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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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Abstract
Sarcoidosis frequently affects the eye and can do so in many different ways. Sarcoidosis causing uveitis can have distinctive features that facilitate identifying sarcoidosis as the cause of the uveitis. Progress is being made in elucidating ocular sarcoidosis, as for example, by transcriptomics, genetics, therapy, and imaging.
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Affiliation(s)
- James T Rosenbaum
- Legacy Devers Eye Institute, 1040 NW 22nd Avenue, Portland, OR 97210, USA; Corvus Pharmaceuticals, 863 Mitten Road Street 102, Burlingame, CA 94010, USA.
| | - Sirichai Pasadhika
- Legacy Devers Eye Institute, 1040 NW 22nd Avenue, Portland, OR 97210, USA
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Qian Z, Xia H, Zhou J, Wang R, Zhu D, Chen L, Kang H, Feng J, Hu X, Wang L, Xu S, Lou Z, Tao Y. Performance of Metagenomic Next-Generation Sequencing of Cell-Free DNA From Vitreous and Aqueous Humor for Diagnoses of Intraocular Infections. J Infect Dis 2024; 229:252-261. [PMID: 37882788 DOI: 10.1093/infdis/jiad363] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/28/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Delayed diagnosis and improper therapy for intraocular infections usually result in poor prognosis. Due to limitations of conventional culture and polymerase chain reaction methods, most causative pathogens cannot be identified from vitreous humor (VH) or aqueous humor (AH) samples with limited volume. METHODS Patients with suspected intraocular infections were enrolled from January 2019 to August 2021. Metagenomic next-generation sequencing (mNGS) was used to detected causative pathogens. RESULTS This multicenter prospective study enrolled 488 patients, from whom VH (152) and AH (336) samples were respectively collected and analyzed using mNGS of cell-free DNA (cfDNA). Taking final comprehensive clinical diagnosis as the gold standard, there were 39 patients with indefinite final diagnoses, whereas 288 and 161 patients were diagnosed as definite infectious and noninfectious diseases, respectively. Based on clinical adjudication, the sensitivity (92.2%) and total coincidence rate (81.3%) of mNGS using VH samples were slightly higher than those of mNGS using AH samples (85.4% and 75.4%, respectively). CONCLUSIONS Using mNGS of cfDNA, an era with clinical experience for more rapid, independent, and impartial diagnosis of bacterial and other intraocular infections can be expected.
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Affiliation(s)
- Zhuyun Qian
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University
- Key Laboratory jointly built by the National Institute for Viral Disease Control and Prevention of China Center for Disease Control and Prevention, Beijing GIANTMED Medical Diagnostics Laboratory
- Department of Medicine, Beijing GIANTMED Medical Diagnostics Laboratory
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co, Ltd, Beijing
| | - Jiemin Zhou
- Department of Scientific Affairs, Hugobiotech Co, Ltd, Beijing
| | - Ruifeng Wang
- Department of Ophthalmology, Zhengzhou Second People's Hospital, Zhengzhou, Henan
| | - Dan Zhu
- Department of Ophthalmology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia
| | - Li Chen
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University
| | - Hao Kang
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University
| | - Jing Feng
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University
| | - Xiaofeng Hu
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University
| | - Lu Wang
- Department of Medicine, Beijing GIANTMED Medical Diagnostics Laboratory
| | - Songtao Xu
- National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, China
| | - Zheng Lou
- Department of Scientific Affairs, Hugobiotech Co, Ltd, Beijing
| | - Yong Tao
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University
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Huang L, Suhler EB, Rosenberg C, Ta Kim D, Winthrop KL, Doan T, Lin P. Acanthamoeba-associated retinitis successfully treated with intravitreal and systemic antimicrobials. Am J Ophthalmol Case Rep 2023; 32:101902. [PMID: 37663996 PMCID: PMC10474359 DOI: 10.1016/j.ajoc.2023.101902] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/03/2023] [Accepted: 07/19/2023] [Indexed: 09/05/2023] Open
Abstract
Purpose To describe a case of unilateral Acanthamoeba-associated retinitis in the absence of concomitant corneal infection in an immunocompetent host without risk factors. Observations A 37-year-old woman presented with unilateral multifocal retinitis with minimal vitritis. Anterior segment was normal. Conventional diagnostics of bacterial, fungal, viral, Toxoplasma and Toxocara etiologies all returned negative. Empiric treatments were unsuccessful, including oral valacyclovir, oral fluconazole, as well as intravitreal injection of vancomycin and ceftazidime. Metagenomic deep sequencing (MDS) identified Acanthamoeba genomic fragments in the vitreous sample. Multiple intravitreal voriconazole injections were performed and achieved partial suppression of lesion growth. Subsequent dual therapy of oral voriconazole and trimethoprim-sulfamethoxazole led to resolution of the lesions and vision improvement without further injections. Conclusions and importance This is an unusual case of unilateral Acanthamoeba-associated retinitis without concomitant corneal infection, diagnosed via unbiased DNA and RNA deep sequencing, with other etiologies ruled out by conventional approaches. Treatment with systemic and intravitreal therapy led to a successful resolution of retinitis and vision improvement. Our case demonstrates the potential of MDS as an unbiased diagnostic tool for rare ocular pathogens and the therapeutic effect of oral voriconazole with trimethoprim-sulfamethoxazole for Acanthamoeba intraocular infection.
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Affiliation(s)
- Lingling Huang
- Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR, USA
| | - Eric B. Suhler
- Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR, USA
- Veterans Affairs Portland Health Care System, 3710 Southwest US Veterans Hospital Road, Portland, OR, USA
| | - Christopher Rosenberg
- Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR, USA
| | - David Ta Kim
- University of British Columbia, 2550 Willow Street, Vancouver, British Columbia, Canada
| | - Kevin L. Winthrop
- Division of Infectious Diseases, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, USA
| | - Thuy Doan
- Francis I. Proctor Foundation, University of California San Francisco, 490 Illinois Street, San Francisco, CA, USA
| | - Phoebe Lin
- Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR, USA
- Cole Eye Institute, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH, USA
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Zinter MS, Dvorak CC, Mayday MY, Reyes G, Simon MR, Pearce EM, Kim H, Shaw PJ, Rowan CM, Auletta JJ, Martin PL, Godder K, Duncan CN, Lalefar NR, Kreml EM, Hume JR, Abdel-Azim H, Hurley C, Cuvelier GDE, Keating AK, Qayed M, Killinger JS, Fitzgerald JC, Hanna R, Mahadeo KM, Quigg TC, Satwani P, Castillo P, Gertz SJ, Moore TB, Hanisch B, Abdel-Mageed A, Phelan R, Davis DB, Hudspeth MP, Yanik GA, Pulsipher MA, Sulaiman I, Segal LN, Versluys BA, Lindemans CA, Boelens JJ, DeRisi JL. Pulmonary microbiome and transcriptome signatures reveal distinct pathobiologic states associated with mortality in two cohorts of pediatric stem cell transplant patients. medRxiv 2023:2023.11.29.23299130. [PMID: 38077035 PMCID: PMC10705623 DOI: 10.1101/2023.11.29.23299130] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Lung injury is a major determinant of survival after pediatric hematopoietic cell transplantation (HCT). A deeper understanding of the relationship between pulmonary microbes, immunity, and the lung epithelium is needed to improve outcomes. In this multicenter study, we collected 278 bronchoalveolar lavage (BAL) samples from 229 patients treated at 32 children's hospitals between 2014-2022. Using paired metatranscriptomes and human gene expression data, we identified 4 patient clusters with varying BAL composition. Among those requiring respiratory support prior to sampling, in-hospital mortality varied from 22-60% depending on the cluster (p=0.007). The most common patient subtype, Cluster 1, showed a moderate quantity and high diversity of commensal microbes with robust metabolic activity, low rates of infection, gene expression indicating alveolar macrophage predominance, and low mortality. The second most common cluster showed a very high burden of airway microbes, gene expression enriched for neutrophil signaling, frequent bacterial infections, and moderate mortality. Cluster 3 showed significant depletion of commensal microbes, a loss of biodiversity, gene expression indicative of fibroproliferative pathways, increased viral and fungal pathogens, and high mortality. Finally, Cluster 4 showed profound microbiome depletion with enrichment of Staphylococci and viruses, gene expression driven by lymphocyte activation and cellular injury, and the highest mortality. BAL clusters were modeled with a random forest classifier and reproduced in a geographically distinct validation cohort of 57 patients from The Netherlands, recapitulating similar cluster-based mortality differences (p=0.022). Degree of antibiotic exposure was strongly associated with depletion of BAL microbes and enrichment of fungi. Potential pathogens were parsed from all detected microbes by analyzing each BAL microbe relative to the overall microbiome composition, which yielded increased sensitivity for numerous previously occult pathogens. These findings support personalized interpretation of the pulmonary microenvironment in pediatric HCT, which may facilitate biology-targeted interventions to improve outcomes.
