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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Tsui E, Sella R, Tham V, Kong AW, McClean E, Goren L, Bahar I, Cherian N, Ramirez J, Hughes RE, Privratsky JK, Onclinx T, Feit-Leichman R, Cheng A, Molina I, Kim P, Yu C, Ruder K, Tan A, Chen C, Liu Y, Abraham T, Hinterwirth A, Zhong L, Porco TC, Lietman TM, Seitzman GD, Doan T. Pathogen Surveillance for Acute Infectious Conjunctivitis. JAMA Ophthalmol 2023; 141:1140-1144. [PMID: 37917077 PMCID: PMC10623299 DOI: 10.1001/jamaophthalmol.2023.4785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 08/31/2023] [Indexed: 11/03/2023]
Abstract
Importance Acute infectious conjunctivitis is a common ocular condition with major public health consequences. Objective To assess regional variations and microbial etiologies of acute infectious conjunctivitis to guide treatment. Design, Setting, and Participants In this cross-sectional study, patients with presumed acute infectious conjunctivitis were enrolled in the study at 5 sites (Honolulu, Hawaii; Los Angeles, San Francisco, and San Diego, California; and Petah-Tikva, Israel) from March 2021 to March 2023. Patients with allergic or toxic conjunctivitis were excluded. Main Outcomes and Measures Pathogens were identified by unbiased RNA deep sequencing. Results In all, 52 patients (mean [range] age, 48 [7-80] years; 31 females [60%]) were enrolled at 5 sites (6 patients from Honolulu, 9 from San Diego, 11 from Los Angeles, 13 from San Francisco, and 13 from Petah-Tikva). RNA deep sequencing detected human adenovirus species D in one-quarter of patients (13 of 52). A wide range of pathogens, including human coronavirus 229E, SARS-CoV-2, and herpes simplex virus type 1, was also identified, as well as several bacteria and fungi. Moreover, 62% (32 of 52) of patients presented with purulent discharge, while only 8% (4 of 52) of patients had confirmed bacterial pathogens. Conclusion and Relevance In this cross-sectional study, pathogens associated with acute infectious conjunctivitis varied between all 5 sites in the US and Israel. Purulent discharge was a common presenting sign in this study, with a low specificity for bacteria-associated conjunctivitis, suggesting that further diagnostic workup may be necessary to inform antibiotic stewardship. Additional research on cost-effectiveness of using RNA deep sequencing is needed to ascertain whether it is better to monitor patients clinically until resolution of disease.
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Affiliation(s)
- Edmund Tsui
- Ocular Inflammatory Disease Center, UCLA Stein Eye Institute, Los Angeles, California
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Ruti Sella
- Department of Ophthalmology, Rabin Medical Center, Petah-Tikva, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Vivien Tham
- Pacific Vision Institute of Hawaii, Honolulu, Hawaii
- Department of Ophthalmology, University of Hawaii John A. Burns School of Medicine, Honolulu
| | - Alan W. Kong
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Esmeralda McClean
- Shiley Eye Institute, University of California, San Diego, San Diego
| | - Lee Goren
- Department of Ophthalmology, Rabin Medical Center, Petah-Tikva, Israel
| | - Irit Bahar
- Department of Ophthalmology, Rabin Medical Center, Petah-Tikva, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nina Cherian
- Ocular Inflammatory Disease Center, UCLA Stein Eye Institute, Los Angeles, California
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Joana Ramirez
- Ocular Inflammatory Disease Center, UCLA Stein Eye Institute, Los Angeles, California
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Reginald E. Hughes
- Ocular Inflammatory Disease Center, UCLA Stein Eye Institute, Los Angeles, California
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Joseph K. Privratsky
- Ocular Inflammatory Disease Center, UCLA Stein Eye Institute, Los Angeles, California
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Tania Onclinx
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Rachel Feit-Leichman
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Angel Cheng
- Pacific Vision Institute of Hawaii, Honolulu, Hawaii
| | - Iliana Molina
- Shiley Eye Institute, University of California, San Diego, San Diego
| | - Phillip Kim
- Shiley Eye Institute, University of California, San Diego, San Diego
| | - Carol Yu
- Shiley Eye Institute, University of California, San Diego, San Diego
| | - Kevin Ruder
- F.I. Proctor Foundation, University of California, San Francisco, San Francisco
| | - Alexander Tan
- Pacific Vision Institute of Hawaii, Honolulu, Hawaii
| | - Cindi Chen
- F.I. Proctor Foundation, University of California, San Francisco, San Francisco
| | - YuHeng Liu
- F.I. Proctor Foundation, University of California, San Francisco, San Francisco
| | - Thomas Abraham
- F.I. Proctor Foundation, University of California, San Francisco, San Francisco
| | - Armin Hinterwirth
- F.I. Proctor Foundation, University of California, San Francisco, San Francisco
| | - Lina Zhong
