1
|
Hammoudeh Y, Suresh L, Ong ZZ, Lister MM, Mohammed I, Thomas DJI, Cottell JL, Holden JM, Said DG, Dua HS, Ting DSJ. Microbiological culture versus 16S/18S rRNA gene PCR-sanger sequencing for infectious keratitis: a three-arm, diagnostic cross-sectional study. Front Med (Lausanne) 2024; 11:1393832. [PMID: 39206175 PMCID: PMC11352289 DOI: 10.3389/fmed.2024.1393832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
Background To compare the diagnostic performance of microbiological culture and 16S/18S rRNA gene polymerase chain reaction (PCR)-Sanger sequencing for infectious keratitis (IK) and to analyse the effect of clinical disease severity on test performance and inter-test concordance. Methods This was a three-arm, diagnostic cross-sectional study. We included all eligible patients who presented with presumed bacterial/fungal keratitis to the Queen's Medical Centre, Nottingham, UK, between June 2021 and September 2022. All patients underwent simultaneous culture (either direct or indirect culture, or both) and 16S (pan-bacterial)/18S (pan-fungal) ribosomal RNA (rRNA) PCR-Sanger sequencing. The bacterial/fungal genus and species identified on culture were confirmed using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. Relevant clinical data were also collected to analyze for any potential clinico-microbiological correlation. Main outcome measures included the diagnostic yield, test accuracy (including sensitivity and specificity), and inter-test agreement [including percent agreement and Cohen's kappa (k)]. Results A total of 81 patients (86 episodes of IK) were included in this study. All organisms identified were of bacterial origin. Diagnostic yields were similar among direct culture (52.3%), indirect culture (50.8%), and PCR (43.1%; p = 0.13). The addition of PCR enabled a positive diagnostic yield in 3 (9.7%) direct culture-negative cases. Based on composite reference standard, direct culture had the highest sensitivity (87.5%; 95% CI, 72.4-95.3%), followed by indirect culture (85.4%; 95% CI, 71.6-93.5%) and PCR (73.5%; 95% CI, 59.0-84.6%), with 100% specificity noted in all tests. Pairwise comparisons showed substantial agreement among the three tests (percent agreement = 81.8-86.2%, Cohen's k = 0.67-0.72). Clinico-microbiological correlation demonstrated higher culture-PCR concordance in cases with greater infection severity. Conclusions This study highlights a similar diagnostic performance of direct culture, indirect culture and 16S rRNA PCR for bacterial keratitis, with substantial inter-test concordance. PCR serves as a useful diagnostic adjuvant to culture, particularly in culture-negative cases or those with lesser disease severity (where culture-PCR concordance is lower).
Collapse
Affiliation(s)
- Yasmeen Hammoudeh
- Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom
| | - Lakshmi Suresh
- Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom
| | - Zun Zheng Ong
- New Cross Hospital Eye Infirmary, Wolverhampton, United Kingdom
| | - Michelle M. Lister
- Department of Microbiology, Queen's Medical Centre, Nottingham, United Kingdom
| | - Imran Mohammed
- School of Optometry and Vision Sciences, College of Biomedical and Life Sciences, Cardiff University, Cardiff, United Kingdom
- Academic Ophthalmology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - D. John I. Thomas
- Micropathology Ltd., Venture Centre, University of Warwick Science Park, Coventry, United Kingdom
| | - Jennifer L. Cottell
- Micropathology Ltd., Venture Centre, University of Warwick Science Park, Coventry, United Kingdom
| | - Jennifer M. Holden
- Micropathology Ltd., Venture Centre, University of Warwick Science Park, Coventry, United Kingdom
| | - Dalia G. Said
- Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom
- Academic Ophthalmology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Harminder S. Dua
- Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom
- Academic Ophthalmology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Darren Shu Jeng Ting
- Academic Ophthalmology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham NHS Trust, Birmingham, United Kingdom
| |
Collapse
|
2
|
Singh RB, Dohlman TH, Ivanov A, Hall N, Ross C, Elze T, Miller JW, Lorch A, Yuksel E, Yin J, Dana R. Corneal Opacity in the United States: An American Academy of Ophthalmology IRIS® Registry (Intelligent Research in Sight) Study. Ophthalmology 2024:S0161-6420(24)00416-0. [PMID: 38986874 DOI: 10.1016/j.ophtha.2024.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024] Open
Abstract
PURPOSE Vision loss associated with opacification of the cornea is one of the leading causes of blindness globally. However, the epidemiological data pertaining to the demographics, associated etiological causes and reduced vision in corneal opacity patients continue to be sparse. This study assesses the case frequencies, underlying etiologies, and vision outcomes in patients diagnosed with corneal opacity, in the United States. DESIGN Retrospective cohort study PARTICIPANTS: Patients in the IRIS® Registry (Intelligent Research in Sight) who were diagnosed with corneal opacity between January 1st, 2013, and November 30th, 2020. METHODS The IRIS Registry contains demographic and clinical data of 79,887,324 patients who presented to eye clinics during the study period. We identified patients with corneal opacity using International Classification of Disease (ICD) codes (ICD-9, and -10) of "371" (corneal scar) and "H17" (corneal opacity), respectively. The analyzed data included demographic parameters included age, sex, race, ethnicity, and geographical location. We evaluated clinical data including laterality, etiology, disease descriptors, and best-corrected visual acuity (VA) up to 1 year before the onset (± 30 days), at the time of diagnosis, and at one year following diagnosis (± 30 days). MAIN OUTCOME MEASURES Case frequencies, etiology, and vision outcomes in patients diagnosed with corneal opacity. RESULTS We identified 5,220,382 patients who were diagnosed with corneal opacity and scars using H17 (ICD-10) and 371.0 (ICD-9) codes over seven years. The case frequency of corneal opacity during the study period was 6,535 cases per 100,000 patients (6.5%). The mean age of the patients was 63.36±18.14 years and the majority were female (57.6%). In the cohort, 38.39% and 30.00% of patients had bilateral and unilateral corneal opacity, respectively. Most of the patients were White (69.13%), followed by Black or African American (6.84%), Asian (2.45%), American Indian or Alaska Native(0.34%), Native Hawaii or other Pacific Islander(0.19%). Among the patients with corneal opacity, 7.34% had Hispanic or Latino ethnicity. The primary etiologies associated with corneal opacity included corneal dystrophies (64.66%) followed by edema (18.25%), ulcer (7.78%), keratoconjunctivitis (7.18%), degeneration (5.62%), neovascularization (6.27%), and trauma (5.28%). Visual acuity of the patients significantly worsened due to corneal opacity (0.46±0.74 logMAR; ∼20/58 in Snellen) and did not improve to the baseline (0.37±0.68 logMAR, ∼20/46 in Snellen) post-management (0.43±0.77 logMAR, ∼20/54 in Snellen). The multiple linear regression analysis showed worse vision outcomes in females (compared to males), and Asian, Black or African American, and American Indian or Alaska Native (compared to White) patients. Additionally, worse vision outcomes were observed in patients with opacity associated with corneal malformation, degenerative disorders, edema, injury, and ulcer compared to those with hereditary corneal dystrophy. CONCLUSIONS Our study shows that the corneal opacity was diagnosed in 6.5% of the patients in the IRIS Registry and it was primarily associated with corneal dystrophies. The final vision outcomes in corneal opacity patients were significantly worse compared to baseline. The worse vision outcomes were associated with sociodemographic differences that might be associated with disparities in access, utilization, and care patterns.
Collapse
Affiliation(s)
- Rohan Bir Singh
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Thomas H Dohlman
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Alexander Ivanov
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Nathan Hall
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Connor Ross
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Tobias Elze
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Joan W Miller
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Alice Lorch
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Erdem Yuksel
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Jia Yin
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Reza Dana
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
3
|
Azzopardi M, Chong YJ, Ng B, Recchioni A, Logeswaran A, Ting DSJ. Diagnosis of Acanthamoeba Keratitis: Past, Present and Future. Diagnostics (Basel) 2023; 13:2655. [PMID: 37627913 PMCID: PMC10453105 DOI: 10.3390/diagnostics13162655] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Acanthamoeba keratitis (AK) is a painful and sight-threatening parasitic corneal infection. In recent years, the incidence of AK has increased. Timely and accurate diagnosis is crucial during the management of AK, as delayed diagnosis often results in poor clinical outcomes. Currently, AK diagnosis is primarily achieved through a combination of clinical suspicion, microbiological investigations and corneal imaging. Historically, corneal scraping for microbiological culture has been considered to be the gold standard. Despite its technical ease, accessibility and cost-effectiveness, the long diagnostic turnaround time and variably low sensitivity of microbiological culture limit its use as a sole diagnostic test for AK in clinical practice. In this review, we aim to provide a comprehensive overview of the diagnostic modalities that are currently used to diagnose AK, including microscopy with staining, culture, corneal biopsy, in vivo confocal microscopy, polymerase chain reaction and anterior segment optical coherence tomography. We also highlight emerging techniques, such as next-generation sequencing and artificial intelligence-assisted models, which have the potential to transform the diagnostic landscape of AK.
