services, Aravind Eye Hospital and Postgraduate Institute of Ophthalmology, Madurai, Tamil Nadu, India
| | - Bethany Mills
- Translational Healthcare Technologies Group, Centre for Inflammation Research, University of Edinburgh, United Kingdom
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Herzog EL, Kreuzer M, Zinkernagel MS, Zysset-Burri DC. Challenges and insights in the exploration of the low abundance human ocular surface microbiome. Front Cell Infect Microbiol 2023; 13:1232147. [PMID: 37727808 PMCID: PMC10505673 DOI: 10.3389/fcimb.2023.1232147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/18/2023] [Indexed: 09/21/2023] Open
Abstract
Purpose The low microbial abundance on the ocular surface results in challenges in the characterization of its microbiome. The purpose of this study was to reveal factors introducing bias in the pipeline from sample collection to data analysis of low-abundant microbiomes. Methods Lower conjunctiva and lower lid swabs were collected from six participants using either standard cotton or flocked nylon swabs. Microbial DNA was isolated with two different kits (with or without prior host DNA depletion and mechanical lysis), followed by whole-metagenome shotgun sequencing with a high sequencing depth set at 60 million reads per sample. The relative microbial compositions were generated using the two different tools MetaPhlan3 and Kraken2. Results The total amount of extracted DNA was increased by using nylon flocked swabs on the lower conjunctiva. In total, 269 microbial species were detected. The most abundant bacterial phyla were Actinobacteria, Firmicutes and Proteobacteria. Depending on the DNA extraction kit and tool used for profiling, the microbial composition and the relative abundance of viruses varied. Conclusion The microbial composition on the ocular surface is not dependent on the swab type, but on the DNA extraction method and profiling tool. These factors have to be considered in further studies about the ocular surface microbiome and other sparsely colonized microbiomes in order to improve data reproducibility. Understanding challenges and biases in the characterization of the ocular surface microbiome may set the basis for microbiome-altering interventions for treatment of ocular surface associated diseases.
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Affiliation(s)
- Elio L. Herzog
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Marco Kreuzer
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Martin S. Zinkernagel
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Denise C. Zysset-Burri
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
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Zhou Y, Sidhu GS, Whitlock JA, Abdelmalik B, Mayer Z, Li Y, Wang GP, Steigleman WA. Effects of Carboxymethylcellulose Artificial Tears on Ocular Surface Microbiome Diversity and Composition, A Randomized Controlled Trial. Transl Vis Sci Technol 2023; 12:5. [PMID: 37555738 PMCID: PMC10424155 DOI: 10.1167/tvst.12.8.5] [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: 04/24/2023] [Accepted: 07/16/2023] [Indexed: 08/10/2023] Open
Abstract
Purpose Carboxymethylcellulose is an artificial tear ingredient known to decrease gut microbiome diversity when ingested. This study examines the effect of carboxymethylcellulose on ocular surface microbiome diversity and composition. Methods Healthy adult participants without significant ophthalmic disease or concurrent carboxymethylcellulose artificial tear use were allocated randomly to take carboxymethylcellulose or control polyethylene glycol artificial tears for seven days. Conjunctival swabs were collected before and after artificial tear treatment. This trial is registered at clinicaltrials.gov (NCT05292755). Primary outcomes included abundance of bacterial taxa and microbiome diversity as measured by the Chao-1 richness estimate, Shannon's phylogenetic diversity index, and UniFrac analysis. Secondary outcomes included Ocular Surface Disease Index scores and artificial tear compliance. Results Of the 80 enrolled participants, 66 completed the trial. Neither intervention affected Chao-1 richness (analysis of variance [ANOVA], P = 0.231) or Shannon's diversity index (ANOVA, P = 0.224). Microbiome samples did not separate by time point (permutation multivariate analysis of variance [PERMANOVA], P = 0.223) or intervention group (PERMANOVA, P = 0.668). LEfSe taxonomic analysis revealed that carboxymethylcellulose depleted several taxa including Bacteroides and Lachnoclostridium, but enriched Enterobacteriaceae, Citrobacter, and Gordonia. Both interventions decreased OSDI scores (Wilcoxon signed rank test, P < 0.05), but there was no significant difference between interventions (Mann-Whitney U, P = 0.54). Conclusions Carboxymethylcellulose artificial tears increased Actinobacteriota but decreased Bacteroides and Firmicutes bacteria. Carboxymethylcellulose artificial tears do not affect ocular surface microbiome diversity and are not significantly more effective than polyethylene glycol artificial tears for dry eye treatment. Translational Relevance The 16S microbiome analysis has revealed small changes in the ocular surface microbiome associated with artificial tear use.
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Affiliation(s)
- Yujia Zhou
- Department of Ophthalmology, University of Florida Shands Hospital, Gainesville, FL, USA
- University of Florida College of Medicine, Gainesville, FL, USA
| | - Gurjit S. Sidhu
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Joan A. Whitlock
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Bishoy Abdelmalik
- Department of Ophthalmology, University of Florida Shands Hospital, Gainesville, FL, USA
- University of Florida College of Medicine, Gainesville, FL, USA
| | - Zachary Mayer
- Department of Ophthalmology, University of Florida Shands Hospital, Gainesville, FL, USA
- University of Florida College of Medicine, Gainesville, FL, USA
| | - Youlei Li
- University of Florida College of Medicine, Gainesville, FL, USA
| | - Gary P. Wang
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Walter A. Steigleman
- Department of Ophthalmology, University of Florida Shands Hospital, Gainesville, FL, USA
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Hu J, Chen J, Hou Q, Xu X, Ren J, Ma L, Yan X. Core-predominant gut fungus Kazachstania slooffiae promotes intestinal epithelial glycolysis via lysine desuccinylation in pigs. MICROBIOME 2023; 11:31. [PMID: 36814349 PMCID: PMC9948344 DOI: 10.1186/s40168-023-01468-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Gut fungi are increasingly recognized as important contributors to host physiology, although most studies have focused on gut bacteria. Post-translational modifications (PTMs) of proteins play vital roles in cell metabolism. However, the contribution of gut fungi to host protein PTMs remains unclear. Mining gut fungi that mediate host protein PTMs and dissecting their mechanism are urgently needed. RESULTS We studied the gut fungal communities of 56 weaned piglets and 56 finishing pigs from seven pig breeds using internal transcribed spacer (ITS) gene amplicon sequencing and metagenomics. The results showed that Kazachstania slooffiae was the most abundant gut fungal species in the seven breeds of weaned piglets. K. slooffiae decreased intestinal epithelial lysine succinylation levels, and these proteins were especially enriched in the glycolysis pathway. We demonstrated that K. slooffiae promoted intestinal epithelial glycolysis by decreasing lysine succinylation by activating sirtuin 5 (SIRT5). Furthermore, K. slooffiae-derived 5'-methylthioadenosine metabolite promoted the SIRT5 activity. CONCLUSIONS These findings provide a landscape of gut fungal communities of pigs and suggest that K. slooffiae plays a crucial role in intestinal glycolysis metabolism through lysine desuccinylation. Our data also suggest a potential protective strategy for pigs with an insufficient intestinal energy supply. Video Abstract.
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Affiliation(s)
- Jun Hu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Jianwei Chen
- BGI Research-Qingdao, BGI, Qingdao, 266555, China
| | - Qiliang Hou
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Xiaojian Xu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Jing Ren
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Libao Ma
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Xianghua Yan
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China.