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Affiliation(s)
- Matt S Zinter
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher C Dvorak
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Madeline Y Mayday
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Departments of Laboratory Medicine and Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Gustavo Reyes
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Miriam R Simon
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Emma M Pearce
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Hanna Kim
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Peter J Shaw
- The Children`s Hospital at Westmead, Sydney, Australia
| | - Courtney M Rowan
- Indiana University, Department of Pediatrics, Division of Critical Care Medicine, Indianapolis, IN, USA
| | - Jeffrey J Auletta
- Hematology/Oncology/BMT and Infectious Diseases, Nationwide Children's Hospital, Columbus, OH, USA
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Paul L Martin
- Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, NC, USA
| | - Kamar Godder
- Cancer and Blood Disorders Center, Nicklaus Children's Hospital, Miami, FL, USA
| | - Christine N Duncan
- Harvard Medical School, Boston, Massachusetts; Division of Pediatric Oncology, Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Nahal R Lalefar
- Division of Pediatric Hematology/Oncology, UCSF Benioff Children's Hospital Oakland, University of California San Francisco, Oakland, CA, USA
| | - Erin M Kreml
- Department of Child Health, Division of Critical Care Medicine, University of Arizona, Phoenix, AZ, USA
| | - Janet R Hume
- University of Minnesota, Department of Pediatrics, Division of Critical Care Medicine, Minneapolis, MN, USA
| | - Hisham Abdel-Azim
- Department of Pediatrics, Division of Hematology/Oncology and Transplant and Cell Therapy, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Loma Linda University School of Medicine, Cancer Center, Children Hospital and Medical Center, Loma Linda, CA, USA
| | - Caitlin Hurley
- Division of Critical Care, Department of Pediatric Medicine, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Geoffrey D E Cuvelier
- CancerCare Manitoba, Manitoba Blood and Marrow Transplant Program, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Amy K Keating
- Center for Cancer and Blood Disorders, Children's Hospital Colorado and University of Colorado, Aurora, CO, USA
- Harvard Medical School, Boston, Massachusetts; Division of Pediatric Oncology, Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Muna Qayed
- Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, GA, USA
| | - James S Killinger
- Division of Pediatric Critical Care, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Julie C Fitzgerald
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Rabi Hanna
- Department of Pediatric Hematology, Oncology and Blood and Marrow Transplantation, Pediatric Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kris M Mahadeo
- Department of Pediatrics, Division of Hematology/Oncology, MD Anderson Cancer Center, Houston, TX, USA
- Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, NC, USA
| | - Troy C Quigg
- Pediatric Blood and Marrow Transplantation Program, Texas Transplant Institute, Methodist Children's Hospital, San Antonio, TX, USA
- Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Prakash Satwani
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Paul Castillo
- University of Florida, Gainesville, UF Health Shands Children's Hospital, Gainesville, FL, USA
| | - Shira J Gertz
- Department of Pediatrics, Division of Critical Care Medicine, Joseph M Sanzari Children's Hospital at Hackensack University Medical Center, Hackensack, NJ, USA
- Department of Pediatrics, St. Barnabas Medical Center, Livingston, NJ, USA
| | - Theodore B Moore
- Department of Pediatric Hematology-Oncology, Mattel Children's Hospital, University of California, Los Angeles, CA, USA
| | - Benjamin Hanisch
- Children's National Hospital, Washington, District of Columbia, USA
| | - Aly Abdel-Mageed
- Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Rachel Phelan
- Division of Pediatric Hematology/Oncology/BMT, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Dereck B Davis
- Department of Pediatrics, Hematology/Oncology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Michelle P Hudspeth
- Adult and Pediatric Blood & Marrow Transplantation, Pediatric Hematology/Oncology, Medical University of South Carolina Children's Hospital/Hollings Cancer Center, Charleston, SC, USA
| | - Greg A Yanik
- Pediatric Blood and Bone Marrow Transplantation, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Michael A Pulsipher
- Division of Hematology, Oncology, Transplantation, and Immunology, Primary Children's Hospital, Huntsman Cancer Institute, Spense Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT, USA
| | - Imran Sulaiman
- Departments of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, NY, USA
| | - Leopoldo N Segal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, NY, USA
| | - Birgitta A Versluys
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Caroline A Lindemans
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, NY, USA
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Jaap J Boelens
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands
- Transplantation and Cellular Therapy, MSK Kids, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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Jiang X, Yan J, Huang H, Ai L, Yu X, Zhong P, Chen Y, Liang Z, Qiu W, Huang H, Yan W, Liang Y, Chen P, Wang R. Development of novel parameters for pathogen identification in clinical metagenomic next-generation sequencing. Front Genet 2023; 14:1266990. [PMID: 38046047 PMCID: PMC10693447 DOI: 10.3389/fgene.2023.1266990] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/27/2023] [Indexed: 12/05/2023] Open
Abstract
Introduction: Metagenomic next-generation sequencing (mNGS) has emerged as a powerful tool for rapid pathogen identification in clinical practice. However, the parameters used to interpret mNGS data, such as read count, genus rank, and coverage, lack explicit performance evaluation. In this study, the developed indicators as well as novel parameters were assessed for their performance in bacterium detection. Methods: We developed several relevant parameters, including 10M normalized reads, double-discard reads, Genus Rank Ratio, King Genus Rank Ratio, Genus Rank Ratio*Genus Rank, and King Genus Rank Ratio*Genus Rank. These parameters, together with frequently used read indicators including raw reads, reads per million mapped reads (RPM), transcript per kilobase per million mapped reads (TPM), Genus Rank, and coverage were analyzed for their diagnostic efficiency in bronchoalveolar lavage fluid (BALF), a common source for detecting eight bacterium pathogens: Acinetobacter baumannii, Klebsiella pneumoniae, Streptococcus pneumoniae, Staphylococcus aureus, Hemophilus influenzae, Stenotrophomonas maltophilia, Pseudomonas aeruginosa, and Aspergillus fumigatus. Results: The results demonstrated that these indicators exhibited good diagnostic efficacy for the eight pathogens. The AUC values of all indicators were almost greater than 0.9, and the corresponding sensitivity and specificity values were almost greater than 0.8, excepted coverage. The negative predictive value of all indicators was greater than 0.9. The results showed that the use of double-discarded reads, Genus Rank Ratio*Genus Rank, and King Genus Rank Ratio*Genus Rank exhibited better diagnostic efficiency than that of raw reads, RPM, TPM, and in Genus Rank. These parameters can serve as a reference for interpreting mNGS data of BALF. Moreover, precision filters integrating our novel parameters were built to detect the eight bacterium pathogens in BALF samples through machine learning. Summary: In this study, we developed a set of novel parameters for pathogen identification in clinical mNGS based on reads and ranking. These parameters were found to be more effective in diagnosing pathogens than traditional approaches. The findings provide valuable insights for improving the interpretation of mNGS reports in clinical settings, specifically in BALF analysis.
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Affiliation(s)
- Xiwen Jiang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Jinghai Yan
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hao Huang
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lu Ai
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xuegao Yu
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Pengqiang Zhong
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yili Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhikun Liang
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Wancen Qiu
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Huiying Huang
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Wenyan Yan
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Yan Liang
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Peisong Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ruizhi Wang
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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7
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Goodman C, Doan T, Mehra D, Betz J, Locatelli E, Mangwani-Mordani S, Kalahasty K, Hernandez M, Hwang JC, Galor A. Case-Control Study Examining the Composition of the Gut Microbiome in Individuals With and Without Immune-Mediated Dry Eye. Cornea 2023; 42:1340-1348. [PMID: 36729650 PMCID: PMC10261549 DOI: 10.1097/ico.0000000000003195] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/11/2022] [Indexed: 02/03/2023]
Abstract
PURPOSE Gut microbiome alterations have been associated with various autoimmune diseases. There are limited data, however, on relationships between gut dysbiosis and immune-related dry eye (DE). Our aim was to compare the gut microbiome composition of individuals with early and late markers of Sjögren syndrome (SS) with controls without DE. METHODS We compared 20 individuals with positive early markers [antisalivary protein 1 (SP1), antiparotid secretory protein (PSP), anticarbonic anhydrase 6 (CA6) IgG, IgA, and IgM, n = 19)], or late markers (anti-Ro/SS-A and anti-La/SS-B, n = 1) of SS with no comorbid autoimmune diagnoses and 20 age-matched and sex-matched controls. Collected stool samples underwent deep RNA sequencing. The main outcomes measured included gut microbiome composition and diversity. RESULTS A total of 20 cases [Dry Eye Questionnaire-5 15.2 ± 3.4, Ocular Surface Disease Index 55.1 ± 22.8, and Schirmer 7.1 ± 5.2 mm] were compared with 20 controls (Dry Eye Questionnaire-5 4.8 ± 3.8, Ocular Surface Disease Index 14.2 ± 12.3, and Schirmer 20.4 ± 9.2 mm). No differences were observed in α-diversity ( P = 0.97) or overall community structure ( P = 0.62). Between groups, 32 species were differentially abundant ( P < 0.01). Among cases, 27 were relatively more abundant, including 10 Lactobacillus and 4 Bifidobacterium species. A relative depletion of 5 species was found in cases compared with controls, notably Fusobacterium varium and Prevotella stercorea . CONCLUSIONS Differences in gut microbiome composition were found in individuals with mostly early markers of SS compared with controls. However, their clinical significance to DE manifestations remains unclear. Further studies are needed to elucidate the role of gut dysbiosis on immune dysregulation and disease activity in the various forms of immune-mediated DE.
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Affiliation(s)
- Courtney Goodman
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Thuy Doan
- Proctor Foundation, San Francisco, CA, USA
- University of California, San Francisco, Department of Ophthalmology, San Fracisco, CA, USA
| | - Divy Mehra
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jason Betz
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Elyana Locatelli
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Simran Mangwani-Mordani
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Karthik Kalahasty
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mireya Hernandez
- Miami Veterans Administration Medical Center, 1201 NW 16th St, Miami, FL 33125, USA
| | - Jodi C Hwang
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anat Galor
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA
- Miami Veterans Administration Medical Center, 1201 NW 16th St, Miami, FL 33125, USA
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8
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Rocha-de-Lossada C, Mazzotta C, Gabrielli F, Papa FT, Gómez-Huertas C, García-López C, Urbinati F, Rachwani-Anil R, García-Lorente M, Sánchez-González JM, Rechichi M, Rubegni G, Borroni D. Ocular Surface Microbiota in Naïve Keratoconus: A Multicenter Validation Study. J Clin Med 2023; 12:6354. [PMID: 37834997 PMCID: PMC10573816 DOI: 10.3390/jcm12196354] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
In the field of Ophthalmology, the mNGS 16S rRNA sequencing method of studying the microbiota and ocular microbiome is gaining more and more weight in the scientific community. This study aims to characterize the ocular microbiota of patients diagnosed with keratoconus who have not undergone any prior surgical treatment using the mNGS 16S rRNA sequencing method. Samples of naïve keratoconus patients were collected with an eNAT with 1 mL of Liquid Amies Medium (Copan Brescia, Italy), and DNA was extracted and analyzed with 16S NGS. The microbiota analysis showed a relative abundance of microorganisms at the phylum level in each sample collected from 38 patients with KC and 167 healthy controls. A comparison between healthy control and keratoconus samples identified two genera unique to keratoconus, Pelomonas and Ralstonia. Our findings suggest that alterations in the microbiota may play a role in the complex scenario of KC development.