Collapse
Affiliation(s)
- Matthew Azzopardi
- Department of Ophthalmology, Royal London Hospital, London E1 1BB, UK;
| | - Yu Jeat Chong
- Birmingham and Midland Eye Centre, Birmingham B18 7QH, UK; (B.N.); (A.R.)
| | - Benjamin Ng
- Birmingham and Midland Eye Centre, Birmingham B18 7QH, UK; (B.N.); (A.R.)
| | - Alberto Recchioni
- Birmingham and Midland Eye Centre, Birmingham B18 7QH, UK; (B.N.); (A.R.)
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
| | | | - Darren S. J. Ting
- Birmingham and Midland Eye Centre, Birmingham B18 7QH, UK; (B.N.); (A.R.)
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
- Academic Ophthalmology, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK
| |
Collapse
|
4
|
Motro Y, Wajnsztajn D, Michael-Gayego A, Mathur S, Marano RB, Salah I, Rosenbluh C, Temper V, Strahilevitz J, Moran-Gilad J. Metagenomic sequencing for investigation of a national keratoconjunctivitis outbreak, Israel, 2022. Euro Surveill 2023; 28:2300010. [PMID: 37535472 PMCID: PMC10401915 DOI: 10.2807/1560-7917.es.2023.28.31.2300010] [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: 01/03/2023] [Accepted: 06/20/2023] [Indexed: 08/05/2023] Open
Abstract
BackgroundEpidemics of keratoconjunctivitis may involve various aetiological agents. Microsporidia are an uncommon difficult-to-diagnose cause of such outbreaks.AimDuring the third quarter of 2022, a keratoconjunctivitis outbreak was reported across Israel, related to common water exposure to the Sea of Galilee. We report a comprehensive diagnostic approach that identified Vittaforma corneae as the aetiology, serving as proof of concept for using real-time metagenomics for outbreak investigation.MethodsCorneal scraping samples from a clinical case were subjected to standard microbiological testing. Samples were tested by calcofluor white staining and metagenomic short-read sequencing. We analysed the metagenome for taxonomical assignment and isolation of metagenome-assembled genome (MAG). Targets for a novel PCR were identified, and the assay was applied to clinical and environmental samples and confirmed by long-read metagenomic sequencing.ResultsFluorescent microscopy was suggestive of microsporidiosis. The most abundant species (96.5%) on metagenomics analysis was V. corneae. Annotation of the MAG confirmed the species assignment. A unique PCR target in the microsporidian rRNA gene was identified and validated against the clinical sample. The assay and metagenomic sequencing confirmed V. corneae in an environmental sludge sample collected at the exposure site.ConclusionsThe real-time utilisation of metagenomics allowed species detection and development of diagnostic tools, which aided in outbreak source tracking and can be applied for future cases. Metagenomics allows a fully culture-independent investigation and is an important modality for public health microbiology.
Collapse
Affiliation(s)
- Yair Motro
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
- These authors contributed equally to the manuscript and share first authorship
| | - Denise Wajnsztajn
- Department of Ophthalmology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- These authors contributed equally to the manuscript and share first authorship
| | - Ayelet Michael-Gayego
- Clinical Microbiology Laboratory, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Shubham Mathur
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Roberto Bm Marano
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Ikram Salah
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Chaggai Rosenbluh
- Department of Genetics, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Violeta Temper
- Clinical Microbiology Laboratory, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Jacob Strahilevitz
- Clinical Microbiology Laboratory, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Jacob Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
- Clinical Microbiology Laboratory, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| |
Collapse
|
5
|
Ung L, Chodosh J. Urgent unmet needs in the care of bacterial keratitis: An evidence-based synthesis. Ocul Surf 2023; 28:378-400. [PMID: 34461290 PMCID: PMC10721114 DOI: 10.1016/j.jtos.2021.08.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 11/21/2022]
Abstract
Bacterial corneal infections, or bacterial keratitis (BK), are ophthalmic emergencies that frequently lead to irreversible visual impairment. Though increasingly recognized as a major cause of global blindness, modern paradigms of evidence-based care in BK have remained at a diagnostic and therapeutic impasse for over half a century. Current standards of management - based on the collection of corneal cultures and the application of broad-spectrum topical antibiotics - are beset by important yet widely underrecognized limitations, including approximately 30% of all patients who will develop moderate to severe vision loss in the affected eye. Though recent advances have involved a more clearly defined role for adjunctive topical corticosteroids, and novel therapies such as corneal crosslinking, overall progress to improve patient and population-based outcomes remains incommensurate to the chronic morbidity caused by this disease. Recognizing that the care of BK is guided by the clinical axiom, "time equals vision", this chapter offers an evidence-based synthesis for the clinical management of these infections, underscoring critical unmet needs in disease prevention, diagnosis, and treatment.
Collapse
Affiliation(s)
- Lawson Ung
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - James Chodosh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
6
|
Tan CL, Sheorey H, Allen PJ, Dawkins RCH. Endophthalmitis: Microbiology and Organism Identification Using Current and Emerging Techniques. Ocul Immunol Inflamm 2023; 31:393-401. [PMID: 35201917 DOI: 10.1080/09273948.2022.2027468] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Endophthalmitis is an ophthalmological emergency requiring timely and appropriate diagnosis and treatment. Microbiological methods of microscopy (Gram's staining) and culture are the current gold standard for organism identification. However, a significant proportion of endophthalmitis remains culture-negative-perhaps the inflammation is non-infectious in origin, results from a novel organism are unidentifiable or because the causative organism is non-culturable often due to pre-treatment with antibiotics. This review outlines the microbiological profile of endophthalmitis, current clinically used methods for organism identification, and the newer molecular techniques of polymerase chain reaction (PCR) and next-generation sequencing (NGS) technology as diagnostic tools for endophthalmitis. They offer the potential to improve organism identification rates and clinical outcomes in infectious diseases, representing an exciting future direction for organism identification in endophthalmitis. Based on the largest ophthalmic hospital in Australia, we highlight the key practical challenges faced by Australian diagnostic laboratories for their use in a clinical setting.
Collapse
Affiliation(s)
- Christine L Tan
- Macular Research Unit, Centre for Eye Research Australia, East Melbourne, Australia.,Department of Ophthalmology, The University of Melbourne, Parkville, Australia
| | - Harsha Sheorey
- Department of Microbiology, St Vincent's Hospital, Fitzroy, Australia
| | - Penelope J Allen
- Macular Research Unit, Centre for Eye Research Australia, East Melbourne, Australia.,Department of Ophthalmology, The University of Melbourne, Parkville, Australia.,Vitreo-retinal Unit, The Royal Victorian Eye and Ear Hospital, East Melbourne, Australia
| | - Rosie C H Dawkins
- Macular Research Unit, Centre for Eye Research Australia, East Melbourne, Australia.,Department of Ophthalmology, The University of Melbourne, Parkville, Australia.,Vitreo-retinal Unit, The Royal Victorian Eye and Ear Hospital, East Melbourne, Australia
| |
Collapse
|
7
|
Borroni D, Bonzano C, Sánchez-González JM, Rachwani-Anil R, Zamorano-Martín F, Pereza-Nieves J, Traverso CE, García Lorente M, Rodríguez-Calvo-de-Mora M, Esposito A, Godin F, Rocha-de-Lossada C. Shotgun metagenomic sequencing in culture negative microbial keratitis. Eur J Ophthalmol 2023:11206721221149077. [PMID: 36617769 DOI: 10.1177/11206721221149077] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
PURPOSE To evaluate the microbiota of culture negative Corneal Impression Membrane (CIM) microbial keratitis samples with the use of shotgun metagenomics analysis. METHODS DNA of microbial keratitis samples were collected with CIM and extracted using the MasterPure™ Complete DNA and RNA Purification Kit (Epicentre). DNA was fragmented by sonication into fragments of 300 to 400 base pairs (bp) using Bioruptor® (Diagenode, Belgium) and then used as a template for library preparation. DNA libraries were sequenced on Illumina® HiSeq2500. The resulting reads were quality controlled, trimmed and mapped against the human reference genome. The unmapped reads were taxonomically classified using the Kraken software. RESULTS 18 microbial keratitis samples were included in the study. Brevundimonas diminuta was found in 5 samples while 6 samples showed the presence of viral infections. Cutibacterium acnes, Staphylococcus aureus, Moraxella lacunata and Pseudomonas alcaligenes were also identified as the presumed putative cause of the infection in 7 samples. CONCLUSIONS Shotgun sequencing can be used as a diagnostic tool in microbial keratitis samples. This diagnostic method expands the available tests to diagnose eye infections and could be clinically significant in culture negative samples.