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Peter VG, Morandi SC, Herzog EL, Zinkernagel MS, Zysset-Burri DC. Investigating the Ocular Surface Microbiome: What Can It Tell Us? Clin Ophthalmol 2023; 17:259-271. [PMID: 36698849 PMCID: PMC9870096 DOI: 10.2147/opth.s359304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
While pathogens of the eye have been studied for a very long time, the existence of resident microbes on the surface of healthy eyes has gained interest only recently. It appears that commensal microbes are a normal feature of the healthy eye, whose role and properties are currently the subject of extensive research. This review provides an overview of studies that have used 16s rRNA gene sequencing and whole metagenome shotgun sequencing to characterize microbial communities associated with the healthy ocular surface from kingdom to genus level. Bacteria are the primary colonizers of the healthy ocular surface, with three predominant phyla: Proteobacteria, Actinobacteria, and Firmicutes, regardless of the host, environment, and method used. Refining the microbial classification to the genus level reveals a highly variable distribution from one individual and study to another. Factors accounting for this variability are intriguing - it is currently unknown to what extent this is attributable to the individuals and their environment and how much is artifactual. Clearly, it is technically challenging to accurately describe the microorganisms of the ocular surface because their abundance is relatively low, thus, permitting substantial contaminations. More research is needed, including better experimental standards to prevent biases, and the exploration of the ocular surface microbiome's role in a spectrum of healthy to pathological states. Outcomes from such research include the opportunity for therapeutic interventions targeting the microbiome.
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Affiliation(s)
- Virginie G Peter
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Correspondence: Virginie G Peter, Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Freiburgstrasse 15, Bern, 3010, Switzerland, Email
| | - Sophia C Morandi
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Elio L Herzog
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Department for BioMedical Research, University of Bern, Bern, Switzerland,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Martin S Zinkernagel
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Denise C Zysset-Burri
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Department for BioMedical Research, University of Bern, Bern, Switzerland
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10
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Jiang S, Chen Y, Han S, Lv L, Li L. Next-Generation Sequencing Applications for the Study of Fungal Pathogens. Microorganisms 2022; 10:microorganisms10101882. [PMID: 36296159 PMCID: PMC9609632 DOI: 10.3390/microorganisms10101882] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) has become a widely used technology in biological research. NGS applications for clinical pathogen detection have become vital technologies. It is increasingly common to perform fast, accurate, and specific detection of clinical specimens using NGS. Pathogenic fungi with high virulence and drug resistance cause life-threatening clinical infections. NGS has had a significant biotechnological impact on detecting bacteria and viruses but is not equally applicable to fungi. There is a particularly urgent clinical need to use NGS to help identify fungi causing infections and prevent negative impacts. This review summarizes current research on NGS applications for fungi and offers a visual method of fungal detection. With the development of NGS and solutions for overcoming sequencing limitations, we suggest clinicians test specimens as soon as possible when encountering infections of unknown cause, suspected infections in vital organs, or rapidly progressive disease.
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Affiliation(s)
- Shiman Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Yanfei Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Shengyi Han
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
- Correspondence: ; Tel.: +86-0571-8723-6458
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11
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Application Progress of High-Throughput Sequencing in Ocular Diseases. J Clin Med 2022; 11:jcm11123485. [PMID: 35743555 PMCID: PMC9225376 DOI: 10.3390/jcm11123485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/11/2022] [Accepted: 06/16/2022] [Indexed: 02/01/2023] Open
Abstract
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.
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12
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Jayasudha R, Chakravarthy SK, Prashanthi GS, Sharma S, Garg P, Murthy SI, Shivaji S. Mycobiomes of the Ocular Surface in Bacterial Keratitis Patients. FRONTIERS IN OPHTHALMOLOGY 2022; 2:894739. [PMID: 38983567 PMCID: PMC11182091 DOI: 10.3389/fopht.2022.894739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/06/2022] [Indexed: 07/11/2024]
Abstract
Inflammation of the cornea is known as keratitis, and bacteria, fungi, protozoans, and viruses are the etiological agents of this disease. Delayed treatment of keratitis could result in loss of vision and, under certain severity conditions, the removal of an eye and its associated structures. In the current study, the ocular surface (conjunctiva and cornea) mycobiomes of individuals with bacterial keratitis were compared with the ocular mycobiome (conjunctiva) of healthy individuals, free of any ocular morbidity. Mycobiomes were generated through NGS approach using conjunctival swabs and corneal scrapings as the source of DNA from which ITS2 was amplified and sequenced, as a proxy to identify fungi. The results indicated significant changes in the alpha-diversity indices and in the abundance at the phylum and genera level. Hierarchical clustering using a heatmap showed that the mycobiomes were different. Furthermore, NMDS plots also differentiated the mycobiomes in the three cohorts, implying dysbiosis in the mycobiomes of the conjunctivae and corneal scrapings of bacterial keratitis individuals compared to control individuals. A preponderance of negative interactions in the hub genera in the conjunctival swabs of bacterial keratitis individuals compared to healthy controls further re-emphasized the differences in the mycobiomes. The dysbiotic changes at the genera level in conjunctivae and corneal scrapings of bacterial keratitis individuals are discussed with respect to their possible role in causing or exacerbating ocular surface inflammation. These results demonstrate dysbiosis in the ocular mycobiome in bacterial keratitis patients compared to healthy controls for the first time.
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Affiliation(s)
| | | | | | - Savitri Sharma
- Prof. Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | - Prashant Garg
- The Cornea Institute, L V Prasad Eye Institute, Hyderabad, India
| | | | - Sisinthy Shivaji
- Prof. Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
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13
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Ozkan J, Willcox M, Coroneo M. A comparative analysis of the cephalic microbiome: The ocular, aural, nasal/nasopharyngeal, oral and facial dermal niches. Exp Eye Res 2022; 220:109130. [DOI: 10.1016/j.exer.2022.109130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/08/2022] [Accepted: 05/22/2022] [Indexed: 12/12/2022]
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14
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Agarwal A. Commentary: Fungal endophthalmitis - Newer insights into the diagnosis and management. Indian J Ophthalmol 2022; 70:777-778. [PMID: 35225511 PMCID: PMC9114599 DOI: 10.4103/ijo.ijo_2878_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Aniruddha Agarwal
- Eye Institute, Cleveland Clinic Abu Dhabi, Al Maryah Island, Abu Dhabi, UAE
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15
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Shivaji S, Jayasudha R, Prashanthi GS, Arunasri K, Das T. Fungi of the human eye: Culture to mycobiome. Exp Eye Res 2022; 217:108968. [PMID: 35120870 DOI: 10.1016/j.exer.2022.108968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 11/02/2021] [Accepted: 01/26/2022] [Indexed: 11/04/2022]
Abstract
The focus of the current review is multi-fold and compares the diversity and abundance of fungi on the ocular surface by the conventional culture-based method with the more sensitive, high throughput, culture-independent NGS method. The aim is to highlight the existence of a core ocular mycobiome and explore the transition of the ocular fungal microbiota from the normal eye to the diseased eye. PubMed, Google Scholar and Medline were used to search for publications and reviews related to cultivable fungi and the mycobiome of the normal and diseased eye. The conventional cultivable approach and the NGS approach confirm that the eye has its own mycobiome and several confounding factors (age, gender, ethnicity etc.) influence the mycobiome. Further, dysbiosis in the mycobiome appears to be associated with ocular diseases and thus impacts the health of the human eye. Considering that the mycobiome of the eye is influenced by several confounding factors and also varies with respect to the disease status of the eye there is a need to extensively explore the mycobiome under different physiological conditions, different ethnicities, geographical regions etc. Such studies would unravel the diversity and abundance of the mycobiomes and contribute to our understanding of ocular health. Research focused on ocular mycobiomes may eventually help to build a targeted and individualized treatment.
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Affiliation(s)
- Sisinthy Shivaji
- Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, Telangana, 500034, India.
| | - Rajagopalaboopathi Jayasudha
- Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, Telangana, 500034, India.
| | - Gumpili Sai Prashanthi
- Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, Telangana, 500034, India.
| | - Kotakonda Arunasri
- Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, Telangana, 500034, India.
| | - Taraprasad Das
- Srimati Kanuri Santhamma Centre for Vitreo Retinal Diseases, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, Telangana, 500034, India.