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Affiliation(s)
- Carlos Rocha-de-Lossada
- Eyemetagenomics Ltd., 71–75, Shelton Street, Covent Garden, London WC2H 9JQ, UK;
- Ophthalmology Department, QVision, Vithas Almería, 04120 Almeria, Spain
- Ophthalmology Department, Hospital Regional Universitario Málaga, 29010 Malaga, Spain; (F.U.); (M.G.-L.)
| | - Cosimo Mazzotta
- Siena Crosslinking Center, 53100 Siena, Italy;
- Departmental Ophthalmology Unit, USL Toscana Sud Est l, 53100 Siena, Italy
- Postgraduate Ophthalmology School, University of Siena, 53100 Siena, Italy;
| | - Federico Gabrielli
- Biolab SRL, Laboratorio di Genetica e Genomica Molecolare, Largo degli Aranci, 9, 63100 Ascoli Piceno, Italy; (F.G.); (F.T.P.)
| | - Filomena Tiziana Papa
- Biolab SRL, Laboratorio di Genetica e Genomica Molecolare, Largo degli Aranci, 9, 63100 Ascoli Piceno, Italy; (F.G.); (F.T.P.)
| | - Carmen Gómez-Huertas
- Department of Ophthalmology, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain; (C.G.-H.); (C.G.-L.)
| | - Celia García-López
- Department of Ophthalmology, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain; (C.G.-H.); (C.G.-L.)
| | - Facundo Urbinati
- Ophthalmology Department, Hospital Regional Universitario Málaga, 29010 Malaga, Spain; (F.U.); (M.G.-L.)
| | | | - María García-Lorente
- Ophthalmology Department, Hospital Regional Universitario Málaga, 29010 Malaga, Spain; (F.U.); (M.G.-L.)
| | | | - Miguel Rechichi
- Centro Polispecialistico Mediterraneo, 88050 Sellia Marina, Italy;
| | - Giovanni Rubegni
- Postgraduate Ophthalmology School, University of Siena, 53100 Siena, Italy;
| | - Davide Borroni
- Eyemetagenomics Ltd., 71–75, Shelton Street, Covent Garden, London WC2H 9JQ, UK;
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He Y, Geng S, Mei Q, Zhang L, Yang T, Zhu C, Fan X, Wang Y, Tong F, Gao Y, Fang X, Bao R, Sheng X, Pan A. Diagnostic Value and Clinical Application of Metagenomic Next-Generation Sequencing for Infections in Critically Ill Patients. Infect Drug Resist 2023; 16:6309-6322. [PMID: 37780531 PMCID: PMC10541086 DOI: 10.2147/idr.s424802] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/14/2023] [Indexed: 10/03/2023] Open
Abstract
Objective To evaluate the diagnostic value and clinical application of metagenomic next-generation sequencing (mNGS) for infections in critically ill patients. Methods Comparison of diagnostic performance of mNGS and conventional microbiological testing for pathogens was analyzed in 234 patients. The differences between immunocompetent and immunocompromised individuals in mNGS-guided anti-infective treatment adjustment were also analyzed. Results The sensitivity and specificity of mNGS for bacterial and fungal detection were 96.6% (95% confidence interval [CI], 93.5%-99.6%) and 83.1% (95% CI, 75.2%-91.1%), and 85.7% (95% CI, 71.9%-99.5%) and 93.2% (95% CI, 89.7%-96.7%), respectively. Overall, 152 viruses were detected by mNGS, but in which 28 viruses were considered causative agents. The proportion of mNGS-guided beneficial anti-infective therapy adjustments in the immunocompromised group was greater than in the immunocompetent group (48.5% vs 30.1%; P=0.008). In addition, mNGS-guided anti-infective regimens with peripheral blood and BALF specimens had the highest proportion (39.0%; 40.0%), but the proportion of patients not helpful due to peripheral blood mNGS was also as high as 22.0%. Conclusion mNGS might be a promising technology to provide precision medicine for critically ill patients with infection.
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Affiliation(s)
- Yuxi He
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Shike Geng
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Qing Mei
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Lei Zhang
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Tianjun Yang
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Chunyan Zhu
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Xiaoqin Fan
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Yinzhong Wang
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Fei Tong
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Yu Gao
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Xiaowei Fang
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Renren Bao
- Department of Intensive Care Unit, the Affiliated Provincial Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China
| | - Ximei Sheng
- Department of Intensive Care Unit, the Training Center of Anhui Provincial Hospital, Wannan Medical College, Wuhu, Anhui, People’s Republic of China
| | - Aijun Pan
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
- Department of Intensive Care Unit, the Affiliated Provincial Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China
- Department of Intensive Care Unit, the Training Center of Anhui Provincial Hospital, Wannan Medical College, Wuhu, Anhui, People’s Republic of China
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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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11
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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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12
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Orr S, Pereira A, Jiang S, Golding J, Choudhry N, Kalevar A, Janetos TM, Goldstein DA. Diagnostic and Therapeutic Challenges. Retina 2023; 43:1628-1632. [PMID: 36996467 DOI: 10.1097/iae.0000000000003789] [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: 04/01/2023]
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13
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Li X, Li Z, Wang M, Fu A, Hao X, Guo X, Gu J, Jin W, Yang A. The diagnostic utility of nanopore targeted sequencing in suspected endophthalmitis. Int Ophthalmol 2023; 43:2653-2668. [PMID: 36941506 PMCID: PMC10371907 DOI: 10.1007/s10792-023-02665-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/19/2023] [Indexed: 03/23/2023]
Abstract
PURPOSE This paper aimed to assess the diagnostic utility of a newly developed gene-based technology-nanopore targeted sequencing (NTS) in suspected endophthalmitis patients. METHODS This retrospective study included 43 patients (44 eyes) with suspected endophthalmitis. NTS was applied along with microbiological culture to detect unknown pathogens in intraocular fluid samples. The diagnostic utility of NTS was mainly evaluated from three aspects, including the positivity rate of bacterial/fungal presence, diagnostic turnaround time and the frequency of change in treatment based on etiology test results. Non-parametric, two-sided Wilcoxon rank sum test, the McNemar's test and the kappa statistic were used for statistical comparisons. RESULTS NTS showed significant advantages over traditional culture in positivity rates and diagnostic time (P < 0.001, kappa = 0.082; Z = -5.805, P < 0. 001). As regards antibiotic strategy, 17 patients (39.53%) and 5 patients (11.63%) underwent medication change following NTS and culture results respectively (P < 0.001, kappa = 0.335). With reasonable use of antibiotic and surgical intervention, most patients responded favorably, judged by significantly improved visual acuity (Z = -4.249, P < 0.001). The mean duration of hospitalization was 8.49 ± 2.45 days (range, 1-16 days). CONCLUSION The high efficiency feature of NTS in pathogen detection renders it a valuable supplementary to traditional culture. Additionally, it has facilitated patients' management for the early and precise diagnosis of endophthalmitis.
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Affiliation(s)
- Xuejie Li
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Ziyue Li
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Ming Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, China
| | - Aisi Fu
- Wuhan Dgensee Clinical Laboratory Co, Ltd. Wuhan 430075, Hubei Province, China
| | - Xinlei Hao
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Xinyang Guo
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Jiashuang Gu
- Wuhan Dgensee Clinical Laboratory Co, Ltd. Wuhan 430075, Hubei Province, China
| | - Wei Jin
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China.
| | - Anhuai Yang
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China.
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14
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Popova G, Retallack H, Kim CN, Wang A, Shin D, DeRisi JL, Nowakowski T. Rubella virus tropism and single-cell responses in human primary tissue and microglia-containing organoids. eLife 2023; 12:RP87696. [PMID: 37470786 PMCID: PMC10370260 DOI: 10.7554/elife.87696] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
Rubella virus is an important human pathogen that can cause neurological deficits in a developing fetus when contracted during pregnancy. Despite successful vaccination programs in the Americas and many developed countries, rubella remains endemic in many regions worldwide and outbreaks occur wherever population immunity is insufficient. Intense interest since rubella virus was first isolated in 1962 has advanced our understanding of clinical outcomes after infection disrupts key processes of fetal neurodevelopment. Yet it is still largely unknown which cell types in the developing brain are targeted. We show that in human brain slices, rubella virus predominantly infects microglia. This infection occurs in a heterogeneous population but not in a highly microglia-enriched monoculture in the absence of other cell types. By using an organoid-microglia model, we further demonstrate that rubella virus infection leads to a profound interferon response in non-microglial cells, including neurons and neural progenitor cells, and this response is attenuated by the presence of microglia.
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Affiliation(s)
- Galina Popova
- Department of Neurological Surgery, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
- Department of Psychiatry and Behavioral Sciences, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Hanna Retallack
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Chang N Kim
- Department of Neurological Surgery, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
- Department of Psychiatry and Behavioral Sciences, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Albert Wang
- Department of Neurological Surgery, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
- Department of Psychiatry and Behavioral Sciences, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - David Shin
- Department of Neurological Surgery, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
- Department of Psychiatry and Behavioral Sciences, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Tomasz Nowakowski
- Department of Neurological Surgery, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
- Department of Psychiatry and Behavioral Sciences, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
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15
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Kaidonis G, Lamy R, Wu J, Yang D, Psaras C, Doan T, Stewart JM. Aqueous Fluid Transcriptome Profiling Differentiates Between Non-Neovascular and Neovascular AMD. Invest Ophthalmol Vis Sci 2023; 64:26. [PMID: 37471072 PMCID: PMC10365141 DOI: 10.1167/iovs.64.10.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
Purpose Early and intermediate non-neovascular AMD (NN-AMD) has the potential to progress to either advanced NN-AMD with geographic atrophy, or to neovascular AMD (N-AMD) with CNV. This exploratory study performed an unbiased analysis of aqueous humor transcriptome in patients with early or intermediate NN-AMD vs. treatment-naïve N-AMD to determine the feasibility of using this method in future studies investigating pathways and triggers for conversion from one form to another. Methods Aqueous humor samples were obtained from 20 patients with early or intermediate NN-AMD and 20 patients with untreated N-AMD, graded on clinical examination and optical coherence tomography. Transcriptome profiles were generated using next-generation sequencing methods optimized for ocular samples. Top-ranked transcripts were compared between groups, and pathway enrichment analysis was performed. Results Seventy-eight differentially expressed transcripts were identified. Unsupervised clustering of differentially expressed transcripts was able to successfully differentiate between the two groups based on aqueous transcriptome alone. Pathway analysis highlighted changes in expression of genes associated with mitochondrial respiration, oxidative stress, ubiquitination, and neurogenesis between the two groups. Conclusions This pilot study compared the aqueous fluid transcriptome of patients with early or intermediate NN-AMD and untreated N-AMD. Differences in transcripts and transcriptome pathways identified in the aqueous of patients with early or intermediate NN-AMD compared with patients with N-AMD are consistent with those previously implicated in the pathogenesis of these distinct AMD subtypes. The findings from this exploratory study warrant further investigation using a larger, prospective study design, with the inclusion of a control group of eyes without AMD.
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Affiliation(s)
- Georgia Kaidonis
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
| | - Ricardo Lamy
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
- Department of Ophthalmology, Zuckerberg San Francisco General Hospital and Trauma Center, San Francisco, California, United States
| | - Joshua Wu
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
- Department of Ophthalmology, Zuckerberg San Francisco General Hospital and Trauma Center, San Francisco, California, United States
| | - Daphne Yang
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
- Department of Ophthalmology, Zuckerberg San Francisco General Hospital and Trauma Center, San Francisco, California, United States
| | - Catherine Psaras
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
- Department of Ophthalmology, Zuckerberg San Francisco General Hospital and Trauma Center, San Francisco, California, United States
| | - Thuy Doan
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
- Francis I. Proctor Foundation, San Francisco, California, United States
| | - Jay M Stewart
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
- Department of Ophthalmology, Zuckerberg San Francisco General Hospital and Trauma Center, San Francisco, California, United States
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16
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Moussa K, Gonzales JA, Shantha J, Acharya NR, Doan T. Prevalence of Epstein-Barr Virus in Patients with Intraocular Inflammation. Ocul Immunol Inflamm 2023; 31:978-980. [PMID: 35708307 PMCID: PMC10424495 DOI: 10.1080/09273948.2022.2075760] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/02/2022] [Accepted: 05/05/2022] [Indexed: 10/18/2022]
Abstract
The relationship between Epstein-Barr virus (EBV) infection and uveitis is unclear. We conducted an observational cross-sectional study to determine the prevalence of EBV in uveitis and to describe the clinical features of EBV-positive uveitis cases. This study was carried out at the F.I. Proctor Foundation at the University of California, San Francisco. All patients with suspected infectious uveitis who underwent unbiased metagenomic deep sequencing (MDS) were included. Demographics, testing information, and clinical features were documented. Eleven out of 288 patients with suspected infectious uveitis had EBV detected by RNA-seq in intraocular fluid. The prevalence of EBV in uveitis in our study sample is 4%. Three out of 11 EBV-positive eyes (27%) were found to have biopsy-proven vitreoretinal lymphoma. Future studies are needed to determine if EBV may drive the development of vitreoretinal lymphoma and if its presence should heighten the suspicion of vitreoretinal lymphoma.
