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Rasheed MW, Mahboob A, Hanif I. On QSAR modeling with novel degree-based indices and thermodynamics properties of eye infection therapeutics. Front Chem 2024; 12:1383206. [PMID: 38860235 PMCID: PMC11163131 DOI: 10.3389/fchem.2024.1383206] [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: 02/07/2024] [Accepted: 04/29/2024] [Indexed: 06/12/2024] Open
Abstract
Topological descriptors are numerical results generated from the structure of a chemical graph that are useful in identifying the physicochemical characteristics of a wide range of drugs. The introduction of molecular descriptors advances quantitative structure-property relationship research. This article focuses on the nine degree-based topological indices and the linear regression model of the eye infection drugs. We introduced two new indices, namely, the "first revised Randic index" and the "second revised Randic index, for the analysis of eye infection drugs. Topological indices are calculated by using edge partitioning, vertex degree counting, and vertex degree labeling. This analysis is done with a scientific calculator and then authenticated with Matlab, a potent tool for examining data. The experimental data and results of the topological indices serve as inputs for the statistical computations and provide the values of intercepts, slopes, and correlation coefficients. All the correlations for the eye-infection drugs are positive, indicating a direct relationship between the experimental and estimated results of the drugs. There are significant results of the p-test for all of the characteristics of eye infection, such as molecular weight, boiling point, enthalpy, flash point, molar refraction, and molar volume, that validate the accuracy of the computations. A significant link was determined in this study between the defined indices with two properties: molar weight and molar refraction. The molar weight and molar refraction have a correlation coefficient ranging from 0.9. These results demonstrate a strong association between the indices and the properties under investigation. The linear regression approach is a valuable tool for chemists and pharmacists to obtain data about different medicines quickly and cost-effectively.
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Affiliation(s)
- Muhammad Waheed Rasheed
- Department of Mathematics, Division of Science and Technology, University of Education, Lahore, Pakistan
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Shahraki K, Shahraki K, Ghasemi Boroumand P, Sheervalilou R. Promotor methylation in ocular surface squamous neoplasia development: epigenetics implications in molecular diagnosis. Expert Rev Mol Diagn 2023; 23:753-769. [PMID: 37493058 DOI: 10.1080/14737159.2023.2240238] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 07/20/2023] [Indexed: 07/27/2023]
Abstract
INTRODUCTION Cancer is heavily influenced by epigenetic mechanisms that include DNA methylation, histone modifications, and non-coding RNA. A considerable proportion of human malignancies are believed to be associated with global DNA hypomethylation, with localized hypermethylation at promoters of certain genes. AREA COVERED The present review aims to emphasize on recent investigations on the epigenetic landscape of ocular surface squamous neoplasia, that could be targeted/explored using novel approaches such as personalized medicine. EXPERT OPINION While the former is thought to contribute to genomic instability, promoter-specific hypermethylation might facilitate tumorigenesis by silencing tumor suppressor genes. Ocular surface squamous neoplasia, the most prevalent type of ocular surface malignancy, is suggested to be affected by epigenetic mechanisms, as well. Although the exact role of epigenetics in ocular surface squamous neoplasia has mostly been unexplored, recent findings have greatly contributed to our understanding regarding this pathology of the eye.
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Affiliation(s)
- Kourosh Shahraki
- Ocular Tissue Engineering Research Center, Ophthalmic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Ophthalmology, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Kianoush Shahraki
- Department of Ophthalmology, Zahedan University of Medical Sciences, Zahedan, Iran
- Cornea Department, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Paria Ghasemi Boroumand
- ENT, Head and Neck Research Center and Department, Iran University of Medical Science, Tehran, Iran
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Yenidünya Konuk E. Molecular Approaches to the Diagnosis of Chlamydia. Infect Dis (Lond) 2023. [DOI: 10.5772/intechopen.109746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
Abstract
Chlamydia trachomatis is known as the most common bacterial infection agent to pass with sexual transition. This microorganism is an obligatory intracellular parasite. A variety of infections are caused by C. trachomatis, including trachoma, pneumonias in newborns, genital and urinary tract infections, and lymphogranuloma venereum (LGV), which is caused by LGV strains. The diagnosis of Chlamydia trachomatis can be made by cultures and isolations, antigens and antibodies (direct fluorescence, enzyme immunoassays), hybridization, or polymerase chain reaction (PCR). Each year, infection and diagnosis rates increase in the developed world. Since Chlamydia is mostly asymptomatic, screening, and treatment are a key to detecting cases. Polymerase chain reaction (PCR), ligase chain reaction (LCR), and nucleic acid sequence-based amplification (NASBAa) molecular methods can be used for the detection, low concentration, quantification, and identification of organisms. While the traditional PCR method confirms its existence, it can quantify real-time PCR (RT-PCR). This method (RT-PCR) may have low sensitivity among variants of the same species. Also, PCR scans, which receive urine service, offer great advantages. PCR from initial void urine (FVU) samples is highly sensitive in detecting the organism. Urine Chlamydia screenings are more acceptable in large populations and asymptomatic detections.
