ArticleInvestigative ophthalmology & visual science2018
Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing.
Article in Investigative ophthalmology & visual science, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 70 citations in OpenAlex.
- Circulating microbiome DNA features and its effect on predicting clinicopathological characteristics of patients with colorectal cancer.Journal of translational medicine · 2025Article
- HPD-Kit: a comprehensive toolkit for pathogen detection and analysis.Frontiers in cellular and infection microbiology · 2025Article
- Preliminary exploration of metagenomic sequencing for pathogenic identification in infectious uveitis.Journal of ophthalmic inflammation and infection · 2024Article
- Clinical and metagenomic characteristics of lymphadenopathy related to fever of unknown origin in children.Pediatric research · 2024Article
- Novel metagenomics analysis of stony coral tissue loss disease.G3 (Bethesda, Md.) · 2024Article
- Unveiling challenging corneal infections: a comprehensive etiological diagnosis through metagenomic next-generation sequencing (mNGS) of corneal tissue samples.International ophthalmology · 2024Article
- Novel metagenomics analysis of stony coral tissue loss disease.bioRxiv : the preprint server for biology · 2024Article
- Herpes simplex keratitis: A brief clinical overview.World journal of virology · 2024Review
- Recent Advances in Diagnosis and Treatment Approaches in Fungal Keratitis: A Narrative Review.Microorganisms · 2024Review
- Application of metagenomic next-generation sequencing in the diagnosis of infectious diseases.Frontiers in cellular and infection microbiology · 2024Review
- Article
- Diagnosis ofDiagnostics (Basel, Switzerland) · 2023Review
- Major data analysis errors invalidate cancer microbiome findings.bioRxiv : the preprint server for biology · 2023Article
- Urgent unmet needs in the care of bacterial keratitis: An evidence-based synthesis.The ocular surface · 2023Article
- Metagenome analysis using the Kraken software suite.Nature protocols · 2022Review
- Metagenomic Sequencing for the Diagnosis ofInternational journal of molecular sciences · 2022Article
- Diagnostic methods for the etiological assessment of infectious corneal pathology (Review).Experimental and therapeutic medicine · 2022Review
- Advances in the microbiological diagnosis of herpetic retinitis.Frontiers in ophthalmology · 2022Review
- Diagnostic armamentarium of infectious keratitis: A comprehensive review.The ocular surface · 2022Review
- Microbiological Profiles of Ocular Fungal Infection at an Ophthalmic Referral Hospital in Southern China: A Ten-Year Retrospective Study.Infection and drug resistance · 2022Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Purpose: We test the ability of next-generation sequencing, combined with computational analysis, to identify a range of organisms causing infectious keratitis. Methods: This retrospective study evaluated 16 cases of infectious keratitis and four control corneas in formalin-fixed tissues from the pathology laboratory. Infectious cases also were analyzed in the microbiology laboratory using culture, polymerase chain reaction, and direct staining. Classified sequence reads were analyzed with two different metagenomics classification engines, Kraken and Centrifuge, and visualized using the Pavian software tool. Results: Sequencing generated 20 to 46 million reads per sample. On average, 96% of the reads were classified as human, 0.3% corresponded to known vectors or contaminant sequences, 1.7% represented microbial sequences, and 2.4% could not be classified. The two computational strategies successfully identified the fungal, bacterial, and amoebal pathogens in most patients, including all four bacterial and mycobacterial cases, five of six fungal cases, three of three Acanthamoeba cases, and one of three herpetic keratitis cases. In several cases, additional potential pathogens also were identified. In one case with cytomegalovirus identified by Kraken and Centrifuge, the virus was confirmed by direct testing, while two where Staphylococcus aureus or cytomegalovirus were identified by Centrifuge but not Kraken could not be confirmed. Confirmation was not attempted for an additional three potential pathogens identified by Kraken and 11 identified by Centrifuge. Conclusions: Next generation sequencing combined with computational analysis can identify a wide range of pathogens in formalin-fixed corneal specimens, with potential applications in clinical diagnostics and research.
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Registered trials
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