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16
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Sharma S, Meyer V. The colors of life: an interdisciplinary artist-in-residence project to research fungal pigments as a gateway to empathy and understanding of microbial life. Fungal Biol Biotechnol 2022; 9:1. [PMID: 35012670 PMCID: PMC8744264 DOI: 10.1186/s40694-021-00130-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/12/2021] [Indexed: 12/13/2022] Open
Abstract
Background Biological pigmentation is one of the most intriguing traits of many fungi. It holds significance to scientists, as a sign of biochemical metabolism and organism-environment interaction, and to artists, as the source of natural colors that capture the beauty of the microbial world. Furthermore, the functional roles and aesthetic appeal of biological pigmentation may be a path to inspiring human empathy for microorganisms, which is key to understanding and preserving microbial biodiversity. A project focused on cross-species empathy was initiated and conducted as part of an artist-in-residence program in 2021. The aim of this residency is to bridge the current divide between science and art through interdisciplinary practice focused on fungi. Results The residency resulted in multiple products that are designed for artistic and scientific audiences with the central theme of biological pigmentation in fungi and other microorganisms. The first product is a video artwork that focuses on Aspergillus niger as a model organism that produces melanin pigment in a biosynthetic process similar to that of humans. The growth and morphology of this commonplace organism are displayed through video, photo, animation, and time-lapse footage, inviting the viewer to examine the likenesses and overlaps between humans and fungi. The second product is The Living Color Database, an online compendium of biological colors for scientists, artists, and designers. It links organisms across the tree of life, focusing on fungi, bacteria, and archaea, and the colors they express through biological pigmentation. Each pigment is represented in terms of its chemistry, its related biosynthesis, and its color expressions according to different indices: HEX, RGB, and Pantone. It is available at color.bio. Conclusions As fungal biotechnology continues to mature into new application areas, it is as important as ever that there is human empathy for these organisms to promote the preservation and appreciation of fungal biodiversity. The products presented here provide paths for artists, scientists, and designers to understand microorganisms through the lens of color, promoting interspecies empathy through research, teaching, and practice.
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Affiliation(s)
- Sunanda Sharma
- Chair of Applied and Molecular Microbiology, Technische Universität Berlin, Str. des 17. Juni 135, 10623, Berlin, Germany.
| | - Vera Meyer
- Chair of Applied and Molecular Microbiology, Technische Universität Berlin, Str. des 17. Juni 135, 10623, Berlin, Germany.
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17
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Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa. J Fungi (Basel) 2021; 7:jof7090703. [PMID: 34575741 PMCID: PMC8467358 DOI: 10.3390/jof7090703] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 01/08/2023] Open
Abstract
Culture techniques are vital in both traditional and modern fungal taxonomy. Establishing sexual-asexual links and synanamorphs, extracting DNA and secondary metabolites are mainly based on cultures. However, it is widely accepted that a large number of species are not sporulating in nature while others cannot be cultured. Recent ecological studies based on culture-independent methods revealed these unculturable taxa, i.e., dark taxa. Recent fungal diversity estimation studies suggested that environmental sequencing plays a vital role in discovering missing species. However, Sanger sequencing is still the main approach in determining DNA sequences in culturable species. In this paper, we summarize culture-based and culture-independent methods in the study of ascomycetous taxa. High-throughput sequencing of leaf endophytes, leaf litter fungi and fungi in aquatic environments is important to determine dark taxa. Nevertheless, currently, naming dark taxa is not recognized by the ICN, thus provisional naming of them is essential as suggested by several studies.
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18
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Abstract
Dry eye disease (DED), a multifactorial condition of the tear film and ocular surface, is one of the leading reasons for patients seeking eye care. Despite the multiple toxic ingredients of eye make-up products and their long-term application close to the ocular surface, few studies have analyzed their role in initiating and worsening DED. Females and the elderly experience the highest prevalence of DED and may be particularly vulnerable to the effects of eye make-up. The multifactorial nature of DED and common mechanisms behind several ocular surface diseases make it difficult to link a particular ingredient-driven mechanism to DED. Therefore, here, we list potential responses to eye cosmetics that may be involved in DED development. The first part of this review introduces the anatomy of the eye and DED, the second section explains the classification of eye cosmetic products, and the final part discusses the undesired effects under physical, pathogenic, and chemical insults.
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Affiliation(s)
- Mazyar Yazdani
- Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, 0027 Oslo, Norway.,Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway.,The Norwegian Dry Eye Clinic, 0366 Oslo, Norway
| | | | - Tor Paaske Utheim
- Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway.,The Norwegian Dry Eye Clinic, 0366 Oslo, Norway.,Department of Plastic and Reconstructive Surgery, Oslo University Hospital, 0450 Oslo, Norway.,Department of Oral Surgery and Oral Medicine, Dentistry, University of Oslo, 0317 Oslo, Norway.,Department of Ophthalmology, Stavanger University Hospital, 4011 Stavanger, Norway.,Department of Ophthalmology, Sørlandet Hospital Arendal, 4604 Arendal, Norway
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19
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Shivaji S. A systematic review of gut microbiome and ocular inflammatory diseases: Are they associated? Indian J Ophthalmol 2021; 69:535-542. [PMID: 33595467 PMCID: PMC7942081 DOI: 10.4103/ijo.ijo_1362_20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The primary focus of this review was to establish the possible association of dysbiotic changes in the gut bacterial microbiomes with both intestinal and extra-intestinal diseases with emphasis on ocular diseases such as bacterial keratitis, fungal keratitis, uveitis, age-related macular degeneration, and ocular mucosal diseases. For this particular purpose, a systematic search was conducted using PubMed and Google Scholar for publications related to gut microbiome and human health (using the keywords: gut microbiome, ocular disease, dysbiosis, keratitis, uveitis, and AMD). The predictions are that microbiome studies would help to unravel dysbiotic changes in the gut bacterial microbiome at the taxonomic and functional level and thus form the basis to mitigate inflammatory diseases of the eye by using nutritional supplements or fecal microbiota transplantation.
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Affiliation(s)
- Sisinthy Shivaji
- Scientist Emeritus and Distinguished Scientist, Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, Telangana, India
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20
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Konduri R, Saiabhilash CR, Shivaji S. Biofilm-Forming Potential of Ocular Fluid Staphylococcus aureus and Staphylococcus epidermidis on Ex Vivo Human Corneas from Attachment to Dispersal Phase. Microorganisms 2021; 9:microorganisms9061124. [PMID: 34067392 PMCID: PMC8224674 DOI: 10.3390/microorganisms9061124] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/14/2022] Open
Abstract
The biofilm-forming potential of Staphylococcus aureus and Staphylococcus epidermidis, isolated from patients with Endophthalmitis, was monitored using glass cover slips and cadaveric corneas as substrata. Both the ocular fluid isolates exhibited biofilm-forming potential by the Congo red agar, Crystal violet and 2,3-bis (2-methoxy-4-nitro-5-sulfophenyl)-5-(phenylamino) carbonyl-2H-tetra-zolium hydroxide (XTT) methods. Confocal microscopy demonstrated that the thickness of the biofilm increased from 4–120 h of biofilm formation. Scanning electron microscopic studies indicated that the biofilms grown on cover slips and ex vivo corneas of both the isolates go through an adhesion phase at 4 h followed by multilayer clumping of cells with intercellular connections and copious amounts of extracellular polymeric substance. Clumps subsequently formed columns and eventually single cells were visible indicative of dispersal phase. Biofilm formation was more rapid when the cornea was used as a substratum. In the biofilms grown on corneas, clumping of cells, formation of 3D structures and final appearance of single cells indicative of dispersal phase occurred by 48 h compared to 96–120 h when biofilms were grown on cover slips. In the biofilm phase, both were several-fold more resistant to antibiotics compared to planktonic cells. This is the first study on biofilm forming potential of ocular fluid S. aureus and S. epidermidis on cadaveric cornea, from attachment to dispersal phase of biofilm formation.