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Affiliation(s)
- Kareem Moussa
- Department of Ophthalmology and Vision Science, University of California, Davis, Sacramento, CA
- F.I. Proctor Foundation, San Francisco, San Francisco, CA
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA
| | - John A. Gonzales
- F.I. Proctor Foundation, San Francisco, San Francisco, CA
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA
| | - Jessica Shantha
- F.I. Proctor Foundation, San Francisco, San Francisco, CA
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA
| | - Nisha R. Acharya
- F.I. Proctor Foundation, San Francisco, San Francisco, CA
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA
| | - Thuy Doan
- F.I. Proctor Foundation, San Francisco, San Francisco, CA
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA
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17
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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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18
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Ung L, Chodosh J. Urgent unmet needs in the care of bacterial keratitis: An evidence-based synthesis. Ocul Surf 2023; 28:378-400. [PMID: 34461290 PMCID: PMC10721114 DOI: 10.1016/j.jtos.2021.08.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 11/21/2022]
Abstract
Bacterial corneal infections, or bacterial keratitis (BK), are ophthalmic emergencies that frequently lead to irreversible visual impairment. Though increasingly recognized as a major cause of global blindness, modern paradigms of evidence-based care in BK have remained at a diagnostic and therapeutic impasse for over half a century. Current standards of management - based on the collection of corneal cultures and the application of broad-spectrum topical antibiotics - are beset by important yet widely underrecognized limitations, including approximately 30% of all patients who will develop moderate to severe vision loss in the affected eye. Though recent advances have involved a more clearly defined role for adjunctive topical corticosteroids, and novel therapies such as corneal crosslinking, overall progress to improve patient and population-based outcomes remains incommensurate to the chronic morbidity caused by this disease. Recognizing that the care of BK is guided by the clinical axiom, "time equals vision", this chapter offers an evidence-based synthesis for the clinical management of these infections, underscoring critical unmet needs in disease prevention, diagnosis, and treatment.
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Affiliation(s)
- Lawson Ung
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - James Chodosh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA.
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19
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Abstract
Endophthalmitis is an ophthalmological emergency requiring timely and appropriate diagnosis and treatment. Microbiological methods of microscopy (Gram's staining) and culture are the current gold standard for organism identification. However, a significant proportion of endophthalmitis remains culture-negative-perhaps the inflammation is non-infectious in origin, results from a novel organism are unidentifiable or because the causative organism is non-culturable often due to pre-treatment with antibiotics. This review outlines the microbiological profile of endophthalmitis, current clinically used methods for organism identification, and the newer molecular techniques of polymerase chain reaction (PCR) and next-generation sequencing (NGS) technology as diagnostic tools for endophthalmitis. They offer the potential to improve organism identification rates and clinical outcomes in infectious diseases, representing an exciting future direction for organism identification in endophthalmitis. Based on the largest ophthalmic hospital in Australia, we highlight the key practical challenges faced by Australian diagnostic laboratories for their use in a clinical setting.
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Affiliation(s)
- Christine L Tan
- Macular Research Unit, Centre for Eye Research Australia, East Melbourne, Australia.,Department of Ophthalmology, The University of Melbourne, Parkville, Australia
| | - Harsha Sheorey
- Department of Microbiology, St Vincent's Hospital, Fitzroy, Australia
| | - Penelope J Allen
- Macular Research Unit, Centre for Eye Research Australia, East Melbourne, Australia.,Department of Ophthalmology, The University of Melbourne, Parkville, Australia.,Vitreo-retinal Unit, The Royal Victorian Eye and Ear Hospital, East Melbourne, Australia
| | - Rosie C H Dawkins
- Macular Research Unit, Centre for Eye Research Australia, East Melbourne, Australia.,Department of Ophthalmology, The University of Melbourne, Parkville, Australia.,Vitreo-retinal Unit, The Royal Victorian Eye and Ear Hospital, East Melbourne, Australia
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20
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Zuo YH, Wu YX, Hu WP, Chen Y, Li YP, Song ZJ, Luo Z, Ju MJ, Shi MH, Xu SY, Zhou H, Li X, Jie ZJ, Liu XD, Zhang J. The Clinical Impact of Metagenomic Next-Generation Sequencing (mNGS) Test in Hospitalized Patients with Suspected Sepsis: A Multicenter Prospective Study. Diagnostics (Basel) 2023; 13. [PMID: 36673134 DOI: 10.3390/diagnostics13020323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/28/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Background: Metagenomic Next Generation Sequencing (mNGS) has the potential to detect pathogens rapidly. We aimed to assess the diagnostic performance of mNGS in hospitalized patients with suspected sepsis and evaluate its role in guiding antimicrobial therapy. Methods: A multicenter, prospective cohort study was performed. We enrolled patients with suspected sepsis, collected clinical characteristics and blood samples, and recorded the 30-day survival. Diagnostic efficacy of mNGS test and blood culture was compared, and the clinical impact of mNGS on antibiotic regimen modification was analyzed. Results: A total of 277 patients were enrolled, and 162 were diagnosed with sepsis. The mortality was 44.8% (121/270). The mNGS test exhibited shorter turn-out time (27.0 (26.0, 29.0) vs. 96.0 (72.0, 140.3) hours, p < 0.001) and higher sensitivity (90.5% vs. 36.0%, p < 0.001) compared with blood culture, especially for fungal infections. The mNGS test showed better performance for patients with mild symptoms, prior antibiotic use, and early stage of infection than blood culture, and was capable of guiding antibiotic regimen modification and improving prognosis. Higher reads of pathogens detected by mNGS were related to 30-day mortality (p = 0.002). Conclusions: Blood mNGS testing might be helpful for early etiological diagnosis of patients with suspected sepsis, guiding the antibiotic regimen modification and improving prognosis.
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21
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Borroni D, Bonzano C, Sánchez-González JM, Rachwani-Anil R, Zamorano-Martín F, Pereza-Nieves J, Traverso CE, García Lorente M, Rodríguez-Calvo-de-Mora M, Esposito A, Godin F, Rocha-de-Lossada C. Shotgun metagenomic sequencing in culture negative microbial keratitis. Eur J Ophthalmol 2023:11206721221149077. [PMID: 36617769 DOI: 10.1177/11206721221149077] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
PURPOSE To evaluate the microbiota of culture negative Corneal Impression Membrane (CIM) microbial keratitis samples with the use of shotgun metagenomics analysis. METHODS DNA of microbial keratitis samples were collected with CIM and extracted using the MasterPure™ Complete DNA and RNA Purification Kit (Epicentre). DNA was fragmented by sonication into fragments of 300 to 400 base pairs (bp) using Bioruptor® (Diagenode, Belgium) and then used as a template for library preparation. DNA libraries were sequenced on Illumina® HiSeq2500. The resulting reads were quality controlled, trimmed and mapped against the human reference genome. The unmapped reads were taxonomically classified using the Kraken software. RESULTS 18 microbial keratitis samples were included in the study. Brevundimonas diminuta was found in 5 samples while 6 samples showed the presence of viral infections. Cutibacterium acnes, Staphylococcus aureus, Moraxella lacunata and Pseudomonas alcaligenes were also identified as the presumed putative cause of the infection in 7 samples. CONCLUSIONS Shotgun sequencing can be used as a diagnostic tool in microbial keratitis samples. This diagnostic method expands the available tests to diagnose eye infections and could be clinically significant in culture negative samples.
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Affiliation(s)
- Davide Borroni
- Department of Ophthalmology, Riga Stradins University, Riga, Latvia
| | - Chiara Bonzano
- DiNOGMI, University of Genoa and IRCCS San Martino Polyclinic Hospital, Genoa, Italy
| | | | | | | | | | - Carlo Enrico Traverso
- DiNOGMI, University of Genoa and IRCCS San Martino Polyclinic Hospital, Genoa, Italy
| | | | | | - Alfonso Esposito
- 18470International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Fernando Godin
- Department of Ophthalmology, Universidad El Bosque, Bogotá, Colombia
| | - Carlos Rocha-de-Lossada
- Qvision, Opththalmology Department, VITHAS Almería Hospital, Almería, Spain.,Ophthalmology Department, VITHAS Málaga, Málaga, Spain.,Hospital Regional Universitario de Málaga, Plaza del Hospital Civil, Málaga, Spain.,Departamento de Cirugía, Universidad de Sevilla, Área de Oftalmología, Doctor Fedriani, Seville, Spain
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22
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Pepple KL, John S, Wilson L, Wang V, Van Gelder RN. Systemic prime exacerbates the ocular immune response to heat-killed Mycobacterium tuberculosis. Exp Eye Res 2022; 223:109198. [PMID: 35921962 PMCID: PMC10240933 DOI: 10.1016/j.exer.2022.109198] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/23/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022]
Abstract
Post-infectious uveitis describes the condition of chronic immune mediated ocular inflammation associated with pathogens such as Mycobacterium tuberculosis (Mtb). Mtb associated post-infectious uveitis can be modeled in mice by intravitreal injection of heat-killed Mtb (HKMtb). To better understand how prior systemic exposure to the pathogen alters the local immune response to Mtb, we used flow cytometry and multiplex ELISAs to compare ocular responses to intravitreal HKMtb in the presence or absence of a systemic "prime" of HKMtb. Priming resulted in exacerbation of local inflammation with significantly increased clinical and histologic inflammation scores and increased vitreous cytokines concentrations one day after intravitreal injection of HKMtb. Seven days after injection, uveitis in unprimed animals had largely resolved. In contrast in primed animals, clinical signs of chronic inflammation were associated with a significant increase in the number of ocular T cells, NK cells, and Ly6Chi macrophages and increasing vitreous concentrations of IL-17, VEGF, MIG(CXCL9), IP-10(CXCL10), IL-12p40 and MIP-1α(CCL3). In mice lacking mature T and B cells (RAG2 deficient), the impact of priming on the ocular immune response was ameliorated with significantly lower vitreous cytokine concentrations and spontaneous resolution of uveitis. Altogether these results suggest that the ocular response to Mtb is exacerbated by prior systemic Mtb infection and chronic post-infectious uveitis is mediated by local production of cytokines and chemokines that amplify Th17 and Th1 responses. This mouse model of chronic Mtb associated uveitis will help elucidate mechanisms of disease in patients with post-infectious uveitis.