- F.I. Proctor Foundation, University of California, San Francisco, San Francisco
| | - Travis C. Porco
- F.I. Proctor Foundation, University of California, San Francisco, San Francisco
- Department of Ophthalmology, University of California, San Francisco, San Francisco
| | - Thomas M. Lietman
- F.I. Proctor Foundation, University of California, San Francisco, San Francisco
- Department of Ophthalmology, University of California, San Francisco, San Francisco
| | - Gerami D. Seitzman
- F.I. Proctor Foundation, University of California, San Francisco, San Francisco
- Department of Ophthalmology, University of California, San Francisco, San Francisco
| | - Thuy Doan
- F.I. Proctor Foundation, University of California, San Francisco, San Francisco
- Department of Ophthalmology, University of California, San Francisco, San Francisco
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Ramachandran PS, Williamson DA. The transformative potential of metagenomics in microbiology: advancements and implications. Intern Med J 2023; 53:1520-1523. [PMID: 37743240 DOI: 10.1111/imj.16228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/20/2023] [Indexed: 09/26/2023]
Affiliation(s)
- Prashanth S Ramachandran
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Melbourne, Australia
- Department of Neurology, Royal Melbourne Hospital, Victoria, Melbourne, Australia
- Department of Neurology, St. Vincent's Hospital, Victoria, Melbourne, Australia
| | - Deborah A Williamson
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Melbourne, Australia
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Victoria, Melbourne, Australia
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Dutta Majumder P, Mochizuki M, González-López JJ, Gonzales J, Sharma M, Sharma K, Biswas J. Laboratory Investigations in Infectious Uveitis. Ocul Immunol Inflamm 2023; 31:1405-1415. [PMID: 36698066 DOI: 10.1080/09273948.2022.2164728] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 01/27/2023]
Abstract
Laboratory investigations can play a significant role in the diagnosis and decision-making of infectious uveitis. Though direct demonstration of the infective organism remains the gold standard of diagnosis, it is not always possible with ocular tissues. Recent advancements in molecular techniques have made it possible to overcome these limitations and to identify the genomic DNA of pathogens associated with infectious uveitis. Techniques such as next-generation sequencing can analyze all DNA-based lifeforms, regardless of whether they are bacteria, fungi, viruses, or parasites and have been used in the laboratory diagnosis of intraocular inflammation. On the other hand, serological tests, though they dominate the diagnostic landscape of various infectious etiologies in uveitis in routine clinical practice, have varied specificities and sensitivities in different infectious uveitis. In this review, we focus on various methods of laboratory diagnosis of infectious uveitis and discuss the recent advances in molecular diagnosis and their role in various infectious clinical entities.
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Affiliation(s)
| | - Manabu Mochizuki
- Miyata Eye Hospital, Miyakonojo, Japan
- Department of Ophthalmology & Visual Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Julio J González-López
- Ophthalmology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Surgery Department, Universidad de Alcalá, Madrid, Spain
| | - John Gonzales
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
- Department of Ophthalmology, University of California, San Francisco, California, USA
| | - Megha Sharma
- Department of Microbiology, All India Institute of Medical Sciences, Bilaspur, India
| | - Kusum Sharma
- Department of Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh (PGIMER), Chandigarh, India
| | - Jyotirmay Biswas
- Director of Uveitis & Ocular Pathology, Sankara Nethralaya, Chennai, India
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Chaudhary M, Sitaula S, Ruder K, Chen C, Zhong L, Heng Lu Y, Abraham T, Yu D, Hinterwirth A, Lietman TM, Doan T, Seitzman GD. Heterogenous pathogen profile associated with acute conjunctivitis in Nepal. Int Health 2023:ihad079. [PMID: 37650684 DOI: 10.1093/inthealth/ihad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/24/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Infectious conjunctivitis is common in Nepal. MATERIALS AND METHODS This prospective study recruited 60 patients with presumed acute infectious conjunctivitis from the B.P. Koirala Lions Center for Ophthalmic Studies in Kathmandu, Nepal. Swabs from the conjunctiva and anterior nares were processed for metagenomic RNA deep sequencing (RNA-seq). RESULTS Pathogens were identified in 55% of cases. RNA viruses were the most common pathogen class identified. Severe acute respiratory syndrome coronavirus 2 was the most common RNA virus identified. CONCLUSIONS Acute infectious conjunctivitis varies by location. Contrary to expectations, RNA viruses predominated. Repeat surveillance may be useful and RNA-seq allows for detection of the unexpected pathogen including RNA viruses.