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21
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Ren Z, Liu Q, Li W, Wu X, Dong Y, Huang Y. Profiling of Diagnostic Information of and Latent Susceptibility to Bacterial Keratitis From the Perspective of Ocular Bacterial Microbiota. Front Cell Infect Microbiol 2021; 11:645907. [PMID: 34055665 PMCID: PMC8155582 DOI: 10.3389/fcimb.2021.645907] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/23/2021] [Indexed: 11/21/2022] Open
Abstract
The ocular surface possesses its own bacterial microbiota. Once given a chance, opportunistic pathogens within ocular microbiota may lead to corneal infection like bacterial keratitis (BK). To reveal the possible factor that makes people vulnerable to BK from the perspective of ocular bacterial microbiota, as well as to compare diagnostic information provided by high-throughput 16S rDNA sequencing and bacterial culture, 20 patients with BK and 42 healthy volunteers were included. Conjunctival swabs and corneal scrapings collected from the diseased eyes of BK patients were subjected for both high-throughput 16S rDNA sequencing and bacterial culture. Conjunctival swabs collected from the normal eyes of BK patients and healthy volunteers were sent only for sequencing. For identifying the pathogens causing BK, high-throughput 16S rDNA sequencing presented a higher positive rate than bacterial culture (98.04% vs. 17.50%), with 92.11% reaching the genus level (including 10.53% down to the species level). However, none of the sequencing results was consistent with the cultural results. The sequencing technique appears to challenge culture, and could be a complement for pathogen identification. Moreover, compared to the eyes of healthy subjects, the ocular microbiota of three sample groups from BK patients contained significantly less Actinobacteria and Corynebacteria (determinate beneficial symbiotic bacteria), but significantly more Gammaproteobacteria, Pseudomonas, Bacteroides, and Escherichia-Shigella (common ocular pathogenic bacteria). Therefore, it is speculated that the imbalance of protective and aggressive bacteria in the ocular microbiota of healthy people may trigger susceptibility to BK. Based on this speculation, it seems promising to prevent and treat infectious oculopathy through regulating ocular microbiota.
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Affiliation(s)
- Zhichao Ren
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China.,State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China.,Qingdao University Medical College, 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, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China
| | - Wenfeng Li
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xian Wu
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China.,State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 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, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 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, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China
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22
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Ozkan J, Majzoub ME, Coroneo M, Thomas T, Willcox M. Comparative analysis of ocular surface tissue microbiome in human, mouse, rabbit, and guinea pig. Exp Eye Res 2021; 207:108609. [PMID: 33932398 DOI: 10.1016/j.exer.2021.108609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/06/2021] [Accepted: 04/21/2021] [Indexed: 01/21/2023]
Abstract
Animal models are a critical element of ocular surface research for investigating therapeutic drops, surgical implants, and infection research. This study was a comparative analysis of the microbial communities on conjunctival tissue samples from humans compared to several commonly used laboratory animals (BALB/c mice, New Zealand white rabbits and IMVS colored stock guinea pigs). Microbial communities were analyzed by extracting total DNA from conjunctival tissue and sequencing the 16 S rRNA gene using the Illumina MiSeq platform. Sequences were quality filtered using the UNOISE pipeline in USEARCH and taxonomically classified using GTDB database. Sequences associated with blank extraction and sampling negative controls were removed with the decontam R software package prior to downstream analysis. There was a difference in the diversity measures of richness (P = 0.0124) and Shannon index (P = 0.0002) between humans and rabbits but not between human, mouse and guinea pigs. There was a difference between the human and any animal for bacterial community structure (P = 0.006). There was a higher degree of similarity between the bacterial composition of the human and mouse samples with each dominated by the phyla Proteobacteria and Firmicutes. The use of mouse models may be more appropriate for studies investigating changes to the ocular microbiome due to interventions such as application of antibiotics due to greater similarities in bacterial community structure and composition to humans.
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Affiliation(s)
- Jerome Ozkan
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia; Centre for Marine Science and Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia.
| | - Marwan E Majzoub
- Centre for Marine Science and Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Minas Coroneo
- Department of Ophthalmology, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Mark Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
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23
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Hur MS, Lee JS, Jang M, Shin HJ, Lee YW. Analysis of the Conjunctival Microbiome in Patients with Atopic Keratoconjunctivitis and Healthy Individuals. Ann Dermatol 2021; 33:163-169. [PMID: 33935458 PMCID: PMC8082000 DOI: 10.5021/ad.2021.33.2.163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/06/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
Background Atopic dermatitis (AD) has been clarified that imbalance of bacterial and fungal communities in the skin and gut play key roles in immunologic dysfunction. Atopic keratoconjunctivitis (AKC), one of severe ophthalmic manifestation of AD, could be related with dysbiosis as same as AD. Objective In this case-control study, the roles of conjunctival microbial communities in AKC were evaluated by a comparative analysis with healthy controls (HCs). Methods 16S rRNA sequencing was used to construct libraries of compositional information for a total of 30 volunteers including 20 patients with AKC and 10 HCs. Results In the results, variation in the conjunctival taxonomic composition was higher in patients with AKC than in the HC group. In an analysis of relative abundance at the genus level, some taxa significantly differed between groups, including Ralstonia, Staphylococcus, Pseudomonas, Proteus, Haemophilus, and Bifidobacterium (p<0.05). Beta diversity was significantly higher in patients with AKC than in HCs (PERMANOVA, p=0.004). Conclusion The results indicated that the diversity and composition of the microbiome differs between patients with AKC and HCs.
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Affiliation(s)
- Min Seok Hur
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea
| | - Ji Su Lee
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea
| | - Minsu Jang
- Department of Ophthalmology, Konkuk University School of Medicine, Seoul, Korea
| | - Hyun Jin Shin
- Department of Ophthalmology, Konkuk University School of Medicine, Seoul, Korea
| | - Yang Won Lee
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea.,Research Institute of Medical Science, Konkuk University, Seoul, Korea
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24
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Vishwakarma P, Mitra S, Beuria T, Barik MR, Sahu SK. Comparative profile of ocular surface microbiome in vernal keratoconjunctivitis patients and healthy subjects. Graefes Arch Clin Exp Ophthalmol 2021; 259:1925-1933. [PMID: 33651203 DOI: 10.1007/s00417-021-05109-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/26/2021] [Accepted: 01/30/2021] [Indexed: 01/07/2023] Open
Abstract
PURPOSE To compare ocular surface microbiome and its antibiotic sensitivity in vernal keratoconjunctivitis (VKC) with normal ocular surface. METHODS In this case-control study, thirty patients each with clinical diagnosis of VKC and age-matched controls with normal ocular surface were enrolled. Tear film samples were collected from each group and subjected to microbial evaluation with microscopy, conventional culture methods, and polymerase chain reaction (PCR). Microbial diversity and antibiotic sensitivity patterns were analyzed. RESULTS Most patients (67%) belonged to severe grades (3 and 4) of VKC, and allergic history could be elicited in 20%. On culture, bacteria were isolated in 50% of VKC patients and 47% of control group. Staphylococcus species were identified in 70% VKC group and 57% control group. S. aureus growth was seen in 52% and 21% of VKC patients and controls, respectively. S. pneumoniae was isolated only in controls (29%) (p<0.05). Confluent colonies (≥10 colonies/μl) were seen in 70% of VKC patients and 14% of controls (p<0.05). Fluoroquinolone resistance was more among higher grades of VKC (50%) (p<0.01) and was observed in 46% of VKC patients and 23% of control group (p<0.01). Both groups were negative for HSV-1 DNA and fungal growth. CONCLUSION Staphylococcus, the most common ocular surface flora, was predominant in VKC patients. Microbial analysis revealed similar microbial diversity in both groups. However, bacterial load was higher in VKC. Increased fluoroquinolone resistance was observed in VKC patients with more resistance among higher grades. Fungi and HSV-1 were not seen in VKC or normal ocular surface.