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Affiliation(s)
- Kathryn L Pepple
- University of Washington, Department of Ophthalmology, Seattle, WA, 98104, USA; University of Washington, Roger and Angie Karalis Johnson Retina Center, Seattle, WA, 98109, USA.
| | - Sarah John
- University of Washington, Department of Ophthalmology, Seattle, WA, 98104, USA
| | - Leslie Wilson
- University of Washington, Department of Ophthalmology, Seattle, WA, 98104, USA
| | - Victoria Wang
- University of Washington, Department of Ophthalmology, Seattle, WA, 98104, USA
| | - Russell N Van Gelder
- University of Washington, Department of Ophthalmology, Seattle, WA, 98104, USA; University of Washington, Department of Biological Structure, Seattle, WA, 98195, USA; University of Washington, Department of Laboratory Medicine and Pathology, Seattle, WA, 98195, USA; University of Washington, Roger and Angie Karalis Johnson Retina Center, Seattle, WA, 98109, USA
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23
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Zhang M, Wang Z, Wang J, Lv H, Xiao X, Lu W, Jin X, Meng J, Pu Y, Zhao M. The Value of Metagenomic Next-Generation Sequencing in Hematological Malignancy Patients with Febrile Neutropenia After Empiric Antibiotic Treatment Failure. Infect Drug Resist 2022; 15:3549-3559. [PMID: 35837537 PMCID: PMC9273631 DOI: 10.2147/idr.s364525] [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: 03/01/2022] [Accepted: 06/30/2022] [Indexed: 11/23/2022] Open
Abstract
Background It was crucial to use empirical antibiotics in febrile neutropenia (FN) patients. However, most patients still died from infection due to poor efficacy. Metagenomic next-generation sequencing (mNGS) is a rapid microbiological diagnostic method. The value of mNGS in patients with FN remains to be studied, especially after empiric antibiotic treatment. Methods We retrospectively analyzed the differences between mNGS and the traditional methods in 192 patients with hematological malignancies who have received empiric antibiotic treatment. Samples were collected when patient had chills or half an hour before peak body temperature. And we compared the differences between FN and non-FN patients, mainly including types of pathogens and the diagnostic value of different pathogens. Results Despite receiving empirical treatment, the pathogen detection rate of mNGS was significantly higher than the traditional method (80.21% vs 25.00%, P<0.001). And it has obvious advantages in detecting mixed pathogens infection (80.21% vs 4.17%, P<0.001). Then, we found that mNGS saw more pathogens in the FN than in the non-FN group, especially fungus. 21/33 (63.63%) of FN patients was diagnosed with fungal infections. The fungal detection rate in FN was significantly higher than non-FN group (32.35% vs 12.22%, P=0.001). Besides, the sensitivity of mNGS was higher than the traditional methods in both FN and non-FN group (P<0.001), but no significant difference in specificity (P>0.05). In the FN group, empiric antibiotic treatment of 46/102 (45.10%) patients did not treat all the pathogens detected by mNGS. After adjusting the antimicrobial regimen according to the results of mNGS, the effective rate at 72 hours and 7 days was 22/46 (47.83%) and 24/102 (52.17%), respectively. Conclusion mNGS had a significant impact on the diagnosis of infection and the second-line antimicrobial therapy in FN. mNGS plays a more important role in FN patients, especially in the diagnosis of fungal infections. Purpose Firstly, we compared the difference between mNGS and the traditional methods in the diagnosis of infection. Secondly, we assessed the value of mNGS in FN patients by comparing it with non-FN patients, including types of pathogens and the diagnostic value of different pathogens. In order to show that mNGS plays a more important role in FN.
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Affiliation(s)
- Meng Zhang
- First Central Clinical College, Tianjin Medical University, Tianjin, 300192, People's Republic of China.,Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People's Republic of China
| | - Zhao Wang
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People's Republic of China
| | - Jiaxi Wang
- First Central Clinical College, Tianjin Medical University, Tianjin, 300192, People's Republic of China
| | - Hairong Lv
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People's Republic of China
| | - Xia Xiao
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People's Republic of China
| | - Wenyi Lu
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People's Republic of China
| | - Xin Jin
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People's Republic of China
| | - Juanxia Meng
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People's Republic of China
| | - Yedi Pu
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People's Republic of China
| | - MingFeng Zhao
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People's Republic of China
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24
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Wu W, Jiang H, Zhang Y, Zhou Y, Bai G, Shen L, Zhou H, Chen X, Hu L. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Secondary Glaucoma in Patients With Cytomegalovirus-Induced Corneal Endotheliitis. Front Microbiol 2022; 13:940818. [PMID: 35865935 PMCID: PMC9295740 DOI: 10.3389/fmicb.2022.940818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022] Open
Abstract
Glaucoma is the second leading cause of blindness globally. Growing scientific evidence indicated that inflammation of the trabecular meshwork induced by corneal endotheliitis could lead to secondary glaucoma. Cytomegalovirus (CMV) has been identified as the most common herpes virus in corneal endotheliitis patients. Early detection is critical in preventing endothelial cell loss, and patient management should vary based on different pathological factors. However, routine culture and real-time polymerase chain reaction (qPCR) have difficult in distinguishing whether CMV, Varicella Zoster Virus (VZV) or Herpes Simplex Virus (HSV) causes endothiliitis. This may result in inappropriate treatment, which may prolong or aggravate the status of disease. We compared the sensitivity and specificity of qPCR and Metagenomic Next-Generation Sequencing (mNGS) in the aqueous humor of patients with suspected CMV endotheliitis in this study. Our results showed that four out of 11 (36.4%) of our patients were positive for CMV by qPCR, whereas mNGS had a 100% detection rate of CMV. Our findings implied that mNGS could be a useful diagnostic tool for CMV-induced endotheliitis.
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Affiliation(s)
- Wei Wu
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hua Jiang
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Zhang
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yang Zhou
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd., Hangzhou, China
| | - Guannan Bai
- The Children’s Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Lingwei Shen
- Department of Clinical Laboratory, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Hongwei Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Xiangjun Chen
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Xiangjun Chen,
| | - Lidan Hu
- The Children’s Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
- Lidan Hu,
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25
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Xu P, Yang K, Yang L, Wang Z, Jin F, Wang Y, Feng J. Next-Generation Metagenome Sequencing Shows Superior Diagnostic Performance in Acid-Fast Staining Sputum Smear-Negative Pulmonary Tuberculosis and Non-tuberculous Mycobacterial Pulmonary Disease. Front Microbiol 2022; 13:898195. [PMID: 35847073 PMCID: PMC9283093 DOI: 10.3389/fmicb.2022.898195] [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: 03/26/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
In this study, we explored the clinical value of next-generation metagenome sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) samples from patients with acid-fast staining (AFS) sputum smear-negative pulmonary tuberculosis (PTB) and non-tuberculous mycobacterial pulmonary disease (NTM-PD). Data corresponding to hospitalized patients with pulmonary infection admitted to the hospital between July 2018 and July 2021, who were finally diagnosed with AFS sputum smear-negative PTB and NTM-PD, were retrospectively analyzed. Bronchoscopy data as well as mNGS, Xpert, AFS (BALF analysis), and T-SPOT (blood) data, were extracted from medical records. Thereafter, the diagnostic performances of these methods with respect to PTB and NTM-PD were compared. Seventy-one patients with PTB and 23 with NTM-PD were included in the study. The sensitivities of mNGS, Xpert, T-SPOT, and AFS for the diagnosis of PTB were 94.4% (67/71), 85.9% (61/71), 64.8% (46/71), and 28.2% (20/71), respectively, and the diagnostic sensitivity of mNGS combined with Xpert was the highest (97.2%, 67/71). The specificity of Xpert was 100%, while those of AFS and T-SPOT were 73.9% (17/23) and 91.3% (21/23), respectively. Further, the 23 patients with NTM-PD could be identified using mNGS, and in the population with immunosuppression, the sensitivities of mNGS, Xpert, T-SPOT, and AFS were 93.5% (29/31), 80.6% (25/31), 48.4% (15/31), and 32.3% (10/31), respectively, and the diagnostic sensitivity of mNGS combined with Xpert was the highest (100%, 31/31). The specificities of Xpert and T-SPOT in this regard were both 100%, while that of AFS was 40% (2/5). Furthermore, using mNGS, all the NTM samples could be identified. Thus, the analysis of BALF samples using mNGS has a high accuracy in the differential diagnosis of MTB and NTM. Further, mNGS combined with Xpert can improve the detection of MTB, especially in AFS sputum smear-negative samples from patients with compromised immune states or poor responses to empirical antibiotics.
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Affiliation(s)
- Peng Xu
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Ke Yang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Lei Yang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhongli Wang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
- Department of Respiratory and Critical Care Medicine, Shandong Second Provincial General Hospital, Jinan, China
| | - Fang Jin
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Yubao Wang
- Institute of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Jing Feng
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
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26
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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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27
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Chen MH, Abernathy E, Icenogle JP, Perelygina LM. Improved diagnostic and multiplex RT-qPCR for detecting rubella viral RNA. J Virol Methods 2022; 306:114555. [PMID: 35654258 DOI: 10.1016/j.jviromet.2022.114555] [Citation(s) in RCA: 2] [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: 04/21/2022] [Revised: 05/19/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022]
Abstract
An examination of the nucleic acid sequence alignment of 48 full-length rubella virus genomes revealed that the 5' terminus of the genome is more conserved than the commonly used detection windows for rubella virus RNA located in the E1 protein coding region, suggesting that the 5' terminus could be a target for improving detection of all rubella virus genotypes. Two candidate primer sets were tested and the window between nucleotides (nts) 98 and 251 was found to have the greatest analytical sensitivity for detection of different genotypes. The new method had a limit of detection of four copies of rubella RNA per reaction with high specificity. The average coefficient variation of Ct was 2.2%. Concordance between the new method and currently used method, based on testing 251 clinical specimens collected from a rubella outbreak, was 99.4%. The assay was further improved upon by the incorporation of detection of both rubella virus RNA and mRNA from a cellular reference gene in a multiplex format. The multiplex format did not reduce the sensitivity or the reproducibility of rubella RNA detection and, of 60 specimens tested, the concordance between the single target and multiplex assays was 85.0%. To assess the utility of the multiplex assay for molecular surveillance, 62 rubella IgM positive serum samples from a rubella outbreak were tested, and eleven tested positive using the multiplex method while none were positive using the method targeting E1. These results show that the assay based on the new detection window near the 5' terminus of the genome can improve the detection of rubella virus for the purpose of molecular surveillance and case confirmation, with the added benefit of improved efficiency due to multiplexing.
