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Buddle S, Forrest L, Akinsuyi N, Martin Bernal LM, Brooks T, Venturini C, Miller C, Brown JR, Storey N, Atkinson L, Best T, Roy S, Goldsworthy S, Castellano S, Simmonds P, Harvala H, Golubchik T, Williams R, Breuer J, Morfopoulou S, Torres Montaguth OE. Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses. Genome Med 2024; 16:111. [PMID: 39252069 PMCID: PMC11382446 DOI: 10.1186/s13073-024-01380-x] [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: 04/16/2024] [Accepted: 08/30/2024] [Indexed: 09/11/2024] Open
Abstract
BACKGROUND Metagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, high sequencing depth requirements, long turnaround times, and limited sensitivity hinder broader adoption. We investigated whether we could overcome these limitations using protocols based on untargeted sequencing with Oxford Nanopore Technologies (ONT), which offers real-time data acquisition and analysis, or a targeted panel approach, which allows the selective sequencing of known pathogens and could improve sensitivity. METHODS We evaluated detection of viruses with readily available untargeted metagenomic workflows using Illumina and ONT, and an Illumina-based enrichment approach using the Twist Bioscience Comprehensive Viral Research Panel (CVRP), which targets 3153 viruses. We tested samples consisting of a dilution series of a six-virus mock community in a human DNA/RNA background, designed to resemble clinical specimens with low microbial abundance and high host content. Protocols were designed to retain the host transcriptome, since this could help confirm the absence of infectious agents. We further compared the performance of commonly used taxonomic classifiers. RESULTS Capture with the Twist CVRP increased sensitivity by at least 10-100-fold over untargeted sequencing, making it suitable for the detection of low viral loads (60 genome copies per ml (gc/ml)), but additional methods may be needed in a diagnostic setting to detect untargeted organisms. While untargeted ONT had good sensitivity at high viral loads (60,000 gc/ml), at lower viral loads (600-6000 gc/ml), longer and more costly sequencing runs would be required to achieve sensitivities comparable to the untargeted Illumina protocol. Untargeted ONT provided better specificity than untargeted Illumina sequencing. However, the application of robust thresholds standardized results between taxonomic classifiers. Host gene expression analysis is optimal with untargeted Illumina sequencing but possible with both the CVRP and ONT. CONCLUSIONS Metagenomics has the potential to become standard-of-care in diagnostics and is a powerful tool for the discovery of emerging pathogens. Untargeted Illumina and ONT metagenomics and capture with the Twist CVRP have different advantages with respect to sensitivity, specificity, turnaround time and cost, and the optimal method will depend on the clinical context.
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Affiliation(s)
- Sarah Buddle
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Leysa Forrest
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Naomi Akinsuyi
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Luz Marina Martin Bernal
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Tony Brooks
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Cristina Venturini
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Charles Miller
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Julianne R Brown
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Nathaniel Storey
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Laura Atkinson
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Timothy Best
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Sunando Roy
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sian Goldsworthy
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sergi Castellano
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Heli Harvala
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Division of Infection and Immunity, University College London, London, UK
- Microbiology Services, NHS Blood and Transplant, Colindale, UK
| | - Tanya Golubchik
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Sydney Infectious Diseases Institute, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Rachel Williams
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Judith Breuer
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK.
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
| | - Sofia Morfopoulou
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK.
- Section for Paediatrics, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK.
| | - Oscar Enrique Torres Montaguth
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK.
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Low L, Rauz S, Ting DSJ. Molecular Sequencing and Biomarkers in Acute Infectious Conjunctivitis. JAMA Ophthalmol 2024; 142:872-873. [PMID: 39145964 DOI: 10.1001/jamaophthalmol.2024.3091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Affiliation(s)
- Liying Low
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham NHS Trust, Birmingham, United Kingdom
| | - Saaeha Rauz
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham NHS Trust, Birmingham, United Kingdom
| | - Darren S J Ting
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham NHS Trust, Birmingham, United Kingdom
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3
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Liu Y, Ma Y. Clinical applications of metagenomics next-generation sequencing in infectious diseases. J Zhejiang Univ Sci B 2024; 25:471-484. [PMID: 38910493 PMCID: PMC11199093 DOI: 10.1631/jzus.b2300029] [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: 01/09/2023] [Accepted: 06/06/2023] [Indexed: 05/23/2024]
Abstract
Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.
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Affiliation(s)
- Ying Liu
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Yongjun Ma
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China.