Collapse
Affiliation(s)
- Davide Borroni
- Department of Ophthalmology, Riga Stradins University, Riga, Latvia
| | - Chiara Bonzano
- DiNOGMI, University of Genoa and IRCCS San Martino Polyclinic Hospital, Genoa, Italy
| | | | | | | | | | - Carlo Enrico Traverso
- DiNOGMI, University of Genoa and IRCCS San Martino Polyclinic Hospital, Genoa, Italy
| | | | | | - Alfonso Esposito
- 18470International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Fernando Godin
- Department of Ophthalmology, Universidad El Bosque, Bogotá, Colombia
| | - Carlos Rocha-de-Lossada
- Qvision, Opththalmology Department, VITHAS Almería Hospital, Almería, Spain.,Ophthalmology Department, VITHAS Málaga, Málaga, Spain.,Hospital Regional Universitario de Málaga, Plaza del Hospital Civil, Málaga, Spain.,Departamento de Cirugía, Universidad de Sevilla, Área de Oftalmología, Doctor Fedriani, Seville, Spain
| |
Collapse
|
8
|
Ludi Z, Sule AA, Samy RP, Putera I, Schrijver B, Hutchinson PE, Gunaratne J, Verma I, Singhal A, Nora RLD, van Hagen PM, Dik WA, Gupta V, Agrawal R. Diagnosis and biomarkers for ocular tuberculosis: From the present into the future. Theranostics 2023; 13:2088-2113. [PMID: 37153734 PMCID: PMC10157737 DOI: 10.7150/thno.81488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/19/2023] [Indexed: 05/10/2023] Open
Abstract
Tuberculosis is an airborne disease caused by Mycobacterium tuberculosis (Mtb) and can manifest both pulmonary and extrapulmonary disease, including ocular tuberculosis (OTB). Accurate diagnosis and swift optimal treatment initiation for OTB is faced by many challenges combined with the lack of standardized treatment regimens this results in uncertain OTB outcomes. The purpose of this study is to summarize existing diagnostic approaches and recently discovered biomarkers that may contribute to establishing OTB diagnosis, choice of anti-tubercular therapy (ATT) regimen, and treatment monitoring. The keywords ocular tuberculosis, tuberculosis, Mycobacterium, biomarkers, molecular diagnosis, multi-omics, proteomics, genomics, transcriptomics, metabolomics, T-lymphocytes profiling were searched on PubMed and MEDLINE databases. Articles and books published with at least one of the keywords were included and screened for relevance. There was no time limit for study inclusion. More emphasis was placed on recent publications that contributed new information about the pathogenesis, diagnosis, or treatment of OTB. We excluded abstracts and articles that were not written in the English language. References cited within the identified articles were used to further supplement the search. We found 10 studies evaluating the sensitivity and specificity of interferon-gamma release assay (IGRA), and 6 studies evaluating that of tuberculin skin test (TST) in OTB patients. IGRA (Sp = 71-100%, Se = 36-100%) achieves overall better sensitivity and specificity than TST (Sp = 51.1-85.7%; Se = 70.9-98.5%). For nuclear acid amplification tests (NAAT), we found 7 studies on uniplex polymerase chain reaction (PCR) with different Mtb targets, 7 studies on DNA-based multiplex PCR, 1 study on mRNA-based multiplex PCR, 4 studies on loop-mediated isothermal amplification (LAMP) assay with different Mtb targets, 3 studies on GeneXpert assay, 1 study on GeneXpert Ultra assay and 1 study for MTBDRplus assay for OTB. Specificity is overall improved but sensitivity is highly variable for NAATs (excluding uniplex PCR, Sp = 50-100%; Se = 10.5-98%) as compared to IGRA. We also found 3 transcriptomic studies, 6 proteomic studies, 2 studies on stimulation assays, 1 study on intraocular protein analysis and 1 study on T-lymphocyte profiling in OTB patients. All except 1 study evaluated novel, previously undiscovered biomarkers. Only 1 study has been externally validated by a large independent cohort. Future theranostic marker discovery by a multi-omics approach is essential to deepen pathophysiological understanding of OTB. Combined these might result in swift, optimal and personalized treatment regimens to modulate the heterogeneous mechanisms of OTB. Eventually, these studies could improve the current cumbersome diagnosis and management of OTB.
Collapse
Affiliation(s)
- Zhang Ludi
- Lee Kong Chian School of Medicine, Nanyang Technological University of Singapore, Singapore
| | - Ashita Ashish Sule
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ramar Perumal Samy
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
| | - Ikhwanuliman Putera
- Department of Ophthalmology, Faculty of Medicine Universitas Indonesia - CiptoMangunkusmoKirana Eye Hospital, Jakarta, Indonesia
- Laboratory Medical Immunology, Department of Immunology, ErasmusMC, UniversityMedical Centre, Rotterdam, the Netherlands
- Department of Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Benjamin Schrijver
- Laboratory Medical Immunology, Department of Immunology, ErasmusMC, UniversityMedical Centre, Rotterdam, the Netherlands
| | - Paul Edward Hutchinson
- Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Indu Verma
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Amit Singhal
- Lee Kong Chian School of Medicine, Nanyang Technological University of Singapore, Singapore
- A*SATR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Rina La Distia Nora
- Department of Ophthalmology, Faculty of Medicine Universitas Indonesia - CiptoMangunkusmoKirana Eye Hospital, Jakarta, Indonesia
- Laboratory Medical Immunology, Department of Immunology, ErasmusMC, UniversityMedical Centre, Rotterdam, the Netherlands
- University of Indonesia Hospital (RSUI), Depok, West Java, Indonesia
| | - P. Martin van Hagen
- Laboratory Medical Immunology, Department of Immunology, ErasmusMC, UniversityMedical Centre, Rotterdam, the Netherlands
- Department of Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Willem A Dik
- Laboratory Medical Immunology, Department of Immunology, ErasmusMC, UniversityMedical Centre, Rotterdam, the Netherlands
| | - Vishali Gupta
- Advanced Eye Centre, Post-Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Rupesh Agrawal
- Lee Kong Chian School of Medicine, Nanyang Technological University of Singapore, Singapore
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
- Duke NUS Medical School, Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
- National Institute for Health Research Biomedical Research Centre, Moorfields Eye Hospital, London, UK
- School of Pharmacy, Nantong University, Nantong, P. R. China
- Department of Mechanical Engineering, University College London, London, United Kingdom
- ✉ Corresponding author: A/Prof (Dr) Rupesh Agrawal, Senior Consultant, National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore 308433,
| |
Collapse
|
9
|
Ting DSJ, Chodosh J, Mehta JS. Achieving diagnostic excellence for infectious keratitis: A future roadmap. Front Microbiol 2022; 13:1020198. [PMID: 36262329 PMCID: PMC9576146 DOI: 10.3389/fmicb.2022.1020198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/20/2022] [Indexed: 02/02/2023] Open
Affiliation(s)
- Darren S. J. Ting
- Academic Ophthalmology, School of Medicine, University of Nottingham, Nottingham, United Kingdom,Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom
| | - James Chodosh
- Department of Ophthalmology, Massachusetts Eye and Ear and Harvard Medical School, Boston, MA, United States
| | - Jodhbir S. Mehta
- Department of Cornea & Refractive Surgery, Singapore National Eye Centre, Singapore, Singapore,Singapore Eye Research Institute, Singapore, Singapore,*Correspondence: Jodhbir S. Mehta
| |
Collapse
|
10
|
Low L, Nakamichi K, Akileswaran L, Lee CS, Lee AY, Moussa G, Murray PI, Wallace GR, Van Gelder RN, Rauz S. Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform. Am J Ophthalmol 2022; 242:243-251. [PMID: 35660421 PMCID: PMC9850836 DOI: 10.1016/j.ajo.2022.05.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 01/22/2023]
Abstract
PURPOSE To evaluate the utility of nanopore sequencing for identifying potential causative pathogens in endophthalmitis, comparing culture results against full-length 16S rRNA nanopore sequencing (16S Nanopore), whole genome nanopore sequencing (Nanopore WGS), and Illumina (Illumina WGS). DESIGN Cross-sectional diagnostic comparison. METHODS Patients with clinically suspected endophthalmitis underwent intraocular vitreous biopsy as per standard care. Clinical samples were cultured by conventional methods, together with full-length 16S rRNA and WGS using nanopore and Illumina sequencing platforms. RESULTS Of 23 patients (median age 68.5 years [range 47-88]; 14 males [61%]), 18 cases were culture-positive. Nanopore sequencing identified the same cultured organism in all of the culture-positive cases and identified potential pathogens in two culture-negative cases (40%). Nanopore WGS was able to additionally detect the presence of bacteriophages in three samples. The agreements at genus level between culture and 16S Nanopore, Nanopore WGS, and Illumina WGS were 75%, 100%, and 78%, respectively. CONCLUSIONS Whole genome sequencing has higher sensitivity and provides a viable alternative to culture and 16S sequencing for detecting potential pathogens in endophthalmitis. Moreover, WGS has the ability to detect other potential pathogens in culture-negative cases. Whilst Nanopore and Illumina WGS provide comparable data, nanopore sequencing provides potential for cost-effective point-of-care diagnostics.