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Jing D, Jiang X, Ren X, Su J, Huang C, Yang J, Hao R, Li X. Metagenomic nanopore sequencing of ocular microbiome in patients with meibomian gland dysfunction. Front Med (Lausanne) 2022; 9:1045990. [PMID: 36438054 PMCID: PMC9682043 DOI: 10.3389/fmed.2022.1045990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/26/2022] [Indexed: 07/30/2023] Open
Abstract
PURPOSE To explore the composition of the ocular microbiome in patients with Meibomian gland dysfunction (MGD) using metagenomic nanopore sequencing. METHODS A total of 98 participants were recruited from September to December 2021, including 86 patients with MGD and 12 controls. Symptoms and signs of dry eye were assessed, and bacterial samples in the conjunctival sac (CS) and meibomian gland (MG) secretions were then identified by bacterial culture identification and metagenomic nanopore sequencing. RESULTS The positive rate of CS bacterial culture in the MGD group was significantly higher than that in the normal group. A more complex composition of bacterial genera was detected in the mild and moderate MGD groups than in the control. However, the severe MGD groups had the simplest composition of bacteria. Metagenomic nanopore sequencing detected more species of bacteria than traditional culture. CONCLUSION The CS and MG of MGD patients may have different degrees of bacterial microbiota imbalance. Metagenomic nanopore sequencing technology provides a new way for us to understand the composition of "real-world" ocular surface microorganisms.
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Affiliation(s)
- Dalan Jing
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Xiaodan Jiang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Xiaotong Ren
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Jie Su
- 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
| | - Jiarui Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Ran Hao
- Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, 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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Zhu J, Xia H, Tang R, Ng TK, Yao F, Liao X, Zhang Q, Ke X, Shi T, Chen H. METAGENOMIC NEXT-GENERATION SEQUENCING DETECTS PATHOGENS IN ENDOPHTHALMITIS PATIENTS. Retina 2022; 42:992-1000. [PMID: 35019890 DOI: 10.1097/iae.0000000000003406] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
PURPOSE To investigate the utility of metagenomic next-generation sequencing (mNGS) in identifying the pathogens in endophthalmitis. METHODS In this prospective study, 36 cases of endophthalmitis were recruited. All patients received surgical treatment and intraocular drug lavage. The samples of vitreous or aqueous humor were extracted for mNGS and microbiological culture. The diagnostic performance of pathogens was compared between mNGS and culture. RESULTS The positive rates of mNGS and culture were 88.89% (32/36) and 27.78% (10/36), respectively. There was a statistically significant difference between mNGS and culture (Chi-square = 27.657; P < 0.01). Staphylococcus epidermidis, Streptococcus pneumoniae, and Klebsiella pneumoniae were the most pathogenic bacteria in traumatic, postoperative, and endogenous endophthalmitis, respectively. The concordance of pathogen identified by mNGS and culture was 70% for culture-positive cases. Antibiotic resistance genes were identified in 9 cases. There was a marginal correlation between the final visual acuity and the microbial sequence read (Spearman correlation coefficient = 0.498; P = 0.05). CONCLUSION Metagenomic next-generation sequencing has a higher positive rate of identifying pathogens in endophthalmitis than in culture. It can also provide information on antibiotic resistance and visual prognosis. However, caution must be taken when interpreting the results of mNGS because they may not be concordant with culture.