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4
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Lee J, Jeong H, Kang HG, Park J, Choi EY, Lee CS, Byeon SH, Kim M. Rapid Pathogen Detection in Infectious Uveitis Using Nanopore Metagenomic Next-Generation Sequencing: A Preliminary Study. Ocul Immunol Inflamm 2024; 32:463-469. [PMID: 36758246 DOI: 10.1080/09273948.2023.2173243] [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: 05/04/2022] [Revised: 12/09/2022] [Accepted: 01/22/2023] [Indexed: 02/11/2023]
Abstract
PURPOSE We establish an accurate and rapid diagnostic method for pathogen detection in infectious uveitis using nanopore metagenomic next-generation sequencing (NGS). METHODS In eight patients with suspected infectious uveitis, we prospectively compared the accuracy and time taken for pathogen identification between conventional diagnostic methods, such as cultures and PCR, and nanopore metagenomic NGS. RESULTS All causative pathogens were identified using nanopore sequencing, while only five of the eight patients were confirmed positive for a specific pathogen using conventional methods. The overall sample-to-answer turnaround time of nanopore sequencing was much shorter than that of conventional methods in the bacterial and fungal infection (mean, 17 h vs. 4d, respectively; P = .028). The pathogens could be detected even when the quantity or quality of DNA was not optimal. CONCLUSION Nanopore metagenomic NGS is a promising diagnostic tool that can rapidly and accurately identify the causative pathogen in infectious uveitis.
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Affiliation(s)
- Junwon Lee
- Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Han Jeong
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun Goo Kang
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Jinkyu Park
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Young Choi
- Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Christopher Seungkyu Lee
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Suk Ho Byeon
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Min Kim
- Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
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Lao HY, Wong LLY, Hui Y, Ng TTL, Chan CTM, Lo HWH, Yau MCY, Leung ECM, Wong RCW, Ho AYM, Yip KT, Lam JYW, Chow VCY, Luk KS, Que TL, Chow FWN, Siu GKH. The clinical utility of Nanopore 16S rRNA gene sequencing for direct bacterial identification in normally sterile body fluids. Front Microbiol 2024; 14:1324494. [PMID: 38264489 PMCID: PMC10803466 DOI: 10.3389/fmicb.2023.1324494] [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: 10/19/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024] Open
Abstract
The prolonged incubation period of traditional culture methods leads to a delay in diagnosing invasive infections. Nanopore 16S rRNA gene sequencing (Nanopore 16S) offers a potential rapid diagnostic approach for directly identifying bacteria in infected body fluids. To evaluate the clinical utility of Nanopore 16S, we conducted a study involving the collection and sequencing of 128 monomicrobial samples, 65 polymicrobial samples, and 20 culture-negative body fluids. To minimize classification bias, taxonomic classification was performed using 3 analysis pipelines: Epi2me, Emu, and NanoCLUST. The result was compared to the culture references. The limit of detection of Nanopore 16S was also determined using simulated bacteremic blood samples. Among the three classifiers, Emu demonstrated the highest concordance with the culture results. It correctly identified the taxon of 125 (97.7%) of the 128 monomicrobial samples, compared to 109 (85.2%) for Epi2me and 102 (79.7%) for NanoCLUST. For the 230 cultured species in the 65 polymicrobial samples, Emu correctly identified 188 (81.7%) cultured species, compared to 174 (75.7%) for Epi2me and 125 (54.3%) for NanoCLUST. Through ROC analysis on the monomicrobial samples, we determined a threshold of relative abundance at 0.058 for distinguishing potential pathogens from background in Nanopore 16S. Applying this threshold resulted in the identification of 107 (83.6%), 117 (91.4%), and 114 (91.2%) correctly detected samples for Epi2me, Emu, and NanoCLUST, respectively, in the monomicrobial samples. Nanopore 16S coupled with Epi2me could provide preliminary results within 6 h. However, the ROC analysis of polymicrobial samples exhibited a random-like performance, making it difficult to establish a threshold. The overall limit of detection for Nanopore 16S was found to be about 90 CFU/ml.