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Affiliation(s)
- Min-Hsin Chen
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | - Emily Abernathy
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Joseph P Icenogle
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Ludmila M Perelygina
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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28
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Gonzales JA, Sundararajan M, Qian Y, Hwang T, Doan T. Detection of Leptospirosis Genome from the Aqueous Humor of a Patient with Bilateral Uveitis. Ocul Immunol Inflamm 2022:1-3. [PMID: 35486672 DOI: 10.1080/09273948.2022.2067779] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Leptospira species are difficult to culture. Thus, when there is suspicion for an infectious etiology to uveitis, bacterial cultures may fail to identify Leptospira. We describe a case of leptospirosis-associated uveitis that evaded culture and molecular assays. DNA sequencing of the aqueous fluid showed the presence of Leptospira spp. METHODS Retrospective case review of clinical and laboratory features of a patient with ocular leptospirosis is presented. RESULTS DNA sequencing identified the genome of Leptospirosis spp. in the aqueous humor. CONCLUSION Metagenomic sequencing, by virtue of its unbiased nature, can be a helpful adjunctive test when a strong clinical suspicion for intraocular infection persists despite negative routine culture and molecular assays.
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Affiliation(s)
- John A Gonzales
- Proctor Foundation, University of California Francis I., San Francisco, California, USA.,Department of Ophthalmology, University of California, San Francisco, California, USA
| | - Miel Sundararajan
- Proctor Foundation, University of California Francis I., San Francisco, California, USA.,Department of Ophthalmology, University of California, San Francisco, California, USA
| | - Ying Qian
- Department of Ophthalmology, Kaiser Permanente, Oakland Medical Center, Oakland, California, USA
| | - Thomas Hwang
- Department of Ophthalmology, Kaiser Permanente, Redwood City Medical Center, Redwood City, California, USA
| | - Thuy Doan
- Proctor Foundation, University of California Francis I., San Francisco, California, USA.,Department of Ophthalmology, University of California, San Francisco, California, USA
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30
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Ma KK, Ung L, Chodosh J. Evidence-based Management of Culture-negative Microbial Keratitis. Int Ophthalmol Clin 2022; 62:111-24. [PMID: 35325914 DOI: 10.1097/IIO.0000000000000411] [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: 11/26/2022]
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31
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Bohl JA, Lay S, Chea S, Ahyong V, Parker DM, Gallagher S, Fintzi J, Man S, Ponce A, Sreng S, Kong D, Oliveira F, Kalantar K, Tan M, Fahsbender L, Sheu J, Neff N, Detweiler AM, Yek C, Ly S, Sath R, Huch C, Kry H, Leang R, Huy R, Lon C, Tato CM, DeRisi JL, Manning JE. Discovering disease-causing pathogens in resource-scarce Southeast Asia using a global metagenomic pathogen monitoring system. Proc Natl Acad Sci U S A 2022; 119:e2115285119. [PMID: 35238677 DOI: 10.1073/pnas.2115285119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
SignificanceMetagenomic pathogen sequencing offers an unbiased approach to characterizing febrile illness. In resource-scarce settings with high biodiversity, it is critical to identify disease-causing pathogens in order to understand burden and to prioritize efforts for control. Here, metagenomic next-generation sequencing (mNGS) characterization of the pathogen landscape in Cambodia revealed diverse vector-borne and zoonotic pathogens irrespective of age and gender as risk factors. Identification of key pathogens led to changes in national program surveillance. This study is a "real world" example of the use of mNGS surveillance of febrile individuals, executed in-country, to identify outbreaks of vector-borne, zoonotic, and other emerging pathogens in a resource-scarce setting.
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32
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Liu C, Li W, Zhang C, Pang F, Wang DW. Previously unexplored etiology for femoral head necrosis: Metagenomics detects no pathogens in necrotic femoral head tissue. World J Clin Cases 2022; 10:2138-2146. [PMID: 35321171 PMCID: PMC8895187 DOI: 10.12998/wjcc.v10.i7.2138] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/17/2021] [Accepted: 01/25/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Osteonecrosis of the femoral head (ONFH) is a frequent and refractory disease whose pathogenesis has not yet been elucidated. Infection and other factors that reduce the local blood supply can lead to bone necrosis.
AIM To aim of this study was to assess the relationship of ONFH with bone infection by use of metagenomic sequencing.
METHODS Twelve patients with idiopathic ONFH and 12 comparable controls who were undergoing hip arthroplasty were followed up in parallel. Necrotic femoral head specimens were collected for bacterial and fungal cultures using standard methods. Bone specimens were subjected to preliminary processing, and metagenomics sequencing of microorganisms was performed. A one-way analysis of variance was used to compare bacterial species in the two groups.
RESULTS Bacterial and fungal cultures exhibited no evidence of microbial growth in all isolated necrotic femoral head tissues. We thus performed metagenomic sequencing and classified the species as suspected pathogens or suspected background microorganisms based on known bacterial pathogenicity. There was no evidence of viruses, fungi, parasites, M. tuberculosis complex, or mycoplasma/chlamydia. There were also no significant differences in suspected pathogens or suspected background microorganisms (P > 0.05).
CONCLUSION Although we found no pathogens specific for ONFH in necrotic femoral head tissue, our research provides a foundation for future research on the metagenomics of bone pathogens.
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Affiliation(s)
- Chao Liu
- Department of Orthopedics, Liaocheng People's Hospital, Liaocheng 252000, Shandong Province, China
- Department of Orthopedics, Shandong The First Medical University, Taian 271016, Shandong Province, China
| | - Wei Li
- Department of Orthopedics, Liaocheng People's Hospital, Liaocheng 252000, Shandong Province, China
| | - Chao Zhang
- Department of Orthopedics, Shandong The First Medical University, Taian 271016, Shandong Province, China
| | - Feng Pang
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng 252000, Shandong Province, China
| | - Da-Wei Wang
- Department of Orthopedics, Liaocheng People's Hospital, Liaocheng 252000, Shandong Province, China
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33
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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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34
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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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35
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Miao S, Lin Q, Li X, Zhao L, Pan Z. Possible association between viral infection and poor survival of the corneal graft after penetrating keratoplasty in patients with congenital corneal opacity: a cohort study. Br J Ophthalmol 2022; 107:763-768. [PMID: 35027353 DOI: 10.1136/bjophthalmol-2021-320031] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 01/03/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Congenital corneal opacity (CCO) is a rare disorder. Penetrating keratoplasty (PK) is the main surgical option for CCO, but many factors affect graft survival. Therefore, this study aimed to perform a virological examination of CCO specimens after PK to explore the relationship between virological factors and graft survival after PK. METHODS This prospective study included consecutive patients (<6 months of age) diagnosed with CCO and treated with PK at Beijing Tongren Hospital from August 2017 to January 2018. Next-generation sequencing was used to detect viral DNA in the CCO specimens. The survival of the primary graft was analysed using the Kaplan-Meier method. RESULTS Overall, 24 eyes of 24 infants were treated with PK during the study period. The mean age at surgery was 4.8±1.1 months. Epstein-Barr virus DNA was detected in two specimens, varicella-zoster virus DNA in one specimen, herpes simplex virus DNA in three specimens and cytomegalovirus DNA in one specimen. In the virus-positive group, only one (14.3%) graft remained clear during follow-up. In contrast, in the virus-negative group (n=17), 13 (76.5%) grafts were still clear at the last follow-up. The mean survival of the grafts in the virus-positive group was significantly shorter than in the virus-negative group (11.0±9.8 months vs 27.1±7.7, p<0.001). CONCLUSION The presence of viral DNA in CCO specimens might be associated with poor graft survival after PK.
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Affiliation(s)
- Sen Miao
- Department of Ophthalmology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Qi Lin
- Department of Ophthalmology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xu Li
- Department of Ophthalmology, Beijing Ophthalmology and Visual Science Key laboratory, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical Unversity, Beijing, China
| | - Lu Zhao
- Department of Ophthalmology, Beijing Ophthalmology and Visual Science Key laboratory, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical Unversity, Beijing, China
| | - Zhiqiang Pan
- Department of Ophthalmology, Beijing Ophthalmology and Visual Science Key laboratory, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical Unversity, Beijing, China
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36
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Redd TK, Lalitha P, Prajna NV, Sikha M, Gunasekaran R, Hinterwirth A, Chen C, Zhong L, Liu Z, Lietman TM, Keenan JD, Doan T, Seitzman GD. Impact of Sample Collection Order on the Diagnostic Performance of Metagenomic Deep Sequencing for Infectious Keratitis. Cornea 2022; 41:39-44. [PMID: 34870622 PMCID: PMC8649208 DOI: 10.1097/ico.0000000000002766] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/26/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE The purpose of this article was to evaluate the impact of sample collection order on the diagnostic yield of metagenomic deep sequencing (MDS) for determining the causative pathogen in infectious keratitis. METHODS We performed a cross-sectional diagnostic test evaluation among subjects with infectious keratitis at Aravind Eye Hospital in Madurai, India. All subjects underwent corneal scrapings of the affected eye to obtain potassium hydroxide smear, Gram stain, bacterial culture, and fungal culture, in this order. The order of MDS specimen collection relative to smear and culture samples was randomized and served as the primary predictor. Outcomes included the normalized copy number of pathogenic RNA detected by MDS, the proportion of MDS samples that were diagnostic, and the agreement of MDS results with cultures. RESULTS MDS samples from 46 subjects with corneal ulcers were evaluated. MDS was positive in 33 subjects (76%) and had 74% overall agreement with culture results. There was no association between order of MDS sample collection and normalized copy number of genetic material detected (P = 0.62) or the likelihood of MDS positivity (P = 0.46). However, the likelihood of agreement between MDS and cultures decreased when MDS corneal swabs were collected after other diagnostic corneal scrapings (P = 0.05). CONCLUSIONS The overall yield of MDS for detecting the cause of infectious keratitis was not affected by sample collection order. However, diagnostic agreement between MDS and cultures decreased when MDS samples were collected after other specimens. Additional investigation is warranted to determine whether this represents increased sensitivity of MDS compared with cultures or higher susceptibility to contaminants.