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Affiliation(s)
- Junfeng Zhu
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Honghe Xia
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Ruqing Tang
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Tsz Kin Ng
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Fen Yao
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Xulong Liao
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Qi Zhang
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Xixuan Ke
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Tingkun Shi
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Haoyu Chen
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
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Xi H, Zhang L, Xu B, Liu H, Li S. Metagenomic Next-Generation Sequencing to Investigate Infectious Endophthalmitis of Brucella: A Case Report. Front Med (Lausanne) 2022; 9:847143. [PMID: 35425780 PMCID: PMC9001913 DOI: 10.3389/fmed.2022.847143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 02/16/2022] [Indexed: 11/26/2022] Open
Abstract
Introduction Brucellosis is a systemic disease that exists prevalently in clinical manifestations. The symptoms present in organs such as the eyes (in ocular brucellosis) can lead to misdiagnosis or even failure to diagnose. Metagenomic Next-Generation Sequencing (mNGS), a high-throughput sequencing approach, could be applied for the detection of microorganisms. Case Presentation A 57-year-old female with acute right-eye vision loss, treated with clindamycin and dexamethasone sodium phosphate for 1.5 months, was difficult to diagnose using regular methods. mNGS was utilized for the aqueous fluid from the patient, and Brucella melitensis was identified. The inflammation was treated with 3 months of antibiotherapy. However, even with specific medicine and surgery, the vision remained poor because severe ocular conditions last for a long time. Conclusion It suggests that brucella should still be a probable pathogen in endophthalmitis despite its low incidence in non-epidemic areas. Moreover, mNGS can achieve early diagnosis and timely treatment for difficult-to-diagnose ocular infections.
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Affiliation(s)
- Huiyu Xi
- Department of Ophthalmology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Xuzhou Eye Disease Prevention and Treatment Institute, Xuzhou, China
| | - Lishuai Zhang
- Department of Ophthalmology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Xuzhou Eye Disease Prevention and Treatment Institute, Xuzhou, China
| | - Bo Xu
- Department of Ophthalmology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Xuzhou Eye Disease Prevention and Treatment Institute, Xuzhou, China
| | - Haiyang Liu
- Department of Ophthalmology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Xuzhou Eye Disease Prevention and Treatment Institute, Xuzhou, China
| | - Suyan Li
- Department of Ophthalmology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Xuzhou Eye Disease Prevention and Treatment Institute, Xuzhou, China
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Diagnostic armamentarium of infectious keratitis: A comprehensive review. Ocul Surf 2021; 23:27-39. [PMID: 34781020 PMCID: PMC8810150 DOI: 10.1016/j.jtos.2021.11.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/05/2021] [Accepted: 11/07/2021] [Indexed: 01/23/2023]
Abstract
Infectious keratitis (IK) represents the leading cause of corneal blindness worldwide, particularly in developing countries. A good outcome of IK is contingent upon timely and accurate diagnosis followed by appropriate interventions. Currently, IK is primarily diagnosed on clinical grounds supplemented by microbiological investigations such as microscopic examination with stains, and culture and sensitivity testing. Although this is the most widely accepted practice adopted in most regions, such an approach is challenged by several factors, including indistinguishable clinical features shared among different causative organisms, polymicrobial infection, long diagnostic turnaround time, and variably low culture positivity rate. In this review, we aim to provide a comprehensive overview of the current diagnostic armamentarium of IK, encompassing conventional microbiological investigations, molecular diagnostics (including polymerase chain reaction and mass spectrometry), and imaging modalities (including anterior segment optical coherence tomography and in vivo confocal microscopy). We also highlight the potential roles of emerging technologies such as next-generation sequencing, artificial intelligence-assisted platforms. and tele-medicine in shaping the future diagnostic landscape of IK.
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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: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [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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Abstract
Metagenomic analysis is the comprehensive study of DNA using clinical specimens of organisms including bacteria, fungi, and viruses. In this study, we investigated the efficacy of metagenomic analysis for diagnosing ocular infections, including 11 keratitis cases, four iridocyclitis cases, and one endophthalmitis case. Corneal scraping, aqueous humor, and vitreous humor, were collected respectively. Ocular specimens were used for bacterial and fungal culture, and PCR for detecting viral DNA. Shotgun metagenomic sequencing for 150 bases of single end was performed by Illumina MiSeq® System. Sequence was retrieved from the database at NCBI using a MegaBLAST search. Since Propionibacterium spp. are commensal bacteria found at the ocular surface, they were excluded from analysis. Six cases (37.5%) were positive for culture or PCR. Metagenome techniques revealed that 9 cases (56.3%) included genomes of organisms that were considered pathogenic in specimens. Five cases (31.3%) possessed genomes of organisms like themselves that were detected by culture and PCR. Six cases (37.5%) were negative for culture, PCR, and metagenome analysis. Moreover, viral pathogens (HSV-1, 2 cases; and VZV, 1 case) were detected by only metagenome analysis. Metagenome analysis using an ocular sample can detect microbial genome comprehensively, and viral pathogens, which were not detected by conventional examination.