Collapse
Affiliation(s)
- Liying Low
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, United Kingdom,Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals NHS Trust, Birmingham, United Kingdom
| | - Kenji Nakamichi
- Department of Ophthalmology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Lakshmi Akileswaran
- Department of Ophthalmology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Cecilia S. Lee
- Department of Ophthalmology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Aaron Y. Lee
- Department of Ophthalmology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - George Moussa
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals NHS Trust, Birmingham, United Kingdom
| | - Philip I. Murray
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, United Kingdom,Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals NHS Trust, Birmingham, United Kingdom
| | - Graham R. Wallace
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, United Kingdom
| | - Russell N. Van Gelder
- Department of Ophthalmology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Saaeha Rauz
- Department of Ophthalmology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | | |
Collapse
|
11
|
Cabrera‐Aguas M, Khoo P, Watson SL. Infectious keratitis: A review. Clin Exp Ophthalmol 2022; 50:543-562. [PMID: 35610943 PMCID: PMC9542356 DOI: 10.1111/ceo.14113] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 12/29/2022]
Abstract
Globally, infectious keratitis is the fifth leading cause of blindness. The main predisposing factors include contact lens wear, ocular injury and ocular surface disease. Staphylococcus species, Pseudomonas aeruginosa, Fusarium species, Candida species and Acanthamoeba species are the most common causal organisms. Culture of corneal scrapes is the preferred initial test to identify the culprit organism. Polymerase chain reaction (PCR) tests and in vivo confocal microscopy can complement the diagnosis. Empiric therapy is typically commenced with fluoroquinolones, or fortified antibiotics for bacterial keratitis; topical natamycin for fungal keratitis; and polyhexamethylene biguanide or chlorhexidine for acanthamoeba keratitis. Herpes simplex keratitis is mainly diagnosed clinically; however, PCR can also be used to confirm the initial diagnosis and in atypical cases. Antivirals and topical corticosteroids are indicated depending on the corneal layer infected. Vision impairment, blindness and even loss of the eye can occur with a delay in diagnosis and inappropriate antimicrobial therapy.
Collapse
Affiliation(s)
- Maria Cabrera‐Aguas
- Save Sight Institute, Discipline of Ophthalmology, Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- Corneal Unit Sydney Eye Hospital Sydney New South Wales Australia
| | - Pauline Khoo
- Save Sight Institute, Discipline of Ophthalmology, Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- Corneal Unit Sydney Eye Hospital Sydney New South Wales Australia
| | - Stephanie L. Watson
- Save Sight Institute, Discipline of Ophthalmology, Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- Corneal Unit Sydney Eye Hospital Sydney New South Wales Australia
| |
Collapse
|
12
|
Omi M, Matsuo Y, Araki-Sasaki K, Oba S, Yamada H, Hirota K, Takahashi K. 16S rRNA nanopore sequencing for the diagnosis of ocular infection: a feasibility study. BMJ Open Ophthalmol 2022; 7:bmjophth-2021-000910. [PMID: 36161861 PMCID: PMC9131114 DOI: 10.1136/bmjophth-2021-000910] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
Objective We conducted a feasibility study to verify the effectiveness of 16S ribosomal RNA (rRNA) gene analysis using the nanopore sequencer MinION for identifying causative bacteria in several types of ocular infections. Methods and Analysis Four cases of corneal ulcers, one case of endophthalmitis and one case of a conjunctival abscess were included in this study. DNA was extracted from corneal scraping, vitreous samples and secretions from the conjunctival abscess. We conducted 16S rRNA gene amplicon sequencing using MinION and metagenomic DNA analysis. The efficacy of bacterial identification was verified by comparing the conventional culture method with smear observations. Results 16S rRNA gene sequencing analysis with MinION identified the causative organisms promptly with high accuracy in approximately 4 hours, from ophthalmic specimens. The results of the conventional culture method and 16S rRNA gene sequencing were consistent in all cases. In four of the six cases, a greater variety of organisms was found in the 16S rRNA gene analysis than in bacterial culture. Conclusion Using our workflow, 16S rRNA gene analysis using MinION enabled rapid and accurate identification possible in various kinds of bacterial ocular infections.
Collapse
Affiliation(s)
- Masatoshi Omi
- Department of Ophthalmology, Kansai Medical University, Hirakata, Japan
| | - Yoshiyuki Matsuo
- Department of Human Stress Response Science, Kansai Medical University, Hirakata, Japan
| | | | - Shimpei Oba
- Department of Ophthalmology, Kansai Medical University, Hirakata, Japan
| | - Haruhiko Yamada
- Department of Ophthalmology, Kansai Medical University, Hirakata, Japan
| | - Kiichi Hirota
- Department of Human Stress Response Science, Kansai Medical University, Hirakata, Japan
| | - Kanji Takahashi
- Department of Ophthalmology, Kansai Medical University, Hirakata, Japan
| |
Collapse
|
13
|
Evidence-based Management of Culture-negative Microbial Keratitis. Int Ophthalmol Clin 2022; 62:111-124. [PMID: 35325914 DOI: 10.1097/iio.0000000000000411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
14
|
Van Gelder RN. Molecular Diagnostics for Ocular Infectious Diseases: LXXVIII Edward Jackson Memorial Lecture. Am J Ophthalmol 2022; 235:300-312. [PMID: 34921773 PMCID: PMC8863649 DOI: 10.1016/j.ajo.2021.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/26/2021] [Accepted: 12/03/2021] [Indexed: 11/01/2022]
Abstract
PURPOSE To review the use of molecular diagnostic techniques in the management of ocular infectious disease. DESIGN Retrospective review. METHODS A combination of literature review and personal recollections are used. RESULTS Although the broad term molecular diagnostics may encompass techniques to identify pathogens via protein or metabolomic signatures, this review concentrates on detection of pathogen nucleic acid as an indicator of infection. The introduction of the polymerase chain reaction (PCR) in 1985 opened a new era in analysis of nucleic acids. This technique was soon applied to the detection of potential pathogen DNA and RNA, including viruses, bacteria, and parasites in infectious eye disease. Advances in PCR have allowed class-specific diagnostics (ie, pan-bacterial and pan-fungal), quantitation of pathogen DNA, and multiplexed testing. The Human Genome Project in the early 2000s greatly accelerated development of DNA sequencers, ushering in the era of "Next Generation Sequencing" and permitting pathogen-agnostic methods for the detection of potential infectious agents. Most recently, new technologies such as nanopore sequencing have reduced both cost and equipment requirements for whole-genome sequencing; when coupled with real-time sequence analysis methods, these methods offer the promise of true, real-time, point-of-service ocular infectious disease diagnostics. CONCLUSIONS Molecular methods for pathogen detection have greatly advanced the diagnosis of ocular infectious disease. Further methodologic advances will have a direct impact on the management of these conditions.