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Affiliation(s)
- Meenu Chaudhary
- B.P. Koira la Lions Center for Ophthalmic Studies, Institute of Medicine, Tribhuvan University, Kathmandu 44600, Nepal
| | - Sanjeeta Sitaula
- B.P. Koira la Lions Center for Ophthalmic Studies, Institute of Medicine, Tribhuvan University, Kathmandu 44600, Nepal
| | - Kevin Ruder
- F. I. Proctor Foundation, University of California San Francisco, San Francisco, California 94158, USA
| | - Cindi Chen
- F. I. Proctor Foundation, University of California San Francisco, San Francisco, California 94158, USA
| | - Lina Zhong
- F. I. Proctor Foundation, University of California San Francisco, San Francisco, California 94158, USA
| | - Yu Heng Lu
- F. I. Proctor Foundation, University of California San Francisco, San Francisco, California 94158, USA
| | - Thomas Abraham
- F. I. Proctor Foundation, University of California San Francisco, San Francisco, California 94158, USA
| | - Danny Yu
- F. I. Proctor Foundation, University of California San Francisco, San Francisco, California 94158, USA
| | - Armin Hinterwirth
- F. I. Proctor Foundation, University of California San Francisco, San Francisco, California 94158, USA
| | - Thomas M Lietman
- F. I. Proctor Foundation, University of California San Francisco, San Francisco, California 94158, USA
- Department of Ophthalmology, University of California San Francisco, San Francisco, California 94158, USA
| | - Thuy Doan
- F. I. Proctor Foundation, University of California San Francisco, San Francisco, California 94158, USA
- Department of Ophthalmology, University of California San Francisco, San Francisco, California 94158, USA
| | - Gerami D Seitzman
- F. I. Proctor Foundation, University of California San Francisco, San Francisco, California 94158, USA
- Department of Ophthalmology, University of California San Francisco, San Francisco, California 94158, USA
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Prajna NV, Prajna L, Teja V, Gunasekaran R, Chen C, Ruder K, Zhong L, Yu D, Liu D, Abraham T, Ao W, Deiner M, Hinterwirth A, Seitzman G, Doan T, Lietman T. Apollo Rising: Acute Conjunctivitis Outbreak in India, 2022. Cornea Open 2023; 2:e0009. [PMID: 37719281 PMCID: PMC10501505 DOI: 10.1097/coa.0000000000000009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Purpose To identify pathogens associated with the 2022 conjunctivitis outbreak in Tamil Nadu, India. Methods This prospective study was conducted in November of 2022. Patients with presumed acute infectious conjunctivitis presenting to the Aravind Eye Clinic in Madurai, India were eligible. Anterior nares and conjunctival samples from participants were obtained and processed for metagenomic RNA deep sequencing (RNA-seq). Results Samples from 29 patients were sequenced. A pathogen was identified in 28/29 (97%) patients. Coxsackievirus A24v, a highly infectious RNA virus, was the predominant pathogen and detected in 23/29 patients. Human adenovirus D (HAdV-D), a DNA virus commonly associated with conjunctivitis outbreaks, was detected in the remaining patients (5/29). Hemorrhagic conjunctiva was documented in both HAdV-D and coxsackievirus A24v affected patients but was not the predominant clinical presentation. Phylogenetic analysis of coxsackievirus A24v revealed a recent divergence from the 2015 outbreak. Conclusions Coxsackievirus A24v and HAdV-D were co-circulating during the 2022 conjunctivitis outbreak in Tamil Nadu, India. Clinical findings were similar between patients with HAD-V and coxsackievirus A24v associated conjunctivitis. As high-throughput technologies become more readily accessible and cost-effective, unbiased pathogen surveillance may prove useful for outbreak surveillance and control.