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Oliveira BB, Veigas B, Carlos FF, Sánchez-Melsió A, Balcázar JL, Borrego CM, Baptista PV. Water safety screening via multiplex LAMP-Au-nanoprobe integrated approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 741:140447. [PMID: 32887010 DOI: 10.1016/j.scitotenv.2020.140447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/20/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
Contaminated water resources remain a major global concern regarding public health. The majority of water safety protocols include indicators of microbial contamination to evaluate the potential risk to public health and are key elements of quality guidelines. Among these, markers for total coliforms and fecal coliforms are strong indicators of co-contamination with other pathogens. Traditional methods, recurring to slow and cumbersome culture-based approaches, have been gradually replaced by molecular methods, capable of faster and more specific screening. These are usually PCR-based methods that may allow for multiple pathogen detection but require dedicated laboratory equipment, hindering the rapid on-site assessment. Here, we used a multiplex Loop-Mediated Isothermal Amplification (mLAMP) strategy for the amplification of two markers associated with the contamination by total and fecal coliforms (e.g. Escherichia coli) - lacZ and uidA genes, respectively - thus allowing for single tube multiplex detection. The mLAMP products were then subject to an Au-nanoprobe colorimetric detection assay for precise discrimination of targets. This approach was validated in 22 water samples that were also screened for the presence of lacZ and uidA using standard and quantitative PCR, with the capability for discriminating the contamination level, e.g. a semi-quantitative evaluation of water quality.
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Affiliation(s)
- Beatriz B Oliveira
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Bruno Veigas
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal; i3N|CENIMAT, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Fábio Ferreira Carlos
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Alexandre Sánchez-Melsió
- Catalan Institute for Water Research (ICRA), H2O Building, Scientific and Technological Park of the University of Girona, Emili Grahit 101, E-17003 Girona, (Spain)
| | - José Luís Balcázar
- Catalan Institute for Water Research (ICRA), H2O Building, Scientific and Technological Park of the University of Girona, Emili Grahit 101, E-17003 Girona, (Spain)
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), H2O Building, Scientific and Technological Park of the University of Girona, Emili Grahit 101, E-17003 Girona, (Spain); Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, M. Aurèlia Capmany 40, E-17003, Girona, (Spain)
| | - Pedro Viana Baptista
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal.
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Lee CS, Hong B, Kasi SK, Aderman C, Talcott KE, Adam MK, Yue B, Akileswaran L, Nakamichi K, Wu Y, Rezaei KA, Olmos de Koo LC, Chee YE, Lee AY, Garg SJ, Van Gelder RN. Prognostic Utility of Whole-Genome Sequencing and Polymerase Chain Reaction Tests of Ocular Fluids in Postprocedural Endophthalmitis. Am J Ophthalmol 2020; 217:325-334. [PMID: 32217118 DOI: 10.1016/j.ajo.2020.03.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE To associate detection of potential pathogen DNA in endophthalmitis with clinical outcomes. DESIGN Prospective cohort study. METHODS Patients in whom endophthalmitis was diagnosed following an intraocular procedure were recruited. Clinical outcome data from baseline, week-1, month-1, and month-3 visits were collected. Intraocular biopsy samples were cultured by standard methods. Quantitative polymerase chain reaction (qPCR) was performed for specific pathogens and whole-genome sequencing (WGS). RESULTS A total of 50 patients (mean age 72 years old; 52% male) were enrolled. Twenty-four cases were culture-positive and 26 were culture-negative. WGS identified the cultured organism in 76% of culture-positive cases and identified potential pathogens in 33% of culture-negative cases. Month-1 and -3 visual acuities did not vary by pathogen-positive versus pathogen-negative cases as detected by either culture or WGS. Visual outcomes of Staphylococcus epidermidis endophthalmitis were no different than those of pathogen-negative cases, whereas the patients infected with other pathogens showed worse outcome. Higher baseline bacterial DNA loads of bacteria other than those of S epidermidis detected by WGS were associated with worse month-1 and -3 visual acuity, whereas the S epidermidis loads did not appear to influence outcomes. Torque teno virus (TTV) and Merkel cell polyomavirus (MCV) were detected by qPCR in 49% and 19% of cases, respectively. Presence of TTV at presentation was associated with a higher rate of secondary pars plana vitrectomy (P = .009) and retinal detachment (P = .022). CONCLUSIONS The presence and higher load of bacteria other than S epidermidis detected by WGS or DNA from TTV by qPCR in ocular fluids is associated with worse outcomes in post-procedure endophthalmitis.