Collapse
Affiliation(s)
- Russell N Van Gelder
- From the Departments of Ophthalmology, Biological Structure, and Laboratory Medicine and Pathology, and Roger and Angie Karalis Johnson Retina Center, University of Washington School of Medicine, Seattle, Washington, USA.
| |
Collapse
|
15
|
An N, Wang C, Dou X, Liu X, Wu J, Cheng Y. Comparison of 16S rDNA Amplicon Sequencing With the Culture Method for Diagnosing Causative Pathogens in Bacterial Corneal Infections. Transl Vis Sci Technol 2022; 11:29. [PMID: 35179557 PMCID: PMC8859490 DOI: 10.1167/tvst.11.2.29] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose The purpose of this study was to explore if 16S rDNA amplicon sequencing can improve the conventional diagnosis of causative pathogens for bacterial corneal infection. Methods Corneal scraping and conjunctiva and eyelid margin swab samples from infected eyes of patients diagnosed with "bacterial corneal infection" and conjunctiva and eyelid margin swab samples from a random eye of healthy participants were collected. Each swab was used for both aerobic and anaerobic cultures and 16S rDNA amplicon sequencing. The V3 to V4 region of the 16S rDNA was amplified using polymerase chain reaction (PCR) and sequenced on the Illumina HiSeq 2500 Sequencing Platform. Results The overall culture positivity rate for all 72 samples was 69% (72% in the bacterial keratitis group and 67% in the healthy control group), whereas 1719 operational taxonomic units in total were generated using 16S rDNA amplicon sequencing with each sample showing 123 to 337 different genera. Staphylococcus, Corynebacterium, Propionibacterium, and Micrococcus most frequently appeared in culture, whereas Streptococcus, Acinetobacter, and Lactobacillus were the most common genera, with large ratios in 16S rDNA amplicon sequencing. The causative pathogens detected by the two methods were inconsistent for most samples, except for several corneal samples. Conclusions We suggest that a combination of different techniques, such as clinical observation, microscopic analysis, culture, and next-generation sequencing techniques including 16S rDNA amplicon sequencing, should be used to comprehensively analyze pathogens in corneal and external ocular infections. Translational Relevance This paper uses a basic research methodology for studying the microbiome in ocular samples to help improve the diagnostic accuracy of corneal and external ocular infections.
Collapse
Affiliation(s)
- Na An
- Department of Ophthalmology, First Affiliated Hospital of Northwest University, Xi'an No.1 Hospital, Xi'an, China.,Shaanxi Key Laboratory of Ophthalmology, Shaanxi Institute of Ophthalmology, Shaanxi Provincial Clinical Research Center for Ophthalmic Diseases, Xi'an, China
| | - Changhao Wang
- School of Life Science, Northwest University, Xi'an, China
| | - Xiuhong Dou
- School of Life Science, Northwest University, Xi'an, China
| | - Xianning Liu
- Department of Ophthalmology, First Affiliated Hospital of Northwest University, Xi'an No.1 Hospital, Xi'an, China.,Shaanxi Key Laboratory of Ophthalmology, Shaanxi Institute of Ophthalmology, Shaanxi Provincial Clinical Research Center for Ophthalmic Diseases, Xi'an, China
| | - Jie Wu
- Department of Ophthalmology, First Affiliated Hospital of Northwest University, Xi'an No.1 Hospital, Xi'an, China
| | - Yan Cheng
- Department of Ophthalmology, First Affiliated Hospital of Northwest University, Xi'an No.1 Hospital, Xi'an, China
| |
Collapse
|
16
|
Ung L, Belanger NL, Chodosh J, Gilmore MS, Bispo PJ. Novel Molecular Barcoding for Rapid Pathogen Detection in Infectious Keratitis. OPHTHALMOLOGY SCIENCE 2021; 1:100066. [PMID: 36246949 PMCID: PMC9559883 DOI: 10.1016/j.xops.2021.100066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/14/2021] [Accepted: 09/20/2021] [Indexed: 11/18/2022]
Affiliation(s)
- Lawson Ung
- Department of Ophthalmology, Massachusetts Eye and Ear, and Infectious Disease Institute, Harvard Medical School, Boston, Massachusetts
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Nicole L. Belanger
- Department of Ophthalmology, Massachusetts Eye and Ear, and Infectious Disease Institute, Harvard Medical School, Boston, Massachusetts
| | - James Chodosh
- Department of Ophthalmology, Massachusetts Eye and Ear, and Infectious Disease Institute, Harvard Medical School, Boston, Massachusetts
| | - Michael S. Gilmore
- Department of Ophthalmology, Massachusetts Eye and Ear, and Infectious Disease Institute, Harvard Medical School, Boston, Massachusetts
| | - Paulo J.M. Bispo
- Department of Ophthalmology, Massachusetts Eye and Ear, and Infectious Disease Institute, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
17
|
Diagnostic armamentarium of infectious keratitis: A comprehensive review. Ocul Surf 2021; 23:27-39. [PMID: 34781020 PMCID: PMC8810150 DOI: 10.1016/j.jtos.2021.11.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/05/2021] [Accepted: 11/07/2021] [Indexed: 01/23/2023]
Abstract
Infectious keratitis (IK) represents the leading cause of corneal blindness worldwide, particularly in developing countries. A good outcome of IK is contingent upon timely and accurate diagnosis followed by appropriate interventions. Currently, IK is primarily diagnosed on clinical grounds supplemented by microbiological investigations such as microscopic examination with stains, and culture and sensitivity testing. Although this is the most widely accepted practice adopted in most regions, such an approach is challenged by several factors, including indistinguishable clinical features shared among different causative organisms, polymicrobial infection, long diagnostic turnaround time, and variably low culture positivity rate. In this review, we aim to provide a comprehensive overview of the current diagnostic armamentarium of IK, encompassing conventional microbiological investigations, molecular diagnostics (including polymerase chain reaction and mass spectrometry), and imaging modalities (including anterior segment optical coherence tomography and in vivo confocal microscopy). We also highlight the potential roles of emerging technologies such as next-generation sequencing, artificial intelligence-assisted platforms. and tele-medicine in shaping the future diagnostic landscape of IK.
Collapse
|
18
|
Clinical Characteristics and Outcomes of Fungal Keratitis in the United Kingdom 2011-2020: A 10-Year Study. J Fungi (Basel) 2021; 7:jof7110966. [PMID: 34829253 PMCID: PMC8624743 DOI: 10.3390/jof7110966] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 12/27/2022] Open
Abstract
Fungal keratitis (FK) is a serious ocular infection that often poses significant diagnostic and therapeutic dilemmas. This study aimed to examine the causes, clinical characteristics, outcomes, and prognostic factors of FK in the UK. All culture-positive and culture-negative presumed FK (with complete data) that presented to Queen’s Medical Centre, Nottingham, and the Queen Victoria Hospital, East Grinstead, between 2011 and 2020 were included. We included 117 patients (n = 117 eyes) with FK in this study. The mean age was 59.0 ± 19.6 years (range, 4–92 years) and 51.3% of patients were female. Fifty-three fungal isolates were identified from 52 (44.4%) culture-positive cases, with Candida spp. (33, 62.3%), Fusarium spp. (9, 17.0%), and Aspergillus spp. (5, 9.4%) being the most common organisms. Ocular surface disease (60, 51.3%), prior corneal surgery (44, 37.6%), and systemic immunosuppression (42, 35.9%) were the three most common risk factors. Hospitalisation for intensive treatment was required for 95 (81.2%) patients, with a duration of 18.9 ± 16.3 days. Sixty-six (56.4%) patients required additional surgical interventions for eradicating the infection. Emergency therapeutic/tectonic keratoplasty was performed in 29 (24.8%) cases, though 13 (44.8%) of them failed at final follow-up. The final corrected-distance-visual-acuity (CDVA) was 1.67 ± 1.08 logMAR. Multivariable logistic regression analyses demonstrated increased age, large infiltrate size (>3 mm), and poor presenting CDVA (<1.0 logMAR) as significant negative predictive factors for poor visual outcome (CDVA of <1.0 logMAR) and poor corneal healing (>60 days of healing time or occurrence of corneal perforation requiring emergency keratoplasty; all p < 0.05). In conclusion, FK represents a difficult-to-treat ocular infection that often results in poor visual outcomes, with a high need for surgical interventions. Innovative treatment strategies are urgently required to tackle this unmet need.