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Affiliation(s)
- Pratima Vishwakarma
- Cornea & Anterior Segment Service, LV Prasad Eye Institute, Bhubaneswar, Odisha, India
| | - Sanchita Mitra
- Ocular Microbiology Service, LV Prasad Eye Institute, Bhubaneswar, Odisha, India
| | - Tushar Beuria
- Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Manas Ranjan Barik
- Ocular Microbiology Service, LV Prasad Eye Institute, Bhubaneswar, Odisha, India
| | - Srikant K Sahu
- Cornea & Anterior Segment Service, LV Prasad Eye Institute, Bhubaneswar, Odisha, India.
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25
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Szczotka-Flynn LB, Shovlin JP, Schnider CM, Caffery BE, Alfonso EC, Carnt NA, Chalmers RL, Collier S, Jacobs DS, Joslin CE, Kroken AR, Lakkis C, Pearlman E, Schein OD, Stapleton F, Tu E, Willcox MDP. American Academy of Optometry Microbial Keratitis Think Tank. Optom Vis Sci 2021; 98:182-198. [PMID: 33771951 PMCID: PMC8075116 DOI: 10.1097/opx.0000000000001664] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
SIGNIFICANCE Think Tank 2019 affirmed that the rate of infection associated with contact lenses has not changed in several decades. Also, there is a trend toward more serious infections associated with Acanthamoeba and fungi. The growing use of contact lenses in children demands our attention with surveillance and case-control studies. PURPOSE The American Academy of Optometry (AAO) gathered researchers and key opinion leaders from around the world to discuss contact lens-associated microbial keratitis at the 2019 AAO Annual Meeting. METHODS Experts presented within four sessions. Session 1 covered the epidemiology of microbial keratitis, pathogenesis of Pseudomonas aeruginosa, and the role of lens care systems and storage cases in corneal disease. Session 2 covered nonbacterial forms of keratitis in contact lens wearers. Session 3 covered future needs, challenges, and research questions in relation to microbial keratitis in youth and myopia control, microbiome, antimicrobial surfaces, and genetic susceptibility. Session 4 covered compliance and communication imperatives. RESULTS The absolute rate of microbial keratitis has remained very consistent for three decades despite new technologies, and extended wear significantly increases the risk. Improved oxygen delivery afforded by silicone hydrogel lenses has not impacted the rates, and although the introduction of daily disposable lenses has minimized the risk of severe disease, there is no consistent evidence that they have altered the overall rate of microbial keratitis. Overnight orthokeratology lenses may increase the risk of microbial keratitis, especially secondary to Acanthamoeba, in children. Compliance remains a concern and a significant risk factor for disease. New insights into host microbiome and genetic susceptibility may uncover new theories. More studies such as case-control designs suited for rare diseases and registries are needed. CONCLUSIONS The first annual AAO Think Tank acknowledged that the risk of microbial keratitis has not decreased over decades, despite innovation. Important questions and research directions remain.
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Affiliation(s)
| | | | | | | | - Eduardo C Alfonso
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Nicole A Carnt
- School of Optometry and Vision Science, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Sarah Collier
- U.S. Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Deborah S Jacobs
- Massachusetts Eye and Ear, Cornea Service, Harvard Medical School, Boston, Massachusetts
| | - Charlotte E Joslin
- Department of Ophthalmology and Visual Science, College of Medicine, Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, Illinois
| | - Abby R Kroken
- School of Optometry, University of California, Berkeley, Berkeley, California
| | | | - Eric Pearlman
- Departments of Ophthalmology, and Physiology and Biophysics, University of California, Irvine, Irvine, California
| | - Oliver D Schein
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Fiona Stapleton
- School of Optometry and Vision Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Elmer Tu
- University of Illinois Eye and Ear Infirmary, Chicago, Illinois
| | - Mark D P Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, New South Wales, Australia
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26
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Kang Y, Lin S, Ma X, Che Y, Chen Y, Wan T, Zhang D, Shao J, Xu J, Xu Y, Lou Y, Zheng M. Strain heterogeneity, cooccurrence network, taxonomic composition and functional profile of the healthy ocular surface microbiome. EYE AND VISION 2021; 8:6. [PMID: 33622400 PMCID: PMC7903678 DOI: 10.1186/s40662-021-00228-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/14/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND There is growing evidence indicating that the microbial communities that dwell on the human ocular surface are crucially important for ocular surface health and disease. Little is known about interspecies interactions, functional profiles, and strain heterogeneity across individuals in healthy ocular surface microbiomes. METHODS To comprehensively characterize the strain heterogeneity, cooccurrence network, taxonomic composition and functional profile of the healthy ocular surface microbiome, we performed shotgun metagenomics sequencing on ocular surface mucosal membrane swabs of 17 healthy volunteers. RESULTS The healthy ocular surface microbiome was classified into 12 phyla, 70 genera, and 140 species. The number of species in each healthy ocular surface microbiome ranged from 6 to 47, indicating differences in microbial diversity among individuals. The species with high relative abundances and high positivity rates were Streptococcus pyogenes, Staphylococcus epidermidis, Propionibacterium acnes, Corynebacterium accolens, and Enhydrobacter aerosaccus. A correlation network analysis revealed a competitive interaction of Staphylococcus epidermidis with Streptococcus pyogenes in ocular surface microbial ecosystems. Staphylococcus epidermidis and Streptococcus pyogenes revealed phylogenetic diversity among different individuals. At the functional level, the pathways related to transcription were the most abundant. We also found that there were abundant lipid and amino acid metabolism pathways in the healthy ocular surface microbiome. CONCLUSION This study explored the strain heterogeneity, cooccurrence network, taxonomic composition, and functional profile of the healthy ocular surface microbiome. These findings have important significance for the future development of probiotic-based eye therapeutic drugs.
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Affiliation(s)
- Yutong Kang
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.,National Clinical Research Center for Ocular Diseases, Wenzhou, Zhejiang, China.,Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Shudan Lin
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xueli Ma
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.,National Clinical Research Center for Ocular Diseases, Wenzhou, Zhejiang, China
| | - Yanlin Che
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yiju Chen
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Tian Wan
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.,National Clinical Research Center for Ocular Diseases, Wenzhou, Zhejiang, China
| | - Die Zhang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jiao Shao
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.,National Clinical Research Center for Ocular Diseases, Wenzhou, Zhejiang, China
| | - Jie Xu
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.,National Clinical Research Center for Ocular Diseases, Wenzhou, Zhejiang, China
| | - Yi Xu
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.,National Clinical Research Center for Ocular Diseases, Wenzhou, Zhejiang, China
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
| | - Meiqin Zheng
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China. .,National Clinical Research Center for Ocular Diseases, Wenzhou, Zhejiang, China. .,Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
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27
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Ranjith K, Sharma S, Shivaji S. Microbes of the human eye: Microbiome, antimicrobial resistance and biofilm formation. Exp Eye Res 2021; 205:108476. [PMID: 33549582 DOI: 10.1016/j.exer.2021.108476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 01/21/2023]
Abstract
BACKGROUND The review focuses on the bacteria associated with the human eye using the dual approach of detecting cultivable bacteria and the total microbiome using next generation sequencing. The purpose of this review was to highlight the connection between antimicrobial resistance and biofilm formation in ocular bacteria. METHODS Pubmed was used as the source to catalogue culturable bacteria and ocular microbiomes associated with the normal eyes and those with ocular diseases, to ascertain the emergence of anti-microbial resistance with special reference to biofilm formation. RESULTS This review highlights the genetic strategies used by microorganisms to evade the lethal effects of anti-microbial agents by tracing the connections between candidate genes and biofilm formation. CONCLUSION The eye has its own microbiome which needs to be extensively studied under different physiological conditions; data on eye microbiomes of people from different ethnicities, geographical regions etc. are also needed to understand how these microbiomes affect ocular health.