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Affiliation(s)
- Cecilia S Lee
- Department of Ophthalmology, University of Washington, Seattle, Washington, USA.
| | - Bryan Hong
- MidAtlantic Retina, The Retina Service of Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Sundeep K Kasi
- MidAtlantic Retina, The Retina Service of Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Christopher Aderman
- MidAtlantic Retina, The Retina Service of Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Katherine E Talcott
- MidAtlantic Retina, The Retina Service of Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Murtaza K Adam
- MidAtlantic Retina, The Retina Service of Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Bryan Yue
- University of Washington, Seattle, Washington, USA
| | - Lakshmi Akileswaran
- Department of Ophthalmology, University of Washington, Seattle, Washington, USA
| | - Kenji Nakamichi
- Department of Ophthalmology, University of Washington, Seattle, Washington, USA
| | - Yue Wu
- Department of Ophthalmology, University of Washington, Seattle, Washington, USA
| | - Kasra A Rezaei
- Department of Ophthalmology, University of Washington, Seattle, Washington, USA
| | - Lisa C Olmos de Koo
- Department of Ophthalmology, University of Washington, Seattle, Washington, USA
| | - Yewlin E Chee
- Department of Ophthalmology, University of Washington, Seattle, Washington, USA
| | - Aaron Y Lee
- Department of Ophthalmology, University of Washington, Seattle, Washington, USA
| | - Sunir J Garg
- Department of Ophthalmology, University of Washington, Seattle, Washington, USA
| | - Russell N Van Gelder
- Department of Ophthalmology, University of Washington, Seattle, Washington, USA; Departments of Biological Structure and Pathology, University of Washington, Seattle, Washington, USA
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12
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A RT-PCR assay for the detection of coronaviruses from four genera. J Clin Virol 2020; 128:104391. [PMID: 32403008 PMCID: PMC7192118 DOI: 10.1016/j.jcv.2020.104391] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 04/20/2020] [Accepted: 04/26/2020] [Indexed: 01/13/2023]
Abstract
We developed a diagnostic to detect all CoVs from the four main genera. This assay can detect and identify all previously recognized CoVs and any future related CoVs that may emerge. The assay was highly specific and sensitive in detecting CoVs, and performed well on different sample types.
Background During the past two decades, three novel coronaviruses (CoVs) have emerged to cause international human epidemics with severe morbidity. CoVs have also emerged to cause severe epidemics in animals. A better understanding of the natural hosts and genetic diversity of CoVs are needed to help mitigate these threats. Objective To design and evaluate a molecular diagnostic tool for detection and identification of all currently recognized and potentially future emergent CoVs from the Orthocoronavirinae subfamily. Study design and Results We designed a semi-nested, reverse transcription RT-PCR assay based upon 38 published genome sequences of human and animal CoVs. We evaluated this assay with 14 human and animal CoVs and 11 other non-CoV respiratory viruses. Through sequencing the assay's target amplicon, the assay correctly identified each of the CoVs; no cross-reactivity with 11 common respiratory viruses was observed. The limits of detection ranged from 4 to 4 × 102 copies/reaction, depending on the CoV species tested. To assess the assay's clinical performance, we tested a large panel of previously studied specimens: 192 human respiratory specimens from pneumonia patients, 5 clinical specimens from COVID-19 patients, 81 poultry oral secretion specimens, 109 pig slurry specimens, and 31 aerosol samples from a live bird market. The amplicons of all RT-PCR-positive samples were confirmed by Sanger sequencing. Our assay performed well with all tested specimens across all sample types. Conclusions This assay can be used for detection and identification of all previously recognized CoVs, including SARS-CoV-2, and potentially any emergent CoVs in the Orthocoronavirinae subfamily.