Collapse
|
19
|
Than T, Morettin CE, Harthan JS, Hartwick ATE, Huecker JB, Johnson SD, Migneco MK, Shorter E, Whiteside M, Olson CK, Alferez CS, van Zyl T, Rodic-Polic B, Storch GA, Gordon MO. Efficacy of a Single Administration of 5% Povidone-Iodine in the Treatment of Adenoviral Conjunctivitis. Am J Ophthalmol 2021; 231:28-38. [PMID: 34102153 DOI: 10.1016/j.ajo.2021.05.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/20/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
PURPOSE To evaluate the safety and efficacy of a single, in-office administration of 5% povidone-iodine (PVP-I) compared to artificial tears (AT) for adenoviral conjunctivitis (Ad-Cs). DESIGN Double-masked pilot randomized trial. METHODS Patients presenting with presumed adenoviral conjunctivitis were screened at 9 U.S. clinics. INCLUSION CRITERIA ≥18 years of age, symptoms ≤4 days, and a positive AdenoPlus test. EXCLUSION CRITERIA thyroid disease, iodine allergy, recent ocular surgery, and ocular findings inconsistent with early-stage Ad-Cs. Randomization was to a single administration of 5% PVP-I or AT in 1 eye and examinations on days 1-2, 4, 7, 14, and 21 with conjunctival swabs taken at each visit for quantitative polymerase chain reaction. Primary outcome was percent reduction from peak viral load. Secondary outcomes were improvement in clinical signs and symptoms. RESULTS Of 56 patients randomized, 28 had detectable viral titers at baseline. Day 4 posttreatment, viral titers in the 5% PVP-I and AT groups were 2.5% ± 2.7% and 14.4% ± 10.5% of peak, respectively (P = .020). Severity of participant-reported tearing, lid swelling, and redness as well as clinician-graded mucoid discharge, bulbar redness, and bulbar edema were lower in the 5% PVP-I group than AT group on day 4 (P < .05). After day 4, viral titers and severity of signs and symptoms decreased markedly in both groups and no differences between groups were detected. CONCLUSIONS Pilot data suggest a single, in-office administration of 5% PVP-I could reduce viral load and hasten improvement of clinical signs and symptoms in patients with Ad-Cs.
Collapse
|
20
|
Ting DSJ, Cairns J, Gopal BP, Ho CS, Krstic L, Elsahn A, Lister M, Said DG, Dua HS. Risk Factors, Clinical Outcomes, and Prognostic Factors of Bacterial Keratitis: The Nottingham Infectious Keratitis Study. Front Med (Lausanne) 2021; 8:715118. [PMID: 34458289 PMCID: PMC8385317 DOI: 10.3389/fmed.2021.715118] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/12/2021] [Indexed: 01/20/2023] Open
Abstract
Background/Aim: To examine the risk factors, clinical characteristics, outcomes, and prognostic factors of bacterial keratitis (BK) in Nottingham, UK. Methods: This was a retrospective study of patients who presented to the Queen's Medical Centre, Nottingham, with suspected BK during 2015–2019. Relevant data, including the demographic factors, risk factors, clinical outcomes, and potential prognostic factors, were analysed. Results: A total of 283 patients (n = 283 eyes) were included; mean age was 54.4 ± 21.0 years and 50.9% were male. Of 283 cases, 128 (45.2%) cases were culture-positive. Relevant risk factors were identified in 96.5% patients, with ocular surface diseases (47.3%), contact lens wear (35.3%) and systemic immunosuppression (18.4%) being the most common factors. Contact lens wear was most commonly associated with P. aeruginosa whereas Staphylococci spp. were most commonly implicated in non-contact lens-related BK cases (p = 0.017). At presentation, culture-positive cases were associated with older age, worse presenting corrected-distance-visual-acuity (CDVA), use of topical corticosteroids, larger epithelial defect and infiltrate, central location and hypopyon (all p < 0.01), when compared to culture-negative cases. Hospitalisation was required in 57.2% patients, with a mean length of stay of 8.0 ± 8.3 days. Surgical intervention was required in 16.3% patients. Significant complications such as threatened/actual corneal perforation (8.8%), loss of perception of light vision (3.9%), and evisceration/enucleation (1.4%) were noted. Poor visual outcome (final corrected-distance-visual-acuity of <0.6 logMAR) and delayed corneal healing (>30 days from initial presentation) were significantly affected by age >50 years, infiltrate size >3 mm, and reduced presenting vision (all p < 0.05). Conclusion: BK represents a significant ocular morbidity in the UK, with ocular surface diseases, contact lens wear, and systemic immunosuppression being the main risk factors. Older age, large infiltrate, and poor presenting vision were predictive of poor visual outcome and delayed corneal healing, highlighting the importance of prevention and early intervention for BK.
Collapse
Affiliation(s)
- Darren Shu Jeng Ting
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom
| | - Jessica Cairns
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Bhavesh P Gopal
- Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom
| | - Charlotte Shan Ho
- Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom
| | - Lazar Krstic
- Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom
| | - Ahmad Elsahn
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom
| | - Michelle Lister
- Department of Microbiology, Queen's Medical Centre, Nottingham, United Kingdom
| | - Dalia G Said
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom.,Research Institute of Ophthalmology, Cairo, Egypt
| | - Harminder S Dua
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom
| |
Collapse
|
21
|
Ung L, Chodosh J. Foundational concepts in the biology of bacterial keratitis. Exp Eye Res 2021; 209:108647. [PMID: 34097906 PMCID: PMC8595513 DOI: 10.1016/j.exer.2021.108647] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/28/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022]
Abstract
Bacterial infections of the cornea, or bacterial keratitis (BK), are notorious for causing rapidly fulminant disease and permanent vision loss, even among treated patients. In the last sixty years, dramatic upward trajectories in the frequency of BK have been observed internationally, driven in large part by the commercialization of hydrogel contact lenses in the late 1960s. Despite this worsening burden of disease, current evidence-based therapies for BK - including broad-spectrum topical antibiotics and, if indicated, topical corticosteroids - fail to salvage vision in a substantial proportion of affected patients. Amid growing concerns of rapidly diminishing antibiotic utility, there has been renewed interest in urgently needed novel treatments that may improve clinical outcomes on an individual and public health level. Bridging the translational gap in the care of BK requires the identification of new therapeutic targets and rational treatment design, but neither of these aims can be achieved without understanding the complex biological processes that determine how bacterial corneal infections arise, progress, and resolve. In this chapter, we synthesize the current wealth of human and animal experimental data that now inform our understanding of basic BK pathophysiology, in context with modern concepts in ocular immunology and microbiology. By identifying the key molecular determinants of clinical disease, we explore how novel treatments can be developed and translated into routine patient care.
Collapse
Affiliation(s)
- Lawson Ung
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - James Chodosh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
22
|
Ting DSJ, Ho CS, Deshmukh R, Said DG, Dua HS. Infectious keratitis: an update on epidemiology, causative microorganisms, risk factors, and antimicrobial resistance. Eye (Lond) 2021; 35:1084-1101. [PMID: 33414529 PMCID: PMC8102486 DOI: 10.1038/s41433-020-01339-3] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/22/2020] [Accepted: 11/24/2020] [Indexed: 01/30/2023] Open
Abstract
Corneal opacity is the 5th leading cause of blindness and visual impairment globally, affecting ~6 million of the world population. In addition, it is responsible for 1.5-2.0 million new cases of monocular blindness per year, highlighting an ongoing uncurbed burden on human health. Among all aetiologies such as infection, trauma, inflammation, degeneration and nutritional deficiency, infectious keratitis (IK) represents the leading cause of corneal blindness in both developed and developing countries, with an estimated incidence ranging from 2.5 to 799 per 100,000 population-year. IK can be caused by a wide range of microorganisms, including bacteria, fungi, virus, parasites and polymicrobial infection. Subject to the geographical and temporal variations, bacteria and fungi have been shown to be the most common causative microorganisms for corneal infection. Although viral and Acanthamoeba keratitis are less common, they represent important causes for corneal blindness in the developed countries. Contact lens wear, trauma, ocular surface diseases, lid diseases, and post-ocular surgery have been shown to be the major risk factors for IK. Broad-spectrum topical antimicrobial treatment is the current mainstay of treatment for IK, though its effectiveness is being challenged by the emergence of antimicrobial resistance, including multidrug resistance, in some parts of the world. In this review, we aim to provide an updated review on IK, encompassing the epidemiology, causative microorganisms, major risk factors and the impact of antimicrobial resistance.