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Affiliation(s)
- Konduri Ranjith
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, Telangana, India.
| | - Savitri Sharma
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, Telangana, India.
| | - Sisinthy Shivaji
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, Telangana, India.
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28
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Walsh ML, Meason-Smith C, Arnold C, Suchodolski JS, Scott EM. Evaluation of the ocular surface mycobiota in clinically normal horses. PLoS One 2021; 16:e0246537. [PMID: 33539431 PMCID: PMC7861450 DOI: 10.1371/journal.pone.0246537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/20/2021] [Indexed: 11/19/2022] Open
Abstract
The eye is host to myriad bacterial, fungal, and viral organisms that likely influence ocular surface physiology in normal and diseased states. The ocular surface mycobiota of horses has not yet been described using NGS techniques. This study aimed to characterize the ocular surface fungal microbiota (mycobiota) in healthy horses in 2 environmental conditions (stalled versus pasture). Conjunctival swabs of both eyes were obtained from 7 adult stallions stabled in an open-air pavilion and 5 adult mares living on pasture. Genomic DNA was extracted from ocular surface swabs and sequenced using primers that target the Internal Transcribed Spacer 1 (ITS1) region of the fungal genome on an Illumina platform. Sequences were processed using Quantitative Insights Into Molecular Ecology (QIIME 2.0) and taxonomy assigned with the Findley et al. 2013 ITS1 database. The most abundant genera identified were Leptosphaerulina (22.7%), unclassified Pleosporaceae (17.3%), Cladosporium (16.2%), Alternaria (9.8%), unclassified Pleosporales (4.4%), unclassified Montagnulaceae (2.9%), Fusarium (2.5%), and Pestalotiopsis (1.4%). Fungal community composition (Jaccard, R = 0.460, p = 0.001) and structure (Bray-Curtis, R = 0.811, p = 0.001) were significantly different between pastured mares and stabled stallions. The ocular surface of pastured mares had significantly increased fungal species richness and diversity compared to stabled stallions (Shannon p = 0.0224, Chao1 p = 0.0118, Observed OTUs p = 0.0241). Relative abundances of Aspergillus (p = 0.005) and Alternaria spp. (p = 0.002) were significantly increased in the mycobiota of pastured mares. This is the first report to describe the mycobiota of the equine ocular surface. Environmental factors such as housing influence the composition, structure, and richness of the equine ocular surface mycobiota.
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Affiliation(s)
- Mary L. Walsh
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Courtney Meason-Smith
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Carolyn Arnold
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Jan S. Suchodolski
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Erin M. Scott
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
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29
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Delbeke H, Younas S, Casteels I, Joossens M. Current knowledge on the human eye microbiome: a systematic review of available amplicon and metagenomic sequencing data. Acta Ophthalmol 2021; 99:16-25. [PMID: 32602257 DOI: 10.1111/aos.14508] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/06/2020] [Accepted: 05/21/2020] [Indexed: 12/23/2022]
Abstract
Insights in the ocular surface microbiome are still at an early stage and many more questions remain unanswered compared with other human-associated microbial communities. The current knowledge on the human microbiome changed our viewpoint on bacteria and human health and significantly enhanced our understanding of human pathophysiology. Also in ocular medicine, microbiome research might impact treatment. Here, we summarize the current knowledge on ocular microbiome research with a particular focus on potential confounding factors and their effects on microbiome composition. Moreover, we present the ocular surface core microbiome based on current available data and defined it as genera present in almost half of the published control cohorts with a relative abundance of at least 1%.
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Affiliation(s)
- Heleen Delbeke
- Department of Ophthalmology University Hospitals Leuven Leuven Belgium
| | - Saif Younas
- Department of Internal Medicine University Hospitals Leuven Leuven Belgium
| | - Ingele Casteels
- Department of Ophthalmology University Hospitals Leuven Leuven Belgium
| | - Marie Joossens
- Department of Molecular Bacteriology REGA institute Catholic University Leuven Leuven Belgium
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30
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Alterations in the conjunctival surface bacterial microbiome in bacterial keratitis patients. Exp Eye Res 2020; 203:108418. [PMID: 33359511 DOI: 10.1016/j.exer.2020.108418] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/17/2020] [Accepted: 12/18/2020] [Indexed: 01/09/2023]
Abstract
Microbial keratitis is an infectious disease of the eye, in which the cornea is inflamed. Under severe conditions, keratitis can lead to significant loss of vision and enucleation of the eye. Ocular trauma is the major risk factor causing keratitis and microorganisms viz., bacteria, fungi, viruses are the causative agents. The current study characterized the conjunctival bacterial microbiomes of healthy individuals and individuals with bacterial keratitis (BK) and assessed whether ocular microbiome dysbiosis is prevalent in BK patients. Ocular bacterial microbiomes were generated from the conjunctival swabs of healthy controls (HC-SW) and conjunctival swabs (BK-SW) and corneal scrapings (BK-CR) of BK patients using V3-V4 amplicon sequencing and data analysed using QIIME and R software. The Alpha diversity indices, diversity and abundance of different phyla and genera, heat map analysis, NMDS plots and inferred functional pathway analysis clearly discriminated the bacterial microbiomes of conjunctival swabs of healthy controls from that of BK patients. Preponderance of negative interactions in the hub genera were observed in BK-CR and BK-SW compared to HC-SW. In addition, a consistent increase in the abundance of pathogenic bacteria, as inferred from published literature, was observed in the conjunctiva of BK patients compared to HC and this may be related to causing or exacerbating ocular surface inflammation. This is the first study demonstrating dysbiosis in the ocular bacterial microbiome of conjunctiva of bacterial keratitis patients compared to the eye of healthy controls. The bacterial microbiome associated with the corneal scrapings of keratitis individuals is also described for the first time.
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31
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Das D, Modaboyina S, Bhandari A, Agrawal S. Lower eyelid aspergillosis infection mimicking a pyogenic granuloma in a pregnant lady. BMJ Case Rep 2020; 13:13/12/e238732. [PMID: 33318280 PMCID: PMC7737053 DOI: 10.1136/bcr-2020-238732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Deepsekhar Das
- Dr Rajendra Prasad Centre for Ophthalmic Sciences, AIIMS, New Delhi, Delhi, India
| | - Sujeeth Modaboyina
- Dr Rajendra Prasad Centre for Ophthalmic Sciences, AIIMS, New Delhi, Delhi, India
| | - Agam Bhandari
- Dr Rajendra Prasad Centre for Ophthalmic Sciences, AIIMS, New Delhi, Delhi, India
| | - Sahil Agrawal
- Dr Rajendra Prasad Centre for Ophthalmic Sciences, AIIMS, New Delhi, Delhi, India
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32
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Mills B, Radhakrishnan N, Karthikeyan Rajapandian SG, Rameshkumar G, Lalitha P, Prajna NV. The role of fungi in fungal keratitis. Exp Eye Res 2020; 202:108372. [PMID: 33249061 DOI: 10.1016/j.exer.2020.108372] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/07/2020] [Accepted: 11/22/2020] [Indexed: 12/20/2022]
Abstract
Fungal keratitis (FK) accounts for approximately half of the microbial keratitis encountered in low middle income countries (LMICs) and predominantly affect the working rural-poor. FK causes significant morbidity with the majority of patients left with moderate or worse visual impairment and approximately 25% requiring expensive and often unsuccessful surgical interventions. The severity of FK and the resultant corneal damage or resolution can be attributed to i) the virulence and bioburden of the fungal pathogen, ii) the host defense mechanism and immune response and iii) sub-optimal diagnostics and anti-fungal treatment strategies. This review provides a comprehensive overview of the multifaceted components that drive FK progression and resolution, highlighting where knowledge gaps exist and areas that warrant further research.