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Affiliation(s)
| | | | | | | | - Cindi Chen
- Francis I. Proctor Foundation, San Francisco, United States
| | - Kevin Ruder
- Francis I. Proctor Foundation, San Francisco, United States
| | - Lina Zhong
- Francis I. Proctor Foundation, San Francisco, United States
| | - Danny Yu
- Francis I. Proctor Foundation, San Francisco, United States
| | - David Liu
- Francis I. Proctor Foundation, San Francisco, United States
| | - Thomas Abraham
- Francis I. Proctor Foundation, San Francisco, United States
| | - Wendy Ao
- Francis I. Proctor Foundation, San Francisco, United States
| | - Michael Deiner
- Department of Ophthalmology, University of California, San Francisco, San Francisco, United States
| | | | - Gerami Seitzman
- Francis I. Proctor Foundation, San Francisco, United States
- Department of Ophthalmology, University of California, San Francisco, San Francisco, United States
| | - Thuy Doan
- Francis I. Proctor Foundation, San Francisco, United States
- Department of Ophthalmology, University of California, San Francisco, San Francisco, United States
| | - Thomas Lietman
- Francis I. Proctor Foundation, San Francisco, United States
- Department of Ophthalmology, University of California, San Francisco, San Francisco, United States
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Vagefi MR, Idowu OO, Miller A, Doan T, Chen C, Hinterwirth A, Zhong L, Ahmad M, Ashraf DC, Grob SR, Kersten RC, Winn BJ. Metagenomic Deep Sequencing for Orbital Inflammatory Disease. Ocul Immunol Inflamm 2023:1-4. [PMID: 37068263 PMCID: PMC10579447 DOI: 10.1080/09273948.2023.2199061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 03/30/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023]
Abstract
PURPOSE Orbital inflammatory disease (OID) is a heterogeneous group of immunologic disorders whose etiology is often non-specific despite routine investigation. In this proof-of-concept study, metagenomic deep sequencing (MDS) is applied to examine host gene expression in two subtypes of OID. METHODS Prospectively collected lacrimal gland tissue from patients with OID was processed for MDS. Differential gene expression analysis was performed to evaluate for host transcriptome signatures. Proof-of-concept comparison was made between histologically confirmed samples of idiopathic dacryoadenitis and IgG4-related disease (IgG4-RD). RESULTS Twelve genes were identified to be differentially expressed between idiopathic dacryoadenitis and IgG4-RD. Differences in innate humoral immunity gene expression were observed. Several additional genes of interests were also found to be upregulated in idiopathic dacryoadenitis. CONCLUSIONS A unique transcriptome signature was found when comparing idiopathic dacryoadenitis to IgG4-RD. This suggests that MDS can identify differentially expressed genes in OID. Such insight could potentially provide a better understanding of host gene expression and the inflammatory pathways involved in OID.
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Affiliation(s)
- M. Reza Vagefi
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Oluwatobi O. Idowu
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Amanda Miller
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Thuy Doan
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
- Francis I. Proctor Foundation, University of California, San Francisco, CA, USA
| | - Cindi Chen
- Francis I. Proctor Foundation, University of California, San Francisco, CA, USA
| | - Armin Hinterwirth
- Francis I. Proctor Foundation, University of California, San Francisco, CA, USA
| | - Lina Zhong
- Francis I. Proctor Foundation, University of California, San Francisco, CA, USA
| | - Meleha Ahmad
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Davin C. Ashraf
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Seanna R. Grob
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Robert C. Kersten
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Bryan J. Winn
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
- Ophthalmology Section, Surgical Service, San Francisco Veterans Affairs Medical Center, 4150 Clement Street, San Francisco, CA 94121
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Kanai K, Whiteside M, Wong M, La T, Nassiri M, Lee S, Yeung SK, Coulter A, Roufail M, Ruder K, Chen C, Liu D, Abraham T, Hinterwirth A, Lietman TM, Doan T, Seitzman GD. Case Series: Unbiased Deep Sequencing Analysis of Acute Infectious Conjunctivitis in an Ambulatory Eye Center in Berkeley, California. Optom Vis Sci 2023; 100:276-280. [PMID: 36880993 PMCID: PMC10133203 DOI: 10.1097/opx.0000000000002010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
SIGNIFICANCE Acute infectious conjunctivitis poses significant challenges to eye care providers. It can be highly transmissible, and because etiology is often presumed, correct treatment and management can be difficult. This study uses unbiased deep sequencing to identify causative pathogens of infectious conjunctivitis, potentially allowing for improved approaches to diagnosis and management. PURPOSES This study aimed to identify associated pathogens of acute infectious conjunctivitis in a single ambulatory eye care center. CASE REPORTS This study included patients who presented to the University of California Berkeley eye center with signs and symptoms suggestive of infectious conjunctivitis. From December 2021 to July 2021, samples were collected from seven subjects (ages ranging from 18 to 38). Deep sequencing identified associated pathogens in five of seven samples, including human adenovirus D, Haemophilus influenzae , Chlamydia trachomatis , and human coronavirus 229E. CONCLUSIONS Unbiased deep sequencing identified some unexpected pathogens in subjects with acute infectious conjunctivitis. Human adenovirus D was recovered from only one patient in this series. Although all samples were obtained during the COVID-19 pandemic, only one case of human coronavirus 229E and no SARS-CoV-2 were identified.