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Affiliation(s)
- Travis K. Redd
- Francis I. Proctor Foundation, University of California San Francisco, CA, USA
- Casey Eye Institute, Oregon Health & Science University, OR, USA
| | | | | | - Misra Sikha
- Aravind Eye Hospital, Madurai, Tamil Nadu, India
| | | | - Armin Hinterwirth
- Francis I. Proctor Foundation, University of California San Francisco, CA, USA
| | - Cindi Chen
- Francis I. Proctor Foundation, University of California San Francisco, CA, USA
| | - Lina Zhong
- Francis I. Proctor Foundation, University of California San Francisco, CA, USA
| | - Zijun Liu
- Francis I. Proctor Foundation, University of California San Francisco, CA, USA
| | - Thomas M. Lietman
- Francis I. Proctor Foundation, University of California San Francisco, CA, USA
| | - Jeremy D. Keenan
- Francis I. Proctor Foundation, University of California San Francisco, CA, USA
| | - Thuy Doan
- Francis I. Proctor Foundation, University of California San Francisco, CA, USA
| | - Gerami D. Seitzman
- Francis I. Proctor Foundation, University of California San Francisco, CA, USA
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37
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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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Li Q, Huang W, Zhang S, Zheng Y, Lv Q, Kong D, Zhang L, Zhang Y, Zhao Z, Wang M, Jiang H, Liu P, Jiang Y. Target-enriched sequencing enables accurate identification of bloodstream infections in whole blood. J Microbiol Methods 2021; 192:106391. [PMID: 34915067 DOI: 10.1016/j.mimet.2021.106391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 11/20/2022]
Abstract
Bloodstream infections are within the top ten causes of death globally, with a mortality rate of up to 70%. Gold standard blood culture testing is time-consuming, resulting in delayed, but accurate, treatment. Molecular methods, such as RT-qPCR, have limited targets in one run. We present a new Ampliseq detection system (ADS) combining target amplification and next-generation sequencing for accurate identification of bacteria, fungi, and antimicrobial resistance determinants directly from blood samples. In this study, we included removal of human genomic DNA during nucleic acid extraction, optimized the target sequence set and drug resistance genes, performed antimicrobial resistance profiling of clinical isolates, and evaluated mock specimens and clinical samples by ADS. ADS successfully identified pathogens at the species-level in 36 h, from nucleic acid extraction to results. Besides pathogen identification, ADS can also present drug resistance profiles. ADS enabled detection of all bacteria and accurate identification of 47 pathogens. In 20 spiked samples and 8 clinical specimens, ADS detected at least 92.81% of reads mapped to pathogens. ADS also showed consistency with the three culture-negative samples, and correctly identified pathogens in four of five culture-positive clinical blood specimens. This Ampliseq-based technology promises broad coverage and accurate pathogen identification, helping clinicians to accurately diagnose and treat bloodstream infections.
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Meredith S, Oakley M, Kumar S. Technologies for Detection of Babesia microti: Advances and Challenges. Pathogens 2021; 10:pathogens10121563. [PMID: 34959518 PMCID: PMC8703551 DOI: 10.3390/pathogens10121563] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 10/05/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 12/26/2022] Open
Abstract
The biology of intraerythrocytic Babesia parasites presents unique challenges for the diagnosis of human babesiosis. Antibody-based assays are highly sensitive but fail to detect early stage Babesia infections prior to seroconversion (window period) and cannot distinguish between an active infection and a previously resolved infection. On the other hand, nucleic acid-based tests (NAT) may lack the sensitivity to detect window cases when parasite burden is below detection limits and asymptomatic low-grade infections. Recent technological advances have improved the sensitivity, specificity and high throughput of NAT and the antibody-based detection of Babesia. Some of these advances include genomics approaches for the identification of novel high-copy-number targets for NAT and immunodominant antigens for superior antigen and antibody-based assays for Babesia. Future advances would also rely on next generation sequencing and CRISPR technology to improve Babesia detection. This review article will discuss the historical perspective and current status of technologies for the detection of Babesia microti, the most common Babesia species causing human babesiosis in the United States, and their implications for early diagnosis of acute babesiosis, blood safety and surveillance studies to monitor areas of expansion and emergence and spread of Babesia species and their genetic variants in the United States and globally.
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40
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Huang Q, Fu A, Wang Y, Zhang J, Zhao W, Cheng Y. Microbiological diagnosis of endophthalmitis using nanopore targeted sequencing. Clin Exp Ophthalmol 2021; 49:1060-1068. [PMID: 34463015 PMCID: PMC9292959 DOI: 10.1111/ceo.13992] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 06/07/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Microorganism identification is critical for the early diagnosis and management of infectious endophthalmitis, but traditional culture can yield false-negative results. Nanopore targeted sequencing (NTS) is a third-generation sequencing technique with multiple advantages. This study aimed to test aqueous humour or vitreous fluid samples from presumed cases of infectious endophthalmitis using NTS to evaluate the feasibility of NTS in diagnosing endophthalmitis, especially for culture-negative cases. METHODS This prospective study enrolled patients who presented to the Department of Ophthalmology of Union Hospital (Wuhan, China) between June 2018 and December 2020. The samples were sent immediately for routine microbiology culture processing and NTS assay. RESULTS NTS identified microorganisms in 17 of 18 cases (94.4%) (eight culture-positive cases, nine culture-negative cases, and one case unavailable for culture). There was a high-quality match between culture and NTS for culture-positive cases. In the eight culture-negative cases and the case unavailable for culture, NTS detected either bacteria, fungi, or a mixture of bacteria and fungi in the intraocular fluids. The average waiting times for the results of bacterial and fungal cultures were 48 and 72 h, respectively. The average time for the NTS results was 12 h. CONCLUSIONS NTS appears to be a promising diagnostic platform for diagnosing infectious endophthalmitis, even for culture-negative cases.
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Affiliation(s)
- Qiong Huang
- Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aisi Fu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Yiyan Wang
- Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jie Zhang
- Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wanxu Zhao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, China.,Wuhan Dgensee Clinical Laboratory Co., Ltd, Wuhan, China
| | - Yang Cheng
- Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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d'Humières C, Salmona M, Dellière S, Leo S, Rodriguez C, Angebault C, Alanio A, Fourati S, Lazarevic V, Woerther PL, Schrenzel J, Ruppé E. The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives. Drugs 2021; 81:1453-1466. [PMID: 34328626 PMCID: PMC8323086 DOI: 10.1007/s40265-021-01572-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Accepted: 07/07/2021] [Indexed: 12/24/2022]
Abstract
Clinical metagenomics (CMg) is the process of sequencing nucleic acid of clinical samples to obtain clinically relevant information such as the identification of microorganisms and their susceptibility to antimicrobials. Over the last decades, sequencing and bioinformatic solutions supporting CMg have much evolved and an increasing number of case reports and series covering various infectious diseases have been published. Metagenomics is a new approach to infectious disease diagnosis that is currently being developed and is certainly one of the most promising for the coming years. However, most CMg studies are retrospective, and few address the potential impact CMg could have on patient management, including initiation, adaptation, or cessation of antimicrobials. In this narrative review, we have discussed the potential role of CMg in bacteriology, virology, mycology, and parasitology. Several reports and case-series confirm that CMg is an innovative tool with which one can (i) identify more microorganisms than with conventional methods in a single test, (ii) obtain results within hours, and (iii) tailor the antimicrobial regimen of patients. However, the cost-efficiency of CMg and its real impact on patient management are still to be determined.
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Affiliation(s)
- Camille d'Humières
- Université de Paris, IAME, INSERM, 75018, Paris, France.,AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018, Paris, France
| | - Maud Salmona
- Unité de Paris, INSERM U976, Insight Team, 75010, Paris, France.,AP-HP, Hôpital Saint-Louis, Laboratoire de Virologie, 75010, Paris, France
| | - Sarah Dellière
- AP-HP, Hôpital Saint-Louis, Laboratoire de Parasitologie-Mycologie, 75010, Paris, France.,Molecular Mycology Unit, Institut Pasteur, CNRS UMR2000, 75015, Paris, France
| | - Stefano Leo
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Christophe Rodriguez
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,INSERM U955, Université Paris-Est, 94000, Créteil, France
| | - Cécile Angebault
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,Université Paris Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, EA7380 Dynamic, 94000, Créteil, France
| | - Alexandre Alanio
- AP-HP, Hôpital Saint-Louis, Laboratoire de Parasitologie-Mycologie, 75010, Paris, France.,Molecular Mycology Unit, Institut Pasteur, CNRS UMR2000, 75015, Paris, France
| | - Slim Fourati
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,INSERM U955, Université Paris-Est, 94000, Créteil, France
| | - Vladimir Lazarevic
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Paul-Louis Woerther
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,Université Paris Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, EA7380 Dynamic, 94000, Créteil, France
| | - Jacques Schrenzel
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Etienne Ruppé
- Université de Paris, IAME, INSERM, 75018, Paris, France. .,AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018, Paris, France.
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Comas I, Cancino-Muñoz I, Mariner-Llicer C, Goig GA, Ruiz-Hueso P, Francés-Cuesta C, García-González N, González-Candelas F. Use of next generation sequencing technologies for the diagnosis and epidemiology of infectious diseases. Enferm Infecc Microbiol Clin 2021; 38 Suppl 1:32-38. [PMID: 32111363 DOI: 10.1016/j.eimc.2020.02.006] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For the first time, next generation sequencing technologies provide access to genomic information at a price and scale that allow their implementation in routine clinical practice and epidemiology. While there are still many obstacles to their implementation, there are also multiple examples of their major advantages compared with previous methods. Their main advantage is that a single determination allows epidemiological information on the causative microorganism to be obtained simultaneously, as well as its resistance profile, although these advantages vary according to the pathogen under study. This review discusses several examples of the clinical and epidemiological use of next generation sequencing applied to complete genomes and microbiomes and reflects on its future in clinical practice.