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Affiliation(s)
- Bethany Mills
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, UK
| | - Naveen Radhakrishnan
- Department of Cornea and Refractive Surgery, Aravind Eye Hospital, Madurai, India
| | | | | | - Prajna Lalitha
- Department of Ocular Microbiology, Aravind Eye Hospital, Madurai, India
| | - N Venkatesh Prajna
- Department of Cornea and Refractive Surgery, Aravind Eye Hospital, Madurai, India.
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Arunasri K, Mahesh M, Sai Prashanthi G, Jayasudha R, Kalyana Chakravarthy S, Tyagi M, Pappuru RR, Shivaji S. Mycobiome changes in the vitreous of post fever retinitis patients. PLoS One 2020; 15:e0242138. [PMID: 33211730 PMCID: PMC7676714 DOI: 10.1371/journal.pone.0242138] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/28/2020] [Indexed: 12/18/2022] Open
Abstract
Fungi have been associated with various diseases of the eye like keratitis, uveitis and endophthalmitis. Despite this fact, fungal microbiome (mycobiome) studies compared to the bacterial microbiome studies have remained neglected. In the present study, using metagenomic sequencing, the mycobiomes of the vitreous of healthy control individuals (VC, n = 15) and individuals with post fever retinitis + non-PFR uveitis (PFR+, n = 9) were analysed and compared. The results indicated that Ascomycota was the most predominant phylum in both VC and PFR+ groups. Further, at the genera level it was observed that the abundance of 17 fungal genera were significantly different in post fever retinitis (PFR, n = 6) group compared to control group. Of these 17 genera, it was observed that 14 genera were relatively more abundant in PFR group and the remaining 3 genera in the VC group. Genus Saccharomyces, a commensal of the gut and skin, was predominantly present in the vitreous of both the cohorts, however it was significantly less abundant in PFR group. Further, significant increase in the genera that have a pathogenic interaction with the host were observed in PFR group. On the whole the mycobiome in both the groups differed significantly and formed two distinct clusters in the heatmap and Principal co-ordinate analysis. These results demonstrate significant changes in the mycobiome from the vitreous of post fever retinitis patients compared to healthy controls thus implying that dysbiotic changes in the fungal vitreous microbiome are associated with PFR.
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Affiliation(s)
- Kotakonda Arunasri
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
| | - Malleswarapu Mahesh
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
| | - Gumpili Sai Prashanthi
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
| | - Rajagopalaboopathi Jayasudha
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
| | - Sama Kalyana Chakravarthy
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
| | - Mudit Tyagi
- Smt. Kanuri Santhamma Centre for Vitreo Retinal Diseases, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
| | - Rajeev R. Pappuru
- Smt. Kanuri Santhamma Centre for Vitreo Retinal Diseases, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
| | - Sisinthy Shivaji
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
- * E-mail:
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Miyazaki D, Eguchi H, Kuwahara T, Nakayama-Imaohji H, Inaba M, Itoi M, Ueda K, Ohashi Y, Sado K, Mizutani S, Miyamoto H, Sasaki SI, Shimizu Y, Inoue Y. Presence of Acanthamoeba and diversified bacterial flora in poorly maintained contact lens cases. Sci Rep 2020; 10:12595. [PMID: 32724150 PMCID: PMC7387515 DOI: 10.1038/s41598-020-69554-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 07/08/2020] [Indexed: 01/11/2023] Open
Abstract
Acanthamoeba can cause visually destructive Acanthamoeba keratitis (AK) in contact lens (CL) users. The purpose of this study was to determine whether Acanthamoeba was present in the CL cases of CL wearers and to develop techniques to prevent the contaminations. To accomplish this, 512 CL case samples were collected from 305 healthy CL wearers. Using real-time PCR, Acanthamoeba DNA was detected in 19.1% of CL cases, however their presence was not directly associated with poor CL case care. Instead, the presence of Acanthamoeba DNA was associated with significant levels of many different bacterial species. When the CL cases underwent metagenomic analysis, the most abundant bacterial orders were Enterobacteriales followed by Burkholderiales, Pseudomonadales, and Flavobacteriales. The presence of Acanthamoeba was characterized by Propionibacterium acnes and Rothia aeria and was also associated with an increase in the α diversity. Collectively, Acanthamoeba contamination occurs when a diversified bacterial flora is present in CL cases. This can effectively be prevented by careful and thorough CL case care.
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Affiliation(s)
- Dai Miyazaki
- Division of Ophthalmology and Visual Science, Faculty of Medicine, Tottori University, 36-1 Nishi-cho, Yonago, Tottori, 683-8504, Japan.
| | - Hiroshi Eguchi
- Department of Ophthalmology, Faculty of Medicine, Kindai University, Higashiōsaka, Japan
| | - Tomomi Kuwahara
- Department of Microbiology, Faculty of Medicine, Kagawa University, 1750-1 Miki, Kagawa, 761-0793, Japan
| | - Haruyuki Nakayama-Imaohji
- Department of Microbiology, Faculty of Medicine, Kagawa University, 1750-1 Miki, Kagawa, 761-0793, Japan
| | | | - Motozumi Itoi
- Dougenzaka Itoi Eye Clinic, Dogenzaka Shibuya-ku, Tokyo, Japan
| | - Kiichi Ueda
- Ueda Eye Clinic, Shimonoseki, Yamaguchi, Japan
| | - Yuichi Ohashi
- School of Medicine, Faculty of Medicine, Ehime University, Matsuyama, Japan
| | | | | | - Hitoshi Miyamoto
- Department of Clinical Laboratory, Ehime University Hospital, Matsuyama, Japan
| | - Shin-Ichi Sasaki
- Division of Ophthalmology and Visual Science, Faculty of Medicine, Tottori University, 36-1 Nishi-cho, Yonago, Tottori, 683-8504, Japan
| | - Yumiko Shimizu
- Division of Ophthalmology and Visual Science, Faculty of Medicine, Tottori University, 36-1 Nishi-cho, Yonago, Tottori, 683-8504, Japan
| | - Yoshitsugu Inoue
- Division of Ophthalmology and Visual Science, Faculty of Medicine, Tottori University, 36-1 Nishi-cho, Yonago, Tottori, 683-8504, Japan
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Assessing the ocular surface microbiome in severe ocular surface diseases. Ocul Surf 2020; 18:706-712. [PMID: 32717380 DOI: 10.1016/j.jtos.2020.07.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 07/05/2020] [Accepted: 07/09/2020] [Indexed: 12/16/2022]
Abstract
PURPOSE There is growing evidence for a critical role of the microbiome in ocular health and disease. We performed a prospective, observational study to characterize the ocular surface microbiome (OSM) in four chronic ocular surface diseases (OSDs) and healthy controls. METHODS Sterile swabs were used to collect samples from each eye of 39 patients (78 eyes). Sterile technique and multiple controls were used to assess contamination during DNA extraction, amplification and sequencing. Concurrent use of topical antibiotics, steroids, and bandage contact lenses (BCLs) was documented. RESULTS Despite the low biomass of the ocular surface, 47/78 (60%) eyes sampled had positive sequencing reads. We observed that half of patients (8/17, 47%) had distinct microbiomes in each eye. Healthy controls had a Lactobacillus/Streptococcus mixture or significant Corynebacterium. Staphylococcus predominated in 4/7 (57%) patients with Stevens-Johnson Syndrome (SJS) in at least one eye, compared to 0/10 healthy controls. Interestingly, 8/11 (73%) eyes with SJS were using BCLs, including 4/5 (80%) eyes dominated by Staphylococcus. Lax eyelid syndrome (LES) and Dry Eye Disease (DED) patients had similar OSMs, with Corynebacterium being the most prevalent bacteria. Alpha diversity was higher in controls and ocular graft-vs-host (oGVHD) patients compared to the other OSDs. CONCLUSIONS Only 50% of the 39 patients had similar microbiomes in each eye. A majority of healthy eyes had a Lactobacillus/Streptococcus mix or Corynebacterium microbiome. Staphylococcus predominated in SJS, Lactobacillus in oGVHD, and Corynebacterium in DED and LES. There may be an association between different OSDs and the microbiome.