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Phadke VK, Shantha JG, O’Keefe G. Relapsing Uveitis due to Human T-lymphotropic Virus Type 1 in a Patient Living With HIV Diagnosed by Metagenomic Deep Sequencing. Open Forum Infect Dis 2020; 7:ofaa078. [PMID: 32206676 PMCID: PMC7081385 DOI: 10.1093/ofid/ofaa078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/06/2020] [Indexed: 12/17/2022] Open
Abstract
HIV infection can result in vision loss from different causes, including HIV retinopathy and uveitis secondary to other infections, such as toxoplasmosis and viral retinitis. It is imperative to identify any infectious causes of uveitis to successfully treat the condition and prevent further vision loss. Metagenomic deep sequencing (MDS) is an emerging technology that presents an unbiased approach to the evaluation of clinical syndromes, including uveitis, that have not been diagnosed by pathogen-specific testing. Herein we present a case of a woman living with HIV with 11 years of relapsing bilateral uveitis refractory to systemic corticosteroid therapy who was diagnosed with human T-lymphotropic virus type 1 (HTLV-1)–associated uveitis by this technology. We also briefly review the literature of MDS as a diagnostic tool and the epidemiology, pathogenesis, and diagnosis of HTLV-1-associated uveitis.
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Affiliation(s)
- Varun K Phadke
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jessica G Shantha
- Emory Eye Center, Department of Ophthalmology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ghazala O’Keefe
- Emory Eye Center, Department of Ophthalmology, Emory University School of Medicine, Atlanta, Georgia, USA
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14
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Abstract
PURPOSE OF REVIEW To review ocular manifestations and complications of herpes simplex virus (HSV) and discuss recent advancements in diagnostic and treatment strategy. RECENT FINDINGS In-vivo confocal microscopy has expanded our understanding of corneal nerve degeneration, corneal dendritic cell activity, and changes in biomechanical properties in HSV keratitis. Although currently available only as a research tool, metagenomic deep sequencing has the potential to improve diagnostic accuracy beyond the well established PCR technology, especially in atypical cases. Development of an HSV vaccine has shown some encouraging results in a murine model. New treatment options for neurotrophic cornea offer promise, specifically cenegermin nerve growth factor. SUMMARY Ocular herpes simplex infection and its complications continue to cause significant visual burden and decreased quality of life. Familiarity with its clinical features, wider adoption of viral PCR diagnostic technology, and recognition of the need for long-term maintenance medications for recurrent or chronic cases form the basis for effective management. Metagenomic deep sequencing, the development of a herpes vaccine, and cenegermin nerve growth factor offer promise as diagnostic, preventive, and therapeutic options, respectively.
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15
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Jerome H, Taylor C, Sreenu VB, Klymenko T, Filipe ADS, Jackson C, Davis C, Ashraf S, Wilson-Davies E, Jesudason N, Devine K, Harder L, Aitken C, Gunson R, Thomson EC. Metagenomic next-generation sequencing aids the diagnosis of viral infections in febrile returning travellers. J Infect 2019; 79:383-388. [PMID: 31398374 PMCID: PMC6859916 DOI: 10.1016/j.jinf.2019.08.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/18/2019] [Accepted: 08/03/2019] [Indexed: 01/20/2023]
Abstract
OBJECTIVES Travel-associated infections are challenging to diagnose because of the broad spectrum of potential aetiologies. As a proof-of-principle study, we used MNGS to identify viral pathogens in clinical samples from returning travellers in a single center to explore its suitability as a diagnostic tool. METHODS Plasma samples from 40 returning travellers presenting with a fever of ≥38°C were sequenced using MNGS on the Illumina MiSeq platform and compared with standard-of-care diagnostic assays. RESULTS In total, 11/40 patients were diagnosed with a viral infection. Standard of care diagnostics revealed 5 viral infections using plasma samples; dengue virus 1 (n = 2), hepatitis E (n = 1), Ebola virus (n = 1) and hepatitis A (n = 1), all of which were detected by MNGS. Three additional patients with Chikungunya virus (n = 2) and mumps virus were diagnosed by MNGS only. Respiratory infections detected by nasal/throat swabs only were not detected by MNGS of plasma. One patient had infection with malaria and mumps virus during the same admission. CONCLUSIONS MNGS analysis of plasma samples improves the sensitivity of diagnosis of viral infections and has potential as an all-in-one diagnostic test. It can be used to identify infections that have not been considered by the treating physician, co-infections and new or emerging pathogens. SUMMARY Next generation sequencing (NGS) has potential as an all-in-one diagnostic test. In this study we used NGS to diagnose returning travellers with acute febrile illness in the UK, highlighting cases where the diagnosis was missed using standard methods.