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Affiliation(s)
- Iñaki Comas
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España; CIBER en Epidemiología y Salud Pública, Valencia, España.
| | | | | | - Galo A Goig
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España
| | - Paula Ruiz-Hueso
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Carlos Francés-Cuesta
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Neris García-González
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Fernando González-Candelas
- CIBER en Epidemiología y Salud Pública, Valencia, España; Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
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Rosenbaum JT, Van Gelder RN. Tautologies and the Telltale Tubercle Bacillus. Ophthalmology 2021; 128:288-9. [PMID: 33485477 DOI: 10.1016/j.ophtha.2020.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 11/23/2022] Open
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Okajima Y, Suzuki T, Miyazaki C, Goto S, Ishikawa S, Suzuki Y, Aoki K, Ishii Y, Tateda K, Hori Y. Metagenomic Shotgun Sequencing Analysis of Canalicular Concretions in Lacrimal Canaliculitis Cases. Curr Issues Mol Biol 2021; 43:676-86. [PMID: 34287258 DOI: 10.3390/cimb43020049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 11/17/2022] Open
Abstract
Lacrimal canaliculitis is a rare infection of the lacrimal canaliculi with canalicular concretions formed by aggregation of organisms. Metagenomic shotgun sequencing analysis using next-generation sequencing has been used to detect pathogens directly from clinical samples. Using this technology, we report cases of successful pathogen detection of canalicular concretions in lacrimal canaliculitis cases. We investigated patients with primary lacrimal canaliculitis examined in the eye clinics of four hospitals from February 2015 to July 2017. Eighteen canalicular concretion specimens collected from 18 eyes of 17 patients were analyzed by shotgun metagenomics sequencing using the MiSeq platform (Illumina). Taxonomic classification was performed using the GenBank NT database. The canalicular concretion diversity was characterized using the Shannon diversity index. This study included 18 eyes (17 patients, 77.1 ± 6.1 years): 82.4% were women with lacrimal canaliculitis; canalicular concretions were obtained from 12 eyes using lacrimal endoscopy and six eyes using canaliculotomy with curettage. Sequencing analysis detected bacteria in all samples (Shannon diversity index, 0.05–1.47). The following genera of anaerobic bacteria (>1% abundance) were identified: Actinomyces spp. in 15 eyes, Propionibacterium spp., Parvimonas spp. in 11 eyes, Prevotella spp. in 9 eyes, Fusobacterium spp. in 6 eyes, Selenomonas spp. in 5 eyes, Aggregatibacter spp. in 3 eyes, facultative and aerobic bacteria such as Streptococcus spp. in 13 eyes, Campylobacter spp. in 6 eyes, and Haemophilus spp. in 3 eyes. The most common combinations were Actinomyces spp. and Streptococcus spp. and Parvinomonas spp. and Streptococcus spp., found in 10 cases. Pathogens were identified successfully using metagenomic shotgun sequencing analysis in patients with canalicular concretions. Canalicular concretions are polymicrobial with anaerobic and facultative, aerobic bacteria.
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Zylberberg M, Van Hemert C, Handel CM, Liu RM, DeRisi JL. POECIVIRUS IS PRESENT IN INDIVIDUALS WITH BEAK DEFORMITIES IN SEVEN SPECIES OF NORTH AMERICAN BIRDS. J Wildl Dis 2021; 57:273-81. [PMID: 33822149 DOI: 10.7589/JWD-D-20-00017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/08/2020] [Indexed: 11/20/2022]
Abstract
Avian keratin disorder (AKD), a disease of unknown etiology characterized by debilitating beak overgrowth, has increasingly affected wild bird populations since the 1990s. A novel picornavirus, poecivirus, is closely correlated with disease status in Black-capped Chickadees (Poecile atricapillus) in Alaska, US. However, our knowledge of the relationship between poecivirus and beak deformities in other species and other geographic areas remains limited. The growing geographic scope and number of species affected by AKD-like beak deformities require a better understanding of the causative agent to evaluate the population-level impacts of this epizootic. Here, we tested eight individuals from six avian species with AKD-consistent deformities for the presence of poecivirus: Mew Gull (Larus canus), Hairy Woodpecker (Picoides villosus), Black-billed Magpie (Pica hudsonia), American Crow (Corvus brachyrhynchos), Red-breasted Nuthatch (Sitta canadensis), and Blackpoll Warbler (Setophaga striata). The birds were sampled in Alaska and Maine (1999-2016). We used targeted PCR followed by Sanger sequencing to test for the presence of poecivirus in each specimen and to obtain viral genome sequence from virus-positive host individuals. We detected poecivirus in all individuals tested, but not in negative controls (water and tissue samples). Furthermore, we used unbiased metagenomic sequencing to test for the presence of other pathogens in six of these specimens (Hairy Woodpecker, two American Crows, two Red-breasted Nuthatches, Blackpoll Warbler). This analysis yielded additional viral sequences from several specimens, including the complete coding region of poecivirus from one Red-breasted Nuthatch, which we confirmed via targeted PCR followed by Sanger sequencing. This study demonstrates that poecivirus is present in individuals with AKD-consistent deformities from six avian species other than Black-capped Chickadee. While further investigation will be required to explore whether there exists a causal link between this virus and AKD, this study demonstrates that poecivirus is not geographically restricted to Alaska, but rather occurs elsewhere in North America.
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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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Fried WA, Soltero-Rivera M, Ramesh A, Lommer MJ, Arzi B, DeRisi JL, Horst JA. Use of unbiased metagenomic and transcriptomic analyses to investigate the association between feline calicivirus and feline chronic gingivostomatitis in domestic cats. Am J Vet Res 2021; 82:381-394. [PMID: 33904799 DOI: 10.2460/ajvr.82.5.381] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To identify associations between microbes and host genes in cats with feline chronic gingivostomatitis (FCGS), a debilitating inflammatory oral mucosal disease with no known cause, compared with healthy cats and cats with periodontitis (control cats). ANIMALS 19 control cats and 23 cats with FCGS. PROCEDURES At least 1 caudal oral mucosal swab specimen was obtained from each cat. Each specimen underwent unbiased metatranscriptomic next-generation RNA sequencing (mNGS). Filtered mNGS reads were aligned to all known genetic sequences from all organisms and to the cat transcriptome. The relative abundances of microbial and host gene read alignments were compared between FCGS-affected cats and control cats and between FCGS-affected cats that did and did not clinically respond to primary treatment. Assembled feline calicivirus (FCV) genomes were compared with reverse transcription PCR (RT-PCR) primers commonly used to identify FCV. RESULTS The only microbe strongly associated with FCGS was FCV, which was detected in 21 of 23 FCGS-affected cats but no control cats. Problematic base pair mismatches were identified between the assembled FCV genomes and RT-PCR primers. Puma feline foamy virus was detected in 9 of 13 FCGS-affected cats that were refractory to treatment and 5 healthy cats but was not detected in FCGS-affected cats that responded to tooth extractions. The most differentially expressed genes in FCGS-affected cats were those associated with antiviral activity. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that FCGS pathogenesis has a viral component. Many FCV strains may yield false-negative results on RT-PCR-based assays. Coinfection of FCGS-affected cats with FCV and puma feline foamy virus may adversely affect response to treatment.
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Mishra D, Satpathy G, Chawla R, Paliwal D, Panda SK. Targeted metagenomics using next generation sequencing in laboratory diagnosis of culture negative endophthalmitis. Heliyon 2021; 7:e06780. [PMID: 33997374 DOI: 10.1016/j.heliyon.2021.e06780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/22/2021] [Accepted: 04/08/2021] [Indexed: 11/29/2022] Open
Abstract
To study the feasibility of 16S rRNA metagenomics using next generation sequencing (NGS) along with broad range PCR assay for 762 bp region of 16S rRNA gene with Sanger's sequencing, in microbial diagnosis of culture negative endophthalmitis. Vitreous fluid from 16 culture negative and one culture positive endophthalmitis patients, admitted to a tertiary care hospital were processed for targeted metagenomics. NGS of 7 variable regions of 16S rRNA gene was done using Ion Torrent Personal Genome Machine (PGM). Sequence data were analyzed using Ion Reporter software using QIIME and BLSATN tools and Greengenes and NCBI–Genbank databases. Bacterial genome sequences were detected in 15 culture negative and culture positive vitreous specimens. The sequence reads varied between 25,245–540,916 with read length between 142bp–228bp and coverage depth was 41.0X and 81.2X. Operational taxonomic unit (OTUs) of multiple bacterial genera and species were detected in 13 culture negative vitreous specimens and OTUs of a single bacterial species were detected in 2 culture negative and 1 culture positive specimens; one negative specimen had no bacterial DNA. Maximum numbers of OTUs detected by NGS for a bacterial species from any vitreous specimen was the one which was detected and identified by Sanger's sequencing in broad range PCR. All the bacteria were belonging to clinically relevant species. Broad range PCR with sequencing failed to identify bacteria from 5 of the 16 (31.25%) culture negative vitreous specimens. Metagenomics could detect and identify bacterial pathogens in 15 of the 16 culture negative vitreous specimen's up to species level. With rapidly decreasing cost, metagenomics has a potential to be used widely in endophthalmitis diagnosis, in which culture negativity is usually high.
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Kobayashi T, Suzuki T, Okajima Y, Aoki K, Ishii Y, Tateda K, Hori Y. Metagenome Techniques for Detection of Pathogens Causing Ocular Infection. Reports 2021; 4:6. [DOI: 10.3390/reports4010006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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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Lee MD, Pasricha N, Driver TH, Lopez SE, Seitzman GD. Microbiological alterations in the conjunctiva of hot tub-soaking ophthalmologists (MACHO): a randomized double-blind clinical trial. Med Hypothesis Discov Innov Ophthalmol 2021; 9:221-230. [PMID: 38249356 PMCID: PMC10798179 DOI: 10.51329/mehdiophthal1409] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Background To determine if there is a difference in the quantity of microbial flora of the conjunctiva in individuals practicing head submersion ("dunk") versus no head submersion ("no-dunk") during hot tub use. Methods In this double-blind randomized clinical trial, healthy volunteers aged ≥ 18 years were recruited. Participants were randomized to head submersion versus no head submersion during a 15-minute hot tub soak. Study personnel, masked to the dunk or no-dunk group assignment, obtained conjunctival cultures before and immediately after hot tub use. De-identified specimens were submitted to the clinical microbiology laboratory for culture and analysis. The main outcome measure was the difference in the quantity of organisms cultured from the conjunctiva before and after hot tub exposure, as determined using a defined ordinal scale. A two-tailed Student's t-test was performed to compare the total microbial colony counts between the two arms. Simpson's diversity was used to measure the changes in organism diversity between the arms. Results Of 36 enrolled subjects, 19 were randomly assigned to the dunk and 17 were assigned to the no-dunk groups. Water samples obtained from all hot tubs were culture negative. Eleven of 19 eyes (58%) from the dunk group and eight of 17 eyes (47%) from the no-dunk group had negative conjunctival bacterial cultures before and after hot tub exposure. However, six of 19 eyes (32%) and four of 17 eyes (24%) of the dunk and no-dunk groups, respectively, were culture-positive after, but not before hot tub exposure. The quantity of organisms before and after hot tub exposure was not significantly different between the two arms (P = 0.12). However, the dunk group only showed a small increase in the quantity of organisms after as compared to before hot tub use (P = 0.03). None of the samples from subjects or hot tubs were culture-positive for Acanthamoeba. Conclusions Head submersion in a public hot tubs during a 15-minute soak does not appear to change conjunctival flora, as determined by culture plate yield, this does not eliminate the association between hot tub use and devastating and painful corneal blindness. Therefore, our recommendation is to remove contact lenses prior to hot tub use, avoid head submersion in a hot tub, and urgently seek ophthalmological help if any eye pain and/or decrease in vision is experienced after hot tub use.
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Affiliation(s)
- Michele D. Lee
- Department of Ophthalmology, University of Washington School of Medicine, Seattle, WA, USA
| | - Neel Pasricha
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
| | - Todd H. Driver
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
- Frances I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA
| | - Sarah E. Lopez
- Frances I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA
| | - Gerami D. Seitzman
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
- Frances I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA
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