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Affiliation(s)
- Kuniyoshi Kanai
- University of California, Berkeley, School of Optometry, Berkeley, California
| | - Meredith Whiteside
- University of California, Berkeley, School of Optometry, Berkeley, California
| | - Michael Wong
- University of California, Berkeley, School of Optometry, Berkeley, California
| | - Tammy La
- University of California, Berkeley, School of Optometry, Berkeley, California
| | - Maryam Nassiri
- University of California, Berkeley, School of Optometry, Berkeley, California
| | - Sam Lee
- University of California, Berkeley, School of Optometry, Berkeley, California
| | - Sze Kei Yeung
- University of California, Berkeley, School of Optometry, Berkeley, California
| | - Adrienne Coulter
- University of California, Berkeley, School of Optometry, Berkeley, California
| | - Mareena Roufail
- University of California, Berkeley, School of Optometry, Berkeley, California
| | - Kevin Ruder
- 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
| | - David Liu
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Thomas Abraham
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Armin Hinterwirth
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
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Johnson K, Taleo F, Willie K, Amel E, Nanu M, Alguet M, Wass J, Rymill P, Solomon A, Ruder K, Chen C, Zhong L, Hinterwirth A, Liu D, Abraham T, Seitzman G, Lietman T, Doan T. Viruses Associated with Acute Conjunctivitis in Vanuatu. Am J Trop Med Hyg 2023; 108:595-598. [PMID: 36646076 PMCID: PMC9978563 DOI: 10.4269/ajtmh.22-0600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/20/2022] [Indexed: 01/18/2023] Open
Abstract
The first manifestation of a viral infection may be conjunctivitis. There are limited data on the etiology of viral conjunctivitis in Vanuatu, a country in the South Pacific Ocean. Patients presenting to one of two Vanuatu health centers with presumed infectious conjunctivitis were eligible if symptom onset was within 14 days of screening. Conjunctival and anterior nasal swabs were obtained and subjected to unbiased RNA deep sequencing (RNA-seq) to identify DNA and RNA viruses. For samples collected from May to November 2021, RNA-seq identified a viral etiology in 12/48 patients. Human adenovirus species were the most common viruses (58%) detected, followed by human herpes viruses (cytomegalovirus, varicella zoster virus, and human herpes 7 virus). Rhinovirus C, Epstein-Barr virus, and bocavirus were also detected. In summary, the etiology for viral conjunctivitis in Vanuatu appears broad. Unbiased testing may be useful for disease surveillance.
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Affiliation(s)
| | - Fasihah Taleo
- Vanuatu Country Office, World Health Organization, Port Vila, Vanuatu
| | | | | | | | | | - Jose Wass
- Ministry of Health Eye Program, Vanuatu
| | | | - Anthony Solomon
- Department of Control of Neglected Tropical Diseases, World Health Organization, Geneva, Switzerland
| | - Kevin Ruder
- 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
| | - Armin Hinterwirth
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
| | - David Liu
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Thomas Abraham
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Gerami Seitzman
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
- Department of Ophthalmology, University of California San Francisco, San Francisco, California
| | - Thomas Lietman
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
- Department of Ophthalmology, University of California San Francisco, 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, San Francisco, California
- Address correspondence to Thuy Doan, Francis I. Proctor Foundation, University of California San Francisco, 490 Illinois St., Fl. 2, San Francisco, CA 94158. E-mail:
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Redd TK, Al-Khaled T, Paul Chan RV, Campbell JP; American Academy of Ophthalmology Task Force on Academic Global Ophthalmology, American Academy of Ophthalmology Task Force on Academic Global Ophthalmology. Technology and Innovation in Global Ophthalmology: The Past, the Potential, and a Path Forward. Int Ophthalmol Clin 2023; 63:25-32. [PMID: 36598831 DOI: 10.1097/IIO.0000000000000450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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12
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Affiliation(s)
- Jennifer Rose-Nussbaumer
- Byers Eye Institute, Stanford University, Palo Alto, California.,Francis I. Proctor Foundation, University of California, San Francisco
| | - Thuy Doan
- Francis I. Proctor Foundation, University of California, San Francisco.,Department of Ophthalmology, University of California, San Francisco
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13
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Gonzales JA, Takhar JS, Joye A, Acharya NR, Chen C, Hinterwirth A, Doan T. Peripheral Blood Transcriptome in Patients with Sarcoidosis-Associated Uveitis. Ocul Immunol Inflamm 2022; 30:1074-1077. [PMID: 33661066 PMCID: PMC9993430 DOI: 10.1080/09273948.2020.1861306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
PURPOSE To identify peripheral blood transcriptome differences in uveitis patients with sarcoidosis compared to those with Vogt-Koyanagi-Harada (VKH) syndrome and controls. METHODS Ten patients with uveitis compatible with sarcoidosis (eight with pulmonary sarcoidosis, one with central nervous system sarcoidosis, and one with conjunctival sarcoidosis), nine patients with VKH, and nine healthy controls were prospectively enrolled. RESULTS Ten genes exhibited a four-fold difference in expression in sarcoidosis patients compared to controls, many being involved in regulating inflammatory processes or cellular responses to microbes. CONCLUSIONS This research suggests that the transcriptome in sarcoidosis is robust enough to be detected in the peripheral blood and that sarcoidosis can be distinguished from healthy controls. Differentially expressed genes may serve as candidates warranting further investigation with respect to disease pathophysiology and may provide additional information, such as ability to stratify patients based on associated disease severity and anatomical location of inflammation within the eye.