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Affiliation(s)
- Hiu-Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Lily Lok-Yee Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Yan Hui
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Hazel Wing-Hei Lo
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Miranda Chong-Yee Yau
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong SAR, China
| | - Eddie Chi-Man Leung
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong SAR, China
| | - River Chun-Wai Wong
- Department of Microbiology, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Alex Yat-Man Ho
- Department of Pathology, Princess Margaret Hospital, Kowloon, Hong Kong SAR, China
| | - Kam-Tong Yip
- Department of Clinical Pathology, Tuen Mun Hospital, Tuen Mun, Hong Kong SAR, China
| | - Jimmy Yiu-Wing Lam
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong SAR, China
| | - Viola Chi-Ying Chow
- Department of Microbiology, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Kristine Shik Luk
- Department of Pathology, Princess Margaret Hospital, Kowloon, Hong Kong SAR, China
| | - Tak-Lun Que
- Department of Clinical Pathology, Tuen Mun Hospital, Tuen Mun, Hong Kong SAR, China
| | - Franklin Wang Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
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6
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Zheng M, Kang Y, Shen Y, Xu Y, Xu F, Chen Y. Genomic Features and Comparative Genomic Analysis of Streptococcus sp. v1. nov., Isolated from an Endophthalmitis Patient. Curr Microbiol 2023; 80:378. [PMID: 37861738 DOI: 10.1007/s00284-023-03460-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/28/2023] [Indexed: 10/21/2023]
Abstract
Endophthalmitis is an acute inflammatory intraocular condition that can cause permanent vision loss. The treatment strategy and visual outcome partly depend on the identification of the agents of pathogens. In this study, metagenomic sequencing was conducted to investigate the microbial and antibiotic resistance genes (ARGs) composition in the vitreous (intraocular body fluid) of an endophthalmitis patient, who progressed rapidly and accompanied by severe pain. Metagenomic sequencing data revealed that the vitreous sample was predominated by Streptococcus, with a low-diversity microbiome in the vitreous. This strain harbor's the ARGs mainly against beta-lactam, macrolide-lincosamide-streptogramin, and multidrug. Additionally, metagenome-assembled genome sequence of Streptococcus sp. v1. nov. was identified. The Tetra Correlation Search (TCS) analysis uncovered that the closest relative of the Streptococcus sp. v1. nov. was Streptococcus mitis SK321. Pan/core genome analysis for Streptococcus sp. v1. nov. and TCS top 25 hits strains revealed that most unique genes of Streptococcus sp. v1. nov. were linked to ATP-binding cassette transport system, which could indicate unique virulence and pathogenic potentials of Streptococcus sp. v1. nov. In addition, a total of 7 virulence factors were identified, and the overwhelming of them were classified into "offensive virulence factors". The high pathogenicity of Streptococcus sp. v1. nov. could be a reason for the patient's rapid disease progression. Our study was first isolated an ocular pathogen with highly virulent based on metagenomic sequencing and bioinformatics analysis, which has important reference value for revealing the composition and genome characteristics of pathogens in endophthalmitis patient in the future.
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Affiliation(s)
- Meiqin Zheng
- Department of Immunology and Pathogenic Biology, College of Basic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shanxi, People's Republic of China
- 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, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yutong Kang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yangyang Shen
- 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
| | - Fangyi Xu
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yanjiong Chen
- Department of Immunology and Pathogenic Biology, College of Basic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shanxi, People's Republic of China.
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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.
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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
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8
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Li X, Li Z, Wang M, Fu A, Hao X, Guo X, Gu J, Jin W, Yang A. The diagnostic utility of nanopore targeted sequencing in suspected endophthalmitis. Int Ophthalmol 2023; 43:2653-2668. [PMID: 36941506 PMCID: PMC10371907 DOI: 10.1007/s10792-023-02665-7] [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: 10/26/2022] [Accepted: 02/19/2023] [Indexed: 03/23/2023]
Abstract
PURPOSE This paper aimed to assess the diagnostic utility of a newly developed gene-based technology-nanopore targeted sequencing (NTS) in suspected endophthalmitis patients. METHODS This retrospective study included 43 patients (44 eyes) with suspected endophthalmitis. NTS was applied along with microbiological culture to detect unknown pathogens in intraocular fluid samples. The diagnostic utility of NTS was mainly evaluated from three aspects, including the positivity rate of bacterial/fungal presence, diagnostic turnaround time and the frequency of change in treatment based on etiology test results. Non-parametric, two-sided Wilcoxon rank sum test, the McNemar's test and the kappa statistic were used for statistical comparisons. RESULTS NTS showed significant advantages over traditional culture in positivity rates and diagnostic time (P < 0.001, kappa = 0.082; Z = -5.805, P < 0. 001). As regards antibiotic strategy, 17 patients (39.53%) and 5 patients (11.63%) underwent medication change following NTS and culture results respectively (P < 0.001, kappa = 0.335). With reasonable use of antibiotic and surgical intervention, most patients responded favorably, judged by significantly improved visual acuity (Z = -4.249, P < 0.001). The mean duration of hospitalization was 8.49 ± 2.45 days (range, 1-16 days). CONCLUSION The high efficiency feature of NTS in pathogen detection renders it a valuable supplementary to traditional culture. Additionally, it has facilitated patients' management for the early and precise diagnosis of endophthalmitis.
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Affiliation(s)
- Xuejie Li
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Ziyue Li
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Ming Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, China
| | - Aisi Fu
- Wuhan Dgensee Clinical Laboratory Co, Ltd. Wuhan 430075, Hubei Province, China
| | - Xinlei Hao
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Xinyang Guo
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Jiashuang Gu
- Wuhan Dgensee Clinical Laboratory Co, Ltd. Wuhan 430075, Hubei Province, China
| | - Wei Jin
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China.
| | - Anhuai Yang
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China.