Collapse
Affiliation(s)
- Darren Shu Jeng Ting
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK
- Department of Ophthalmology, Queen's Medical Centre, Nottingham, UK
| | | | - Rashmi Deshmukh
- Department of Ophthalmology, Queen's Medical Centre, Nottingham, UK
| | - Dalia G Said
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK
- Department of Ophthalmology, Queen's Medical Centre, Nottingham, UK
| | - Harminder S Dua
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK.
- Department of Ophthalmology, Queen's Medical Centre, Nottingham, UK.
| |
Collapse
|
23
|
Ting DSJ, Ho CS, Cairns J, Elsahn A, Al-Aqaba M, Boswell T, Said DG, Dua HS. 12-year analysis of incidence, microbiological profiles and in vitro antimicrobial susceptibility of infectious keratitis: the Nottingham Infectious Keratitis Study. Br J Ophthalmol 2021; 105:328-333. [PMID: 32580955 PMCID: PMC7907586 DOI: 10.1136/bjophthalmol-2020-316128] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/01/2020] [Accepted: 04/27/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND/AIMS To examine the incidence, causative microorganisms and in vitro antimicrobial susceptibility and resistance profiles of infectious keratitis (IK) in Nottingham, UK. METHODS A retrospective study of all patients who were diagnosed with IK and underwent corneal scraping between July 2007 and October 2019 (a 12-year period) at a UK tertiary referral centre. Relevant data, including demographic factors, microbiological profiles and in vitro antibiotic susceptibility of IK, were analysed. RESULTS The estimated incidence of IK was 34.7 per 100 000 people/year. Of the 1333 corneal scrapes, 502 (37.7%) were culture-positive and 572 causative microorganisms were identified. Sixty (4.5%) cases were of polymicrobial origin (caused by ≥2 different microorganisms). Gram-positive bacteria (308, 53.8%) were most commonly isolated, followed by Gram-negative bacteria (223, 39.0%), acanthamoeba (24, 4.2%) and fungi (17, 3.0%). Pseudomonas aeruginosa (135, 23.6%) was the single most common organism isolated. There was a significant increase in Moraxella spp (p<0.001) and significant decrease in Klebsiella spp (p=0.004) over time. The in vitro susceptibilities of Gram-positive and Gram-negative bacteria to cephalosporin, fluoroquinolone and aminoglycoside were 100.0% and 81.3%, 91.9% and 98.1%, and 95.2% and 98.3%, respectively. An increase in resistance against penicillin was observed in Gram-positive (from 3.5% to 12.7%; p=0.005) and Gram-negative bacteria (from 52.6% to 65.4%; p=0.22). CONCLUSION IK represents a relatively common and persistent burden in the UK and the reported incidence is likely underestimated. Current broad-spectrum antimicrobial treatment provides a good coverage for IK, although challenged by some level of antimicrobial resistance and polymicrobial infection.
Collapse
Affiliation(s)
| | | | - Jessica Cairns
- School of Medicine, University of Nottingham, Nottingham, UK
| | - Ahmad Elsahn
- Academic Ophthalmology, University of Nottingham, Nottingham, UK
| | | | - Tim Boswell
- Department of Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Dalia G Said
- Academic Ophthalmology, University of Nottingham, Nottingham, UK
- Ophthalmology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Harminder Singh Dua
- Division of Ophthalmology and Visual Sciences, University of Nottingham, Nottingham, UK
| |
Collapse
|
24
|
Lalitha P, Prajna NV, Sikha M, Gunasekaran R, Hinterwirth A, Worden L, Chen C, Zhong L, Liu Z, Lietman TM, Seitzman GD, Doan T. Evaluation of Metagenomic Deep Sequencing as a Diagnostic Test for Infectious Keratitis. Ophthalmology 2021; 128:473-475. [PMID: 32682834 PMCID: PMC7856230 DOI: 10.1016/j.ophtha.2020.07.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/13/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023] Open
Affiliation(s)
| | | | - Misra Sikha
- Aravind Eye Hospital, Madurai, Tamil Nadu, India
| | | | - Armin Hinterwirth
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Lee Worden
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Cindi Chen
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Lina Zhong
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Zijun Liu
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Thomas M Lietman
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California; Department of Ophthalmology, University of California, San Francisco, California
| | - Gerami D Seitzman
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California; Department of Ophthalmology, University of California, San Francisco, California.
| | - Thuy Doan
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California; Department of Ophthalmology, University of California, San Francisco, California
| |
Collapse
|
25
|
Low L, Fuentes-Utrilla P, Hodson J, O’Neil JD, Rossiter AE, Begum G, Suleiman K, Murray PI, Wallace GR, Loman NJ, Rauz S. Evaluation of full-length nanopore 16S sequencing for detection of pathogens in microbial keratitis. PeerJ 2021; 9:e10778. [PMID: 33628638 PMCID: PMC7891086 DOI: 10.7717/peerj.10778] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/22/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Microbial keratitis is a leading cause of preventable blindness worldwide. Conventional sampling and culture techniques are time-consuming, with over 40% of cases being culture-negative. Nanopore sequencing technology is portable and capable of generating long sequencing reads in real-time. The aim of this study is to evaluate the potential of nanopore sequencing directly from clinical samples for the diagnosis of bacterial microbial keratitis. METHODS Using full-length 16S rRNA amplicon sequences from a defined mock microbial community, we evaluated and benchmarked our bioinformatics analysis pipeline for taxonomic assignment on three different 16S rRNA databases (NCBI 16S RefSeq, RDP and SILVA) with clustering at 97%, 99% and 100% similarities. Next, we optimised the sample collection using an ex vivo porcine model of microbial keratitis to compare DNA recovery rates of 12 different collection methods: 21-gauge needle, PTFE membrane (4 mm and 6 mm), Isohelix™ SK-2S, Sugi® Eyespear, Cotton, Rayon, Dryswab™, Hydraflock®, Albumin-coated, Purflock®, Purfoam and Polyester swabs. As a proof-of-concept study, we then used the sampling technique that provided the highest DNA recovery, along with the optimised bioinformatics pipeline, to prospectively collected samples from patients with suspected microbial keratitis. The resulting nanopore sequencing results were then compared to standard microbiology culture methods. RESULTS We found that applying alignment filtering to nanopore sequencing reads and aligning to the NCBI 16S RefSeq database at 100% similarity provided the most accurate bacterial taxa assignment. DNA concentration recovery rates differed significantly between the collection methods (p < 0.001), with the Sugi® Eyespear swab providing the highest mean rank of DNA concentration. Then, applying the optimised collection method and bioinformatics pipeline directly to samples from two patients with suspected microbial keratitis, sequencing results from Patient A were in agreement with culture results, whilst Patient B, with negative culture results and previous antibiotic use, showed agreement between nanopore and Illumina Miseq sequencing results. CONCLUSION We have optimised collection methods and demonstrated a novel workflow for identification of bacterial microbial keratitis using full-length 16S nanopore sequencing.