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Affiliation(s)
- John A Gonzales
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA.,Department of Ophthalmology, University of California, San Francisco, California, USA
| | - Jaskirat S Takhar
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA.,John Burns Medical School, University of Hawaii, Honolulu, Hawaii, USA
| | - Ashlin Joye
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Nisha R Acharya
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA.,Department of Ophthalmology, University of California, San Francisco, California, USA
| | - Cindi Chen
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Armin Hinterwirth
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Thuy Doan
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA.,Department of Ophthalmology, University of California, San Francisco, California, USA
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14
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He X, Zhang N, Cao W, Xing Y, Yang N. Application Progress of High-Throughput Sequencing in Ocular Diseases. J Clin Med 2022; 11:3485. [PMID: 35743555 DOI: 10.3390/jcm11123485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/11/2022] [Accepted: 06/16/2022] [Indexed: 02/01/2023] Open
Abstract
Ocular diseases affect multiple eye parts and can be caused by pathogenic infections, complications of systemic diseases, genetics, environment, and old age. Understanding the etiology and pathogenesis of eye diseases and improving their diagnosis and treatment are critical for preventing any adverse consequences of these diseases. Recently, the advancement of high-throughput sequencing (HTS) technology has paved wide prospects for identifying the pathogenesis, signaling pathways, and biomarkers involved in eye diseases. Due to the advantages of HTS in nucleic acid sequence recognition, HTS has not only identified several normal ocular surface microorganisms but has also discovered many pathogenic bacteria, fungi, parasites, and viruses associated with eye diseases, including rare pathogens that were previously difficult to identify. At present, HTS can directly sequence RNA, which will promote research on the occurrence, development, and underlying mechanism of eye diseases. Although HTS has certain limitations, including low effectiveness, contamination, and high cost, it is still superior to traditional diagnostic methods for its efficient and comprehensive diagnosis of ocular diseases. This review summarizes the progress of the application of HTS in ocular diseases, intending to explore the pathogenesis of eye diseases and improve their diagnosis.
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15
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Prajna NV, Lalitha P, Chen C, Zhong L, Lietman TM, Doan T, Seitzman GD. Acute Keratoconjunctivitis Resulting From Coinfection With Avian Newcastle Virus and Human Adenovirus. Cornea 2022; 41:630-631. [PMID: 34483275 PMCID: PMC8894503 DOI: 10.1097/ico.0000000000002853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/25/2021] [Indexed: 11/25/2022]
Abstract
PURPOSE The aim of this study was to report a case of human keratoconjunctivitis caused by both Newcastle disease virus (NDV) and human adenovirus. METHODS A 32-year-old-man presented with an acute unilateral keratoconjunctivitis that resolved with corneal scarring. On presentation, his conjunctival swab was collected for metagenomic sequencing. RESULTS The highest number of pathogen sequencing reads in the conjunctival sample mapped to the NDV. The second highest number of reads mapped to human adenovirus. Confirmation testing with directed reverse-transcription polymerase chain reaction also identified NDV in the specimen. CONCLUSIONS Newcastle conjunctivitis has not been reported for more than 40 years. Mixed infections, including zoonotic pathogens, may be more common than realized.
