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Benador-Shen C, Shantha J, Lee J, Qian Y, Doan T, Gonzales JA. Multiple Anterior Chamber Paracenteses May Be Needed to Identify Cytomegalovirus Anterior Uveitis. Am J Ophthalmol 2024; 269:189-194. [PMID: 39218387 DOI: 10.1016/j.ajo.2024.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/17/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
PURPOSE To demonstrate cases of anterior uveitis requiring more than one anterior chamber paracenesis to elucidate CMV as the causative etiology. DESIGN Retrospective chart review. METHODS Patients were seen at the Francis I. Proctor Foundation at the University of California, San Francisco between 2013 and 2024. Patients who required more than one anterior chamber paracentesis to detect CMV as the etiologic agent of their anterior uveitis were included. Number of anterior chamber paracenteses required to detect CMV, demographic and clinical features, viral load at time of positive anterior chamber paracentesis and association between topical corticosteroid use and viral load at time of positive anterior chamber paracentesis. RESULTS Fourteen patients required a median of 2 (range 2-4) anterior chamber paracenteses to detect CMV. Mean age was 48.2 years, and 57.1% were male. Most patients (64.3%) were born in East and Southeast Asia. All affected eyes featured ocular hypertension. Five patients (35.7%) were initially treated with systemic immunosuppression before CMV was detected. Increasing frequency of topical corticosteroid use was significantly associated with higher CMV viral loads (P < .001). Five patients (35.7%) required glaucoma surgery. In 13 patients with available data, uveitis was present for an average of 2776 days (range 23-7889 days) prior to CMV detection. Once diagnosed, most patients were treated with oral valganciclovir, with one patient transitioning to letermovir due to side effects. CONCLUSIONS CMV anterior uveitis may be more prevalent than previously recognized and often requires multiple anterior chamber paracenteses for diagnosis. Reliance on a signle negative test may lead to misdiagnosis and inappropriate treatment. Clinicians should maintain a high index of suspicion for CMV in cases of recurrent anterior uveitis, particularly in patients of East and Southeast Asian descent. This study highlights the importance of repeated testing and appropriate antiviral treatment to prevent complications such as glaucoma.
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Affiliation(s)
- Christine Benador-Shen
- From the Kaiser Permanente Northern California (C.B.-S.), San Francisco, California, USA
| | - Jessica Shantha
- Francis I. Proctor Foundation, University of California San Francisco (J.S., T.D.), San Francisco, California, USA; Department of Ophthalmology, University of California San Francisco (J.S.,T.D.), San Francisco, California, USA
| | - Jennifer Lee
- Sharp-Rees-Stealy and Rady Childrens Hospital (J.L.), San Diego, California, USA
| | - Ying Qian
- Kaiser Permanente Northern California (Y.Q.), Oakland, California, USA
| | - Thuy Doan
- Francis I. Proctor Foundation, University of California San Francisco (J.S., T.D.), San Francisco, California, USA; Department of Ophthalmology, University of California San Francisco (J.S.,T.D.), San Francisco, California, USA
| | - John A Gonzales
- Francis I. Proctor Foundation, University of California San Francisco (J.S., T.D.), San Francisco, California, USA; Department of Ophthalmology, University of California San Francisco (J.S.,T.D.), San Francisco, California, USA.
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Choo C, Cote O, Bostwick K, Regueiro M, Wells J, Grossniklaus HE, Gonzales J, Yeh S, Hinterwirth A, Doan T, Shantha JG. Deep sequencing as a diagnostic tool in patients with suspected primary vitreoretinal lymphoma. Br J Ophthalmol 2024:bjo-2023-324769. [PMID: 39122354 DOI: 10.1136/bjo-2023-324769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/08/2024] [Indexed: 08/12/2024]
Abstract
PURPOSE To compare the diagnostic utility of metagenomic deep sequencing (MDS) to cytology, flow cytometry and gene rearrangement by PCR in ocular samples of patients with suspected vitreoretinal lymphoma (VRL). METHODS Patients with suspected VRL underwent ocular sampling of one or both eyes at the Emory Eye Center from September 2017 to June 2022. Ocular samples were evaluated with MDS and conventional diagnostics. MDS was performed at the Ralph and Sophie Heintz Laboratory at the F.I. Proctor Foundation. Relevant demographic and clinical data were retrospectively collected from medical records. Patients were diagnosed with VRL based on clinical assessment and conventional diagnostic testing. RESULTS This study included 13 patients with suspected VRL who underwent diagnostic vitrectomy, including 1 patient who had an additional subretinal biopsy. Six patients (46.2%) were diagnosed with VRL. Among patients diagnosed with VRL, MDS detected pathogenic mutations in 5 out of 6 patients (83.3%) while cytology was positive for VRL in 4 out of 6 patients (66.7%), flow cytometry in 4 out of 4 patients (100.0%) and PCR in 4 out of 4 patients (100.0%). MDS detected mutations in MYD88 in 2 out of 6 patients diagnosed with VRL. In 7 patients (53.8%) not diagnosed with VRL, MDS detected pathogenic lymphoma mutations in 2 patients (28.6%). DISCUSSION MDS detected pathogenic mutations in five out of six patients diagnosed with VRL, including in two patients with negative cytology, demonstrating its potential to improve diagnostic rates of VRL as an adjunctive test.