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36
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Garza A, Diaz G, Hamdan M, Shetty A, Hong BY, Cervantes J. Homeostasis and Defense at the Surface of the Eye. The Conjunctival Microbiota. Curr Eye Res 2020; 46:1-6. [PMID: 32584612 DOI: 10.1080/02713683.2020.1788100] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The literature on ocular microbiome has grown tremendously over the past decade, and our knowledge of the different aspects and roles in homeostasis and protection is continuously growing. The development of 16 S rRNA sequencing has allowed the field to characterize communities of bacteria in health and ocular disease. Efforts should continue to further elucidate the interplay between microbiome and key players, such as age, comorbidities, and contact lens usage in order to have better control of the sight-threatening complications.
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Affiliation(s)
- Arnulfo Garza
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center , El Paso, TX, USA
| | - Giancarlo Diaz
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center , El Paso, TX, USA
| | - Marah Hamdan
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center , El Paso, TX, USA
| | - Akaanksh Shetty
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center , El Paso, TX, USA
| | - Bo-Young Hong
- The Jackson Laboratory for Genomic Medicine , Farmington, CT, USA
| | - Jorge Cervantes
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center , El Paso, TX, USA
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Arunasri K, Mahesh M, Sai Prashanthi G, Jayasudha R, Kalyana Chakravarthy S, Tyagi M, Pappuru RR, Shivaji S. Comparison of the Vitreous Fluid Bacterial Microbiomes between Individuals with Post Fever Retinitis and Healthy Controls. Microorganisms 2020; 8:E751. [PMID: 32429503 PMCID: PMC7285296 DOI: 10.3390/microorganisms8050751] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/23/2020] [Accepted: 05/04/2020] [Indexed: 12/21/2022] Open
Abstract
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.
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Affiliation(s)
- Kotakonda Arunasri
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Malleswarapu Mahesh
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Gumpili Sai Prashanthi
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Rajagopalaboopathi Jayasudha
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Sama Kalyana Chakravarthy
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Mudit Tyagi
- Smt. Kanuri Santhamma Centre for Vitreo Retinal Diseases, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (M.T.); (R.R.P.)
| | - Rajeev R. Pappuru
- Smt. Kanuri Santhamma Centre for Vitreo Retinal Diseases, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (M.T.); (R.R.P.)
| | - Sisinthy Shivaji
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
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Diagnostic information Profiling and Evaluation of Causative Fungi of Fungal Keratitis Using High-throughput Internal Transcribed Spacer Sequencing. Sci Rep 2020; 10:1640. [PMID: 32015395 PMCID: PMC6997210 DOI: 10.1038/s41598-020-58245-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/06/2020] [Indexed: 11/23/2022] Open
Abstract
Early and accurate diagnosis is essential for the targeted management of fungal keratitis (FK), which is one of the major blinding eye diseases worldwide. To elucidate the diagnostic information of high-throughput internal transcribed spacer (ITS) sequencing for identifying causative fungi of FK, 38 patients who were highly suspected of having FK were included in this research. In vivo confocal microscopy, potassium hydroxide smear, and fungal culture were performed to diagnose FK. Culture and ITS sequencing were used to identify causative fungi. We hypothesized that the dominant genus was the result of pathogen identification by ITS sequencing. Thirty-five patients were eventually diagnosed with FK, with fungal pathogens found by confocal microscopy in 27 patients (77.14%), by smear examination in 27 patients (77.14%), by culture in 25 patients (71.43%), and by ITS sequencing in 26 patients (74.29%). Eight causative fungal genera were determined by ITS sequencing, while five causative fungal genera were identified based on the morphology of the cultured pathogens. The results of ITS sequencing and culture were coincident in 10 patients with FK (28.57%). It is concluded that ITS sequencing, to some extent, challenged fungal culture and might be an optional complement in identifying fungal pathogens in corneas.
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Ung L, Bispo PJM, Doan T, Van Gelder RN, Gilmore MS, Lietman T, Margolis TP, Zegans ME, Lee CS, Chodosh J. Clinical metagenomics for infectious corneal ulcers: Rags to riches? Ocul Surf 2020; 18:1-12. [PMID: 31669750 PMCID: PMC9837861 DOI: 10.1016/j.jtos.2019.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/21/2019] [Indexed: 01/17/2023]
Abstract
The emergence of clinical metagenomics as an unbiased, hypothesis-free approach to diagnostic testing is set to fundamentally alter the way infectious diseases are detected. Long envisioned as the solution to the limitations of culture-based conventional microbiology, next generation sequencing methods will soon mature, and our attention will inevitably turn to how they can be applied to areas of medicine which need it most urgently. In ophthalmology, the demand for this technology is particularly pressing for the care of infectious corneal ulcers, where current diagnostic tests may fail to identify a causative organism in over half of cases. However, the optimism found in the budding discourse surrounding clinical metagenomics belies the reality that clinicians and scientists will soon be inundated by oppressive volumes of sequencing data, much of which will be foreign and unfamiliar. Therefore, our success in translating clinical metagenomics is likely to hinge on how we make sense of these data, and understanding its implications for the interpretation and implementation of sequencing into routine clinical care. In this consortium-led review, we provide an outline of these data-related issues and how they may be used to inform technical workflows, with the hope that we may edge closer to realizing the potential of clinical metagenomics for this important unmet need.
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Affiliation(s)
- Lawson Ung
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Paulo J M Bispo
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Thuy Doan
- Francis I. Proctor Foundation, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | | | - Michael S Gilmore
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Thomas Lietman
- Francis I. Proctor Foundation, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Todd P Margolis
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in Saint Louis, Saint Louis, USA
| | - Michael E Zegans
- Department of Surgery (Ophthalmology), and Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | - Cecilia S Lee
- Department of Ophthalmology, University of Washington, Seattle, WA, USA.
| | - James Chodosh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA.
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41
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Alterations in the Ocular Surface Fungal Microbiome in Fungal Keratitis Patients. Microorganisms 2019; 7:microorganisms7090309. [PMID: 31480776 PMCID: PMC6780152 DOI: 10.3390/microorganisms7090309] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/28/2019] [Accepted: 08/31/2019] [Indexed: 12/17/2022] Open
Abstract
Keratitis, an inflammatory disease of the eye, when neglected could lead to sight-threatening complications and ultimately blindness. Globally, over a million people are affected by keratitis annually. Keratitis has a microbial etiology and is caused by bacteria, fungi, viruses, etc. The present study compared the ocular surface fungal microbiome of healthy individuals and individuals with fungal keratitis. Fungal microbiomes from the conjunctival swabs of healthy individuals and from conjunctival swabs and corneal scrapings of individuals with fungal keratitis were generated using ITS2 region amplicons. Microbiomes were sequenced using Illumina MiSeq 2 × 250 base pair chemistry with a paired-end protocol. Based on Alpha diversity indices, phylum and genera level diversity, abundance differences, and heat map analysis, the fungal microbiomes of conjunctival swabs and corneal scrapings of individuals with fungal keratitis exhibited dysbiosis (alterations in the diversity and abundance) compared to the ocular surface microbiome of the healthy control individuals. This is the first report indicating dysbiosis in the fungal microbiome of conjunctival swabs and corneal scrapings in individuals with fungal keratitis. A total of 11 genera present in the majority of the eyes constituted the variable core ocular microbiome.
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