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Affiliation(s)
| | | | - Cindi Chen
- Francis I. Proctor Foundation and Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Lina Zhong
- Francis I. Proctor Foundation and Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Thomas M Lietman
- Francis I. Proctor Foundation and Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Thuy Doan
- Francis I. Proctor Foundation and Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Gerami D Seitzman
- Francis I. Proctor Foundation and Department of Ophthalmology, University of California San Francisco, San Francisco, CA
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16
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Zhao M, Ma P, Xie Q, Bui A, Yonamine S, Hinterwirth A, Zhong L, Chen C, Doan T, Han Y. Biomarkers for primary open-angle glaucoma progression. Exp Eye Res 2022. [DOI: 10.1016/j.exer.2022.109025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/16/2021] [Accepted: 03/02/2022] [Indexed: 11/22/2022]
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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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18
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Miller S, Chiu C. The Role of Metagenomics and Next-Generation Sequencing in Infectious Disease Diagnosis. Clin Chem 2021; 68:115-124. [PMID: 34969106 DOI: 10.1093/clinchem/hvab173] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) for pathogen detection is becoming increasingly available as a method to identify pathogens in cases of suspected infection. mNGS analyzes the nucleic acid content of patient samples with high-throughput sequencing technologies to detect and characterize microorganism DNA and/or RNA. This unbiased approach to organism detection enables diagnosis of a broad spectrum of infection types and can identify more potential pathogens than any single conventional test. This can lead to improved ability to diagnose patients, although there remains concern regarding contamination and detection of nonclinically significant organisms. CONTENT We describe the laboratory approach to mNGS testing and highlight multiple considerations that affect diagnostic performance. We also summarize recent literature investigating the diagnostic performance of mNGS assays for a variety of infection types and recommend further studies to evaluate the improvement in clinical outcomes and cost-effectiveness of mNGS testing. SUMMARY The majority of studies demonstrate that mNGS has sensitivity similar to specific PCR assays and will identify more potential pathogens than conventional methods. While many of these additional organism detections correlate with the expected pathogen spectrum based on patient presentations, there are relatively few formal studies demonstrating whether these are true-positive infections and benefits to clinical outcomes. Reduced specificity due to contamination and clinically nonsignificant organism detections remains a major concern, emphasizing the importance of careful interpretation of the organism pathogenicity and potential association with the clinical syndrome. Further research is needed to determine the possible improvement in clinical outcomes and cost-effectiveness of mNGS testing.
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Affiliation(s)
- Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
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19
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Shimokawa A, Kobayashi A, Saeki Y, Uchio E. A case of fungal conjunctivitis with giant papillae treated surgically. Taiwan J Ophthalmol 2021; 11:417-420. [PMID: 35070676 PMCID: PMC8757520 DOI: 10.4103/tjo.tjo_46_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/11/2020] [Indexed: 12/03/2022] Open
Abstract
Fungal conjunctivitis is a rare disorder, with low incidence and difficulty in diagnosis due to a lack of specific clinical findings. We report a case of fungal conjunctivitis which exhibited a specific clinical feature of giant papilla formation, and its diagnosis was a complex process. A 19-year-old woman with a history of atopic dermatitis and hard contact lens use was referred to us with a 3-month history of giant papillary conjunctivitis of the right eye in spite of treatment with antiallergic and corticosteroid eye drops, complicated by intraocular pressure elevation. The left eye showed no symptom of ocular surface disorder throughout the clinical course. The right eye did not respond to oral corticosteroid. Polymerase chain reaction of conjunctival scrapings against Chlamydia trachomatis was negative, and she was treated surgically by total papilla resection. Conjunctival giant papilla recurrence was not observed after surgery. Although the primary histopathological diagnosis was chronic inflammation due to atopic keratoconjunctivitis, repeated histopathological survey of excised conjunctival tissue including immunohistochemical staining revealed histiocytes, yeast type spores and hyphae, and phagocytosed spores and hyphae in macrophages. The causative organism was identified morphologically as a Candida species. Later, histopathological examination of a cervical swab revealed the presence of Candida sp. This rare case indicates that a fungal organism may underlie refractory conjunctivitis with specific giant papillary hypertrophy mimicking vernal keratoconjunctivitis.
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Affiliation(s)
- Asami Shimokawa
- Department of Ophthalmology, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Ayaka Kobayashi
- Department of Ophthalmology, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Yusuke Saeki
- Department of Ophthalmology, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Eiichi Uchio
- Department of Ophthalmology, Fukuoka University School of Medicine, Fukuoka, Japan
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20
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Leal SM Jr, Rodino KG, Fowler WC, Gilligan PH. Practical Guidance for Clinical Microbiology Laboratories: Diagnosis of Ocular Infections. Clin Microbiol Rev 2021; 34:e0007019. [PMID: 34076493 DOI: 10.1128/CMR.00070-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The variety and complexity of ocular infections have increased significantly in the last decade since the publication of Cumitech 13B, Laboratory Diagnosis of Ocular Infections (L. D. Gray, P. H. Gilligan, and W. C. Fowler, Cumitech 13B, Laboratory Diagnosis of Ocular Infections, 2010). The purpose of this practical guidance document is to review, for individuals working in clinical microbiology laboratories, current tools used in the laboratory diagnosis of ocular infections. This document begins by describing the complex, delicate anatomy of the eye, which often leads to limitations in specimen quantity, requiring a close working bond between laboratorians and ophthalmologists to ensure high-quality diagnostic care. Descriptions are provided of common ocular infections in developed nations and neglected ocular infections seen in developing nations. Subsequently, preanalytic, analytic, and postanalytic aspects of laboratory diagnosis and antimicrobial susceptibility testing are explored in depth.