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Affiliation(s)
- Charlene Choo
- Francis I Proctor Foundation, San Francisco, California, USA
| | - Olivia Cote
- Emory University School of Medicine, Atlanta, Georgia, USA
| | | | | | | | | | - John Gonzales
- Francis I Proctor Foundation, San Francisco, California, USA
- Department of Ophthalmology, University of California San Francisco, San Francisco, California, USA
| | - Steven Yeh
- Department of Ophthalmology and Visual Sciences, Truhlsen Eye Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | | | - Thuy Doan
- Francis I Proctor Foundation, San Francisco, California, USA
- Department of Ophthalmology, University of California San Francisco, San Francisco, California, USA
| | - Jessica G Shantha
- Francis I Proctor Foundation, San Francisco, California, USA
- Department of Ophthalmology, University of California San Francisco, San Francisco, California, USA
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Naik S, Kashyap D, Deep J, Darwish S, Cross J, Mansoor E, Garg VK, Honnavar P. Utilizing Next-Generation Sequencing: Advancements in the Diagnosis of Fungal Infections. Diagnostics (Basel) 2024; 14:1664. [PMID: 39125540 PMCID: PMC11311512 DOI: 10.3390/diagnostics14151664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Next-generation sequencing (NGS) has emerged as a promising tool for diagnosing fungal infections. It enables the identification of a wide range of fungal species and provides more accurate and rapid results than traditional diagnostic methods. NGS-based approaches involve the sequencing of DNA or RNA from clinical samples, which can be used to detect and identify fungal pathogens in complex clinical samples. The development of targeted gene panels and whole-genome sequencing has allowed for identifying genetic markers associated with antifungal drug resistance, enabling clinicians to tailor patient treatment options. NGS can also provide insights into the pathogenesis of fungal infections and aid in discovering novel drug targets. Although NGS has some limitations, such as cost and data analysis, it can potentially revolutionize the future diagnosis and treatment of fungal infections.
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Affiliation(s)
- Sheetal Naik
- Department of Physiology, American University of Antigua College of Medicine, St. Johns 1451, Antigua and Barbuda
| | - Dharambir Kashyap
- Brown Center for Immunotherapy, Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Jashan Deep
- Basic Medical Science, American University of Antigua College of Medicine, St. Johns 1451, Antigua and Barbuda
| | - Saif Darwish
- Basic Medical Science, American University of Antigua College of Medicine, St. Johns 1451, Antigua and Barbuda
| | - Joseph Cross
- Department of Biochemistry, Cell Biology and Genetics; American University of Antigua College of Medicine, St. Johns 1451, Antigua and Barbuda
- Department of Microbial Pathogenesis and Immunology, Texas A & M University, College Station, TX 77843, USA
| | - Edmond Mansoor
- Department of Clinical Medicine; American University of Antigua College of Medicine, St. Johns 1451, Antigua and Barbuda
| | - Vivek Kumar Garg
- University Institute of Allied Health Sciences, Chandigarh University, Gharuan, Mohali 140413, Punjab, India
| | - Prasanna Honnavar
- Department of Microbiology and Immunology; American University of Antigua College of Medicine, St. Johns 1451, Antigua and Barbuda
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Fashina T, Hariprasad SM, Yeh S. Molecular Diagnostics for Infectious Uveitis: Current Practice and Future Directions. Ophthalmic Surg Lasers Imaging Retina 2024; 55:368-373. [PMID: 39012195 DOI: 10.3928/23258160-20240603-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
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Lee J, Jeong H, Kang HG, Park J, Choi EY, Lee CS, Byeon SH, Kim M. Rapid Pathogen Detection in Infectious Uveitis Using Nanopore Metagenomic Next-Generation Sequencing: A Preliminary Study. Ocul Immunol Inflamm 2024; 32:463-469. [PMID: 36758246 DOI: 10.1080/09273948.2023.2173243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 12/09/2022] [Accepted: 01/22/2023] [Indexed: 02/11/2023]
Abstract
PURPOSE We establish an accurate and rapid diagnostic method for pathogen detection in infectious uveitis using nanopore metagenomic next-generation sequencing (NGS). METHODS In eight patients with suspected infectious uveitis, we prospectively compared the accuracy and time taken for pathogen identification between conventional diagnostic methods, such as cultures and PCR, and nanopore metagenomic NGS. RESULTS All causative pathogens were identified using nanopore sequencing, while only five of the eight patients were confirmed positive for a specific pathogen using conventional methods. The overall sample-to-answer turnaround time of nanopore sequencing was much shorter than that of conventional methods in the bacterial and fungal infection (mean, 17 h vs. 4d, respectively; P = .028). The pathogens could be detected even when the quantity or quality of DNA was not optimal. CONCLUSION Nanopore metagenomic NGS is a promising diagnostic tool that can rapidly and accurately identify the causative pathogen in infectious uveitis.