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9
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Astley RA, Mursalin MH, Coburn PS, Livingston ET, Nightengale JW, Bagaruka E, Hunt JJ, Callegan MC. Ocular Bacterial Infections: A Ten-Year Survey and Review of Causative Organisms Based on the Oklahoma Experience. Microorganisms 2023; 11:1802. [PMID: 37512974 PMCID: PMC10386592 DOI: 10.3390/microorganisms11071802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Ocular infections can be medical emergencies that result in permanent visual impairment or blindness and loss of quality of life. Bacteria are a major cause of ocular infections. Effective treatment of ocular infections requires knowledge of which bacteria are the likely cause of the infection. This survey of ocular bacterial isolates and review of ocular pathogens is based on a survey of a collection of isolates banked over a ten-year span at the Dean McGee Eye Institute in Oklahoma. These findings illustrate the diversity of bacteria isolated from the eye, ranging from common species to rare and unique species. At all sampled sites, staphylococci were the predominant bacteria isolated. Pseudomonads were the most common Gram-negative bacterial isolate, except in vitreous, where Serratia was the most common Gram-negative bacterial isolate. Here, we discuss the range of ocular infections that these species have been documented to cause and treatment options for these infections. Although a highly diverse spectrum of species has been isolated from the eye, the majority of infections are caused by Gram-positive species, and in most infections, empiric treatments are effective.
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Affiliation(s)
- Roger A Astley
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Md Huzzatul Mursalin
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Phillip S Coburn
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Erin T Livingston
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - James W Nightengale
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Eddy Bagaruka
- Department of Biology, Oklahoma Christian University, Edmond, OK 73013, USA
| | - Jonathan J Hunt
- Department of Biology, Oklahoma Christian University, Edmond, OK 73013, USA
| | - Michelle C Callegan
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
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10
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Sugita S, Takase H, Nakano S. Role of Recent PCR Tests for Infectious Ocular Diseases: From Laboratory-Based Studies to the Clinic. Int J Mol Sci 2023; 24:ijms24098146. [PMID: 37175854 PMCID: PMC10179472 DOI: 10.3390/ijms24098146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/22/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Infectious uveitis is a vision-threatening condition that requires prompt clinical diagnosis and proper treatment. However, rapid and proper diagnosis in infectious uveitis remains challenging. Several examination tests, including polymerase chain reaction (PCR) tests, are transitioning from laboratory-based basic research-level tests to bedside clinical tests, and recently tests have changed to where they can be performed right next to clinicians. In this review, we introduce an updated overview of recent studies that are representative of the current trends in clinical microbiological techniques including PCR tests for infectious uveitis.
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Affiliation(s)
- Sunao Sugita
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe 650-0047, Japan
| | - Hiroshi Takase
- Department of Ophthalmology & Visual Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Satoko Nakano
- Department of Ophthalmology, Oita University, Oita 879-5593, Japan
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11
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Schwartz SG, Flynn HW, Smiddy WE. Infectious Endophthalmitis vs Noninfectious "Pseudohypopyon" After Intravitreal Triamcinolone Acetonide. JOURNAL OF VITREORETINAL DISEASES 2023; 7:178-181. [PMID: 37006659 PMCID: PMC10037753 DOI: 10.1177/24741264231153027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Introduction: To describe a patient who presented with visual loss and an apparent hypopyon but none of the other symptoms or signs most common with infectious endophthalmitis. Methods: A case and its findings were analyzed. Results: A 73-year-old woman was treated with intravitreal triamcinolone acetonide (IVTA) for cystoid macular edema. The eye had 12 previous injections without complication. After the 13th injection, the patient noted painless visual loss. An examination showed a visual acuity (VA) of finger counting and an apparent hypopyon, which shifted after a head-tilt test, suggesting a noninfectious "pseudohypopyon." Two days later, the VA worsened to hand motions and the hypopyon had increased in size. The eye was treated with a vitreous tap and injection with vancomycin and ceftazidime. The inflammation resolved, VA improved to 20/40, and cultures showed no growth. Conclusions: Distinguishing infectious endophthalmitis from noninfectious inflammation remains challenging. There is no definitive technique by which to distinguish between the 2 conditions; thus, clinicians must use their best judgment and follow the patient closely.
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Affiliation(s)
- Stephen G. Schwartz
- Department of Ophthalmology, Bascom Palmer
Eye Institute, University of Miami Miller School of Medicine, Naples, FL, USA
| | - Harry W. Flynn
- Department of Ophthalmology, Bascom Palmer
Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - William E. Smiddy
- Department of Ophthalmology, Bascom Palmer
Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
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