Collapse
Affiliation(s)
- Liying Low
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals National Health Service (NHS) Trust, Birmingham, West Midlands, UK
| | - Pablo Fuentes-Utrilla
- MicrobesNG/School of Biosciences, University of Birmingham, Birmingham, West Midlands, UK
| | - James Hodson
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, West Midlands, UK
| | - John D. O’Neil
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
| | - Amanda E. Rossiter
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, West Midlands, UK
| | - Ghazala Begum
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
- National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Birmingham, UK
| | - Kusy Suleiman
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
| | - Philip I. Murray
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals National Health Service (NHS) Trust, Birmingham, West Midlands, UK
| | - Graham R. Wallace
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals National Health Service (NHS) Trust, Birmingham, West Midlands, UK
| | - Nicholas J. Loman
- MicrobesNG/School of Biosciences, University of Birmingham, Birmingham, West Midlands, UK
| | - Saaeha Rauz
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals National Health Service (NHS) Trust, Birmingham, West Midlands, UK
| | | |
Collapse
|
26
|
Doan T, Sahoo MK, Ruder K, Huang C, Zhong L, Chen C, Hinterwirth A, Lin C, Gonzales JA, Pinsky BA, Acharya NR. Comprehensive pathogen detection for ocular infections. J Clin Virol 2021; 136:104759. [PMID: 33609933 DOI: 10.1016/j.jcv.2021.104759] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND Molecular diagnostics such as pathogen-directed PCRs have transformed testing for ocular infections since the late 1990s. Although these assays remain important diagnostic tools for samples with low biomass, the lack of diagnostic range motivates alternative molecular approaches for ocular infections. The aim of this study was to determine the performance of a high-throughput RNA sequencing approach, RNA-seq, to detect infectious agents in ocular samples from patients with presumed ocular infections. METHODS We compared the performance of RNA-seq to pathogen-directed PCRs using remnant nucleic acids from 41 aqueous or vitreous samples of patients with presumed ocular infections. Pathogen-directed PCRs were performed at the CLIA-certified Stanford Clinical Virology Laboratory. RNA-seq was performed in a masked manner at the Proctor Foundation at the University of California San Francisco. Percent positive and negative agreement between the two testing approaches were calculated. Discordant results were subjected to orthogonal testing. RESULTS The positive percent agreement between RNA-seq and pathogen-directed PCRs was 100% (95% confidence interval (CI): 78.5%-100%). The negative percent agreement was 92.6% (95% CI: 76.6%-97.9%). RNA-seq identified pathogens not on the differential diagnosis for 9.7% (4/41) of the samples. Two pathogens solely identified with RNA-seq were confirmed with orthogonal testing. CONCLUSIONS RNA-seq can accurately identify common and rare pathogens in aqueous and vitreous samples of patients with presumed ocular infections. Such an unbiased approach to testing has the potential to improve diagnostics although practical clinical utility warrants additional studies.
Collapse
Affiliation(s)
- Thuy Doan
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA; Department of Ophthalmology, University of California, San Francisco, CA, USA.
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kevin Ruder
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lina Zhong
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA
| | - Cindi Chen
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA
| | - Armin Hinterwirth
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA
| | - Charles Lin
- Byers Eye Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - John A Gonzales
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA; Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nisha R Acharya
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA; Department of Ophthalmology, University of California, San Francisco, CA, USA
| |
Collapse
|
27
|
Ting DSJ, Ho CS, Cairns J, Gopal BP, Elsahn A, Al-Aqaba M, Boswell T, Said DG, Dua HS. Seasonal patterns of incidence, demographic factors and microbiological profiles of infectious keratitis: the Nottingham Infectious Keratitis Study. Eye (Lond) 2020; 35:2543-2549. [PMID: 33184491 DOI: 10.1038/s41433-020-01272-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 10/22/2020] [Accepted: 10/28/2020] [Indexed: 01/08/2023] Open
Abstract
PURPOSE The purpose of this study is to examine the seasonal patterns of incidence, demographic factors and microbiological profiles of infectious keratitis (IK) in Nottingham, UK. METHODS A retrospective study of all patients who were diagnosed with IK and underwent corneal scraping during 2008-2019 at a UK tertiary referral centre. Seasonal patterns of incidence (in per 100,000 population-year), demographic factors, culture positivity rate and microbiological profiles of IK were analysed. RESULTS A total of 1272 IK cases were included. The overall incidence of IK was highest during summer (37.7, 95% confidence interval (CI): 31.3-44.1), followed by autumn (36.7, 95% CI: 31.0-42.4), winter (36.4, 95% CI: 32.1-40.8) and spring (30.6, 95% CI: 26.8-34.3), though not statistically significant (p = 0.14). The incidence of IK during summer increased significantly over the 12 years of study (r = 0.58, p = 0.049), but the incidence of IK in other seasons remained relatively stable throughout the study period. Significant seasonal variations were observed in patients' age (younger age in summer) and causative organisms, including Pseudomonas aeruginosa (32.9% in summer vs. 14.8% in winter; p < 0.001) and gram-positive bacilli (16.1% in summer vs. 4.7% in winter; p = 0.014). CONCLUSION The incidence of IK in Nottingham was similar among four seasons. No temporal trend in the annual incidence of IK was observed, as reported previously, but there was a significant yearly increase in the incidence of IK during summer in Nottingham over the past decade. The association of younger age, P. aeruginosa and gram-positive bacilli infection with summer was likely attributed to contact lens wear, increased outdoor/water activity and warmer temperature conducive for microbial growth.
Collapse
Affiliation(s)
- Darren Shu Jeng Ting
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK.,Department of Ophthalmology, Queen's Medical Centre, Nottingham, UK
| | | | - Jessica Cairns
- School of Medicine, University of Nottingham, Nottingham, UK
| | - Bhavesh P Gopal
- Department of Ophthalmology, Queen's Medical Centre, Nottingham, UK
| | - Ahmad Elsahn
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK.,Department of Ophthalmology, Queen's Medical Centre, Nottingham, UK
| | - Mouhamed Al-Aqaba
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK.,Department of Ophthalmology, Queen's Medical Centre, Nottingham, UK
| | - Tim Boswell
- Department of Microbiology, Nottingham University Hospital, Nottingham, UK
| | - Dalia G Said
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK.,Department of Ophthalmology, Queen's Medical Centre, Nottingham, UK
| | - Harminder S Dua
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK. .,Department of Ophthalmology, Queen's Medical Centre, Nottingham, UK.
| |
Collapse
|
28
|
Abstract
Purpose: to summarize the origin and very recent history of the use of metagenomic sequencing for the diagnosis of infectious uveitis, convey the technique as described by one of the primary institutions experimenting with the technology, and present recent successful applications of the technology as well as potential advantages and pitfalls compared to other current diagnostic tools.Methods: review of peer-reviewed literature concerning metagenomic sequencing for the diagnosis of infectious uveitis.Conclusion: compared to existing diagnostic methods, metagenomic deep sequencing is a sensitive, unbiased, and comprehensive technique with great potential for diagnosing the causative pathogens of cases of infectious uveitis. However, many issues remain to be addressed in the process of developing this technology, including but not limited to the potentially overwhelming amount of information generated, definition of diagnostic thresholds, demonstration of validity, contamination, and cost.
Collapse
Affiliation(s)
- Lianna Valdes
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School , Boston, MA, USA
| | - Paulo Bispo
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School , Boston, MA, USA
| | - Lucia Sobrin
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School , Boston, MA, USA
| |
Collapse
|
29
|
Kirubakaran R, ArulJothi KN, Revathi S, Shameem N, Parray JA. Emerging priorities for microbial metagenome research. BIORESOURCE TECHNOLOGY REPORTS 2020; 11:100485. [PMID: 32835181 PMCID: PMC7319936 DOI: 10.1016/j.biteb.2020.100485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022]
Abstract
Overwhelming anthropogenic activities lead to deterioration of natural resources and the environment. The microorganisms are considered desirable, due to their suitability for easy genetic manipulation and handling. With the aid of modern biotechnological techniques, the culturable microorganisms have been widely exploited for the benefit of mankind. Metagenomics, a powerful tool to access the abundant biodiversity of the environmental samples including the unculturable microbes, to determine microbial diversity and population structure, their ecological roles and expose novel genes of interest. This review focuses on the microbial adaptations to the adverse environmental conditions, metagenomic techniques employed towards microbial biotechnology. Metagenomic approach helps to understand microbial ecology and to identify useful microbial derivatives like antibiotics, toxins, and enzymes with diverse and enhanced function. It also summarizes the application of metagenomics in clinical diagnosis, improving microbial ecology, therapeutics, xenobiotic degradation and impact on agricultural crops.
Collapse
Affiliation(s)
| | - K N ArulJothi
- Department of Genetic Engineering, SRM Institute of Science and Technology, Chennai, India
- Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | | | - Nowsheen Shameem
- Department of Environmental Science, Cluster University Srinagar, J&K, India
| | - Javid A Parray
- Department of Environmental Science, Govt SAM Degree College Budgam, J&K, India
| |
Collapse
|