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Affiliation(s)
- Hanna Jerome
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Callum Taylor
- Department of Infectious Diseases, Queen Elizabeth University Hospital, 1345 Govan Rd, Govan, Glasgow G51 4TF, UK
| | - Vattipally B. Sreenu
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Tanya Klymenko
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Ana Da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Celia Jackson
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G31 2ER, UK
| | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Shirin Ashraf
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Eleri Wilson-Davies
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G31 2ER, UK
| | - Natasha Jesudason
- Queen Elizabeth University Hospital, 1345 Govan Rd, Govan, Glasgow G51 4TF, UK
| | - Karen Devine
- Department of Infectious Diseases, Queen Elizabeth University Hospital, 1345 Govan Rd, Govan, Glasgow G51 4TF, UK
| | - Lisbeth Harder
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Celia Aitken
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G31 2ER, UK
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G31 2ER, UK
| | - Emma C. Thomson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
- Department of Infectious Diseases, Queen Elizabeth University Hospital, 1345 Govan Rd, Govan, Glasgow G51 4TF, UK
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16
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Ma L, Jakobiec FA, Dryja TP. A Review of Next-Generation Sequencing (NGS): Applications to the Diagnosis of Ocular Infectious Diseases. Semin Ophthalmol 2019; 34:223-231. [PMID: 31170015 DOI: 10.1080/08820538.2019.1620800] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Purpose: To review the value of next-generation sequencing (NGS) in identifying the pathogens which cause ocular infections, thereby facilitating prompt initiation of treatment with an optimal anti-microbial regimen. Both contemporary and futuristic approaches to identifying pathogens in ocular infections are covered in this brief overview. Methods: Review of the peer reviewed literature on conventional and advanced methods as applied to the diagnosis of infectious diseases of the eye. Conclusion: NGS is a novel technology for identifying the pathogens responsible for ocular infections with the potential to improve the accuracy and speed of diagnosis and hastening the selection of the best therapy.
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Affiliation(s)
- Lina Ma
- a David G Cogan Laboratory of Ophthalmic Pathology, Massachusetts Eye and Ear Infirmary , Harvard Medical School , Boston , MA , USA
| | - Frederick A Jakobiec
- a David G Cogan Laboratory of Ophthalmic Pathology, Massachusetts Eye and Ear Infirmary , Harvard Medical School , Boston , MA , USA
| | - Thaddeus P Dryja
- a David G Cogan Laboratory of Ophthalmic Pathology, Massachusetts Eye and Ear Infirmary , Harvard Medical School , Boston , MA , USA
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17
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Borroni D, Romano V, Kaye SB, Somerville T, Napoli L, Fasolo A, Gallon P, Ponzin D, Esposito A, Ferrari S. Metagenomics in ophthalmology: current findings and future prospectives. BMJ Open Ophthalmol 2019; 4:e000248. [PMID: 31276030 PMCID: PMC6557081 DOI: 10.1136/bmjophth-2018-000248] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 02/04/2019] [Accepted: 02/19/2019] [Indexed: 01/14/2023] Open
Abstract
Less than 1% of all microorganisms of the available environmental microbiota can be cultured with the currently available techniques. Metagenomics is a new methodology of high-throughput DNA sequencing, able to provide taxonomic and functional profiles of microbial communities without the necessity to culture microbes in the laboratory. Metagenomics opens to a ‘hypothesis-free’ approach, giving important details for future research and treatment of ocular diseases in ophthalmology, such as ocular infection and ocular surface diseases.