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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Abstract
ABSTRACT Metagenomic next-generation sequencing is a powerful method for pathogen detection that combines advanced genome sequencing technology with cutting-edge bioinformatics to analyze microbial populations. Metagenomic next-generation sequencing has the potential to identify uncommon, unculturable, and even previously unidentified pathogens from a clinical isolate. Of particular interest to ophthalmology, this robust data extraction can occur from very small volume clinical samples. Here we discuss the opportunities and limitations of this technique and their current and future application to ophthalmic diagnostics.
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Affiliation(s)
- Sharon L Sabapathypillai
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO
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23
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Wang Z, Huang C, Li X. Research Trends and Hotspot Analysis of Conjunctival Bacteria Based on CiteSpace Software. Biomed Res Int 2020; 2020:2580795. [PMID: 33083458 PMCID: PMC7556104 DOI: 10.1155/2020/2580795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/28/2020] [Accepted: 09/28/2020] [Indexed: 12/26/2022]
Abstract
OBJECTIVE To sort out the literature related to conjunctival bacteria and summarize research hotspots and trends of this field. MATERIALS AND METHODS The relevant literature data from 1900 to 2019 was retrieved from the Web of Science Core Collection database. After manual selection, each document record includes title, author, keywords, abstract, year, organization, and citation. We imported the downloaded data into CiteSpace V (version 5.5R2) to draw the knowledge map and conduct cooperative network analysis, discipline and journal analysis, cluster analysis, and burst keyword analysis. RESULTS After manual screening, there were 285 relevant papers published in the last 28 years (from 1991 to 2019), and the number is increasing year by year. The publications of conjunctival bacteria were dedicated by 1381 authors of 451 institutions in 56 countries/regions. The United States dominates this field (82 literatures), followed by Germany (23 literatures) and Japan (23 literatures). Overall, most cited papers were published with a focus on molecular biology, genetics, nursing, and toxicology. Most papers fall into the category of ophthalmology, veterinary sciences, and pharmacology and pharmacy. The only organized cluster is the "postantibiotic effect," and the top 5 keywords with the strongest citation bursts include "postoperative endophthalmiti(s)," "infectious keratoconjunctiviti(s)," "conjunctiviti(s)," "resistance," and "diversity". CONCLUSION The global field of conjunctival bacteria has expanded in the last 28 years. The United States contributes most. However, there are little cooperation among authors and institutions. Overall, this bibliometric study organized one cluster, "postantibiotic effect", and identified the top 5 hotspots in conjunctival bacteria research: "postoperative endophthalmiti(s)," "infectious keratoconjunctiviti(s)," "conjunctiviti(s)," "resistance," and "diversity". Thus, further research focuses on these topics that may be more helpful to prevent ocular infection and improve prophylaxis strategies to bring a benefit to patients in the near future.
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Affiliation(s)
- Zhenyu Wang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Chen Huang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
- Medical Research Center, Peking University Third Hospital, Beijing, China
| | - Xuemin Li
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
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24
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Sutra P, Rose-Nussbaumer J, Gonzales JA, Wang K, Hinterwirth A, Seitzman G, Bloomer M, Acharya N, Doan T. Metagenomic Deep Sequencing to Investigate for an Infectious Etiology of Iridocorneal Endothelial Syndrome. Cornea 2020; 39:1307-10. [PMID: 32398422 DOI: 10.1097/ICO.0000000000002368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE Iridocorneal endothelial (ICE) syndrome is a group of rare ocular conditions that result from abnormal corneal endothelial cells, leading to secondary glaucoma, iris distortions, and corneal edema. The etiology of ICE is unknown, although it has been associated with viral infections, such as herpes simplex virus. In this study, we sought to identify an infectious etiology for ICE using advanced molecular techniques. METHODS Metagenomic RNA sequencing (MDS) is a high-throughput sequencing approach that can identify all pathogens in any clinical sample, including RNA viruses. Descemet membrane and aqueous fluid from patients with ICE syndrome were subjected to MDS testing. RESULTS Samples from 3 patients with ICE were analyzed. MDS was performed on the aqueous fluid of 3 patients and Descemet membrane and endothelial cell tissue from 1 patient. Viral pathogens were not identified in any of the samples. CONCLUSIONS We were unable to identify a viral etiology in the tissues of patients with the Chandler variant of ICE syndrome, although this study was limited by sample size.
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