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Affiliation(s)
- Davide Borroni
- St Paul's Eye Unit, Department of Corneal and External Eye Diseases, Royal Liverpool University Hospital, Liverpool, United Kingdom.,Department of Doctoral Studies, Riga Stradins University, Riga, Latvia.,Department of Eye and Vision Science, University of Liverpool, Liverpool, United Kingdom.,Fondazione Banca Degli Occhi Del Veneto Onlus, Zelarino, Venezia, Italy
| | - Vito Romano
- St Paul's Eye Unit, Department of Corneal and External Eye Diseases, Royal Liverpool University Hospital, Liverpool, United Kingdom.,Department of Eye and Vision Science, University of Liverpool, Liverpool, United Kingdom
| | - Stephen B Kaye
- St Paul's Eye Unit, Department of Corneal and External Eye Diseases, Royal Liverpool University Hospital, Liverpool, United Kingdom.,Department of Eye and Vision Science, University of Liverpool, Liverpool, United Kingdom
| | - Tobi Somerville
- St Paul's Eye Unit, Department of Corneal and External Eye Diseases, Royal Liverpool University Hospital, Liverpool, United Kingdom.,Department of Eye and Vision Science, University of Liverpool, Liverpool, United Kingdom
| | - Luca Napoli
- Dipartimento di Specialità Medico-Chirurgiche, Scienze Radiologiche e Sanita Pubblica, Universita degli Studi di Brescia, Brescia, Italy
| | - Adriano Fasolo
- Fondazione Banca Degli Occhi Del Veneto Onlus, Zelarino, Venezia, Italy
| | - Paola Gallon
- Fondazione Banca Degli Occhi Del Veneto Onlus, Zelarino, Venezia, Italy
| | - Diego Ponzin
- Fondazione Banca Degli Occhi Del Veneto Onlus, Zelarino, Venezia, Italy
| | - Alfonso Esposito
- Centre for Integrative Biology (CIBIO), Trento University, Trento, Italy
| | - Stefano Ferrari
- Fondazione Banca Degli Occhi Del Veneto Onlus, Zelarino, Venezia, Italy
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18
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Gomez CA, Sahoo MK, Kahn GY, Zhong L, Montoya JG, Pinsky BA, Doan T. Dual-target, real-time PCR for the diagnosis of intraocular Toxoplasma gondii infections. Br J Ophthalmol 2019; 103:569-572. [PMID: 30636207 PMCID: PMC6691874 DOI: 10.1136/bjophthalmol-2018-313064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/25/2018] [Accepted: 11/14/2018] [Indexed: 11/04/2022]
Abstract
BACKGROUND Toxoplasma gondii is the most common infectious cause of posterior uveitis worldwide. Two multicopy targets (B1 and Rep529) are commonly used in T. gondii PCR assays, but studies evaluating these targets in ocular fluid samples are limited. Herein, we determine the analytical characteristics of a single-reaction, internally controlled, dual-target, real-time T. gondii PCR and evaluate the clinical performance of this assay in intraocular fluid samples obtained at a reference ophthalmologic centre in the USA. METHODS Lower limits of detection for the B1 and Rep529 components of the dual-target assay were determined using serial dilutions of cultured T. gondii strain Z185. The dual-target assay was then used to test 148 archived intraocular samples (132 vitreous,16 aqueous humour) collected at the Francis I. Proctor Foundation between January 2010 and December 2015 for testing by a nested, conventional PCR targeting the B1 gene. RESULTS The 95% lower limits of detection for the dual-target assay was determined to be 1.05 tachyzoites/mL for B1 and 0.83 tachyzoites/mL for Rep529. Using archived clinical intraocular specimens, the dual-target assay demonstrated 97.2% positive per cent agreement (n=35/36; 95% CI 83.7% to 99.9%) and 99.1% negative per cent agreement (n=111/112; 95% CI 94.4% to 100%) compared with the nested, conventional B1 PCR. CONCLUSION This single-reaction, internally controlled, dual-target (B1, Rep529) real-time PCR for the detection of T. gondii DNA in intraocular specimens demonstrated excellent agreement with nested, conventional, B1 PCR. The dual-target design may ensure T. gondii detection when variation is present in one of two target regions.
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Affiliation(s)
- Carlos A Gomez
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Palo Alto Medical Foundation Toxoplasma Serology Laboratory, National Reference Center for the Study and Diagnosis of Toxoplasmosis, Palo Alto, California, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Ghazala Yasmeen Kahn
- Clinical Virology Laboratory, Stanford Health Care and Stanford Children's Health, Stanford, California, USA
| | - Lina Zhong
- F.I. Proctor Foundation, University of California San Francisco, San Francisco, California, USA
| | - José G Montoya
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Palo Alto Medical Foundation Toxoplasma Serology Laboratory, National Reference Center for the Study and Diagnosis of Toxoplasmosis, Palo Alto, California, USA
| | - Benjamin A Pinsky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA .,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Clinical Virology Laboratory, Stanford Health Care and Stanford Children's Health, Stanford, California, USA
| | - Thuy Doan
- F.I. Proctor Foundation, University of California San Francisco, San Francisco, California, USA.,Department of Ophthalmology, University of California, San Francisco, California, USA
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