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Affiliation(s)
- Junwon Lee
- Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Han Jeong
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun Goo Kang
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Jinkyu Park
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Young Choi
- Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Christopher Seungkyu Lee
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Suk Ho Byeon
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Min Kim
- Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
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Tan J, Wu L, Zhan L, Sheng M, Tang Z, Xu J, Ma H. Optimal selection of specimens for metagenomic next-generation sequencing in diagnosing periprosthetic joint infections. Front Cell Infect Microbiol 2024; 14:1356804. [PMID: 38500507 PMCID: PMC10945027 DOI: 10.3389/fcimb.2024.1356804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Objective This study aimed to assess the diagnostic value of metagenomic next-generation sequencing (mNGS) across synovial fluid, prosthetic sonicate fluid, and periprosthetic tissues among patients with periprosthetic joint infection (PJI), intending to optimize specimen selection for mNGS in these patients. Methods This prospective study involved 61 patients undergoing revision arthroplasty between September 2021 and September 2022 at the First Affiliated Hospital of Zhengzhou University. Among them, 43 cases were diagnosed as PJI, and 18 as aseptic loosening (AL) based on the American Musculoskeletal Infection Society (MSIS) criteria. Preoperative or intraoperative synovial fluid, periprosthetic tissues, and prosthetic sonicate fluid were collected, each divided into two portions for mNGS and culture. Comparative analyses were conducted between the microbiological results and diagnostic efficacy derived from mNGS and culture tests. Furthermore, the variability in mNGS diagnostic efficacy for PJI across different specimen types was assessed. Results The sensitivity and specificity of mNGS diagnosis was 93% and 94.4% for all types of PJI specimens; the sensitivity and specificity of culture diagnosis was 72.1% and 100%, respectively. The diagnostic sensitivity of mNGS was significantly higher than that of culture (X2 = 6.541, P=0.011), with no statistically significant difference in specificity (X2 = 1.029, P=0.310). The sensitivity of the synovial fluid was 83.7% and the specificity was 94.4%; the sensitivity of the prosthetic sonicate fluid was 90.7% and the specificity was 94.4%; and the sensitivity of the periprosthetic tissue was 81.4% and the specificity was 100%. Notably, the mNGS of prosthetic sonicate fluid displayed a superior pathogen detection rate compared to other specimen types. Conclusion mNGS can function as a precise diagnostic tool for identifying pathogens in PJI patients using three types of specimens. Due to its superior ability in pathogen identification, prosthetic sonicate fluid can replace synovial fluid and periprosthetic tissue as the optimal sample choice for mNGS.
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Affiliation(s)
- Jun Tan
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
| | - Lingxiao Wu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lijuan Zhan
- Department of Neurology, People’s Hospital of Zhengzhou, Zhengzhou, Henan, China
| | - Minkui Sheng
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
| | - Zhongxin Tang
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jianzhong Xu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haijun Ma
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
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Wang N, Gao Z, He S, Han M, Han W, Liu X, Cao H, Jing M, Sun T, Xu J. Lung abscess by Fusobacterium nucleatum and Streptococcus spp. co-infection by mNGS: A case series. Open Life Sci 2023; 18:20220651. [PMID: 37483431 PMCID: PMC10358748 DOI: 10.1515/biol-2022-0651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/15/2023] [Accepted: 06/05/2023] [Indexed: 07/25/2023] Open
Abstract
A lung abscess is a necrotizing infection caused by microbiomes that lead to the loss of healthy lung tissue. The routine culture is a waste of time and yields false-negative results, and clinicians could only choose empiric therapy or use broad-spectrum antibiotics, which could significantly contribute to the problem of resistance or aggravate the condition. We report three patients with a routine-culture-negative lung abscess. The presenting symptoms included fever, cough, dyspnea, and chest pain, and a computed tomography scan revealed a lesion in the lungs. The bronchoalveolar lavage fluid and pleural fluid were tested for pathogens using metagenome next-generation sequencing (mNGS), and the results revealed Fusobacterium nucleatum and Streptococcus spp. (S. constellatus, S. intermedius) as the most represented microbial pathogens. Our data demonstrated that mNGS could be a promising alternative diagnostic tool for pathogen detection, and the pathogen lists indicate that it will be important to focus on the Streptococcus genus rather than the dominant Streptococcus spp. in terms of co-infection of pathogen determined by shotgun mNGS.
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Affiliation(s)
- Na Wang
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Pharmacology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Zhichao Gao
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Breast Medicine, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Shuai He
- Department of Imaging, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Mengzhen Han
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Pharmacology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Wenjie Han
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Pharmacology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Xiaolin Liu
- Liaoning Kanghui Biotechnology Co., Ltd, Zhihuier Street, Hunnan District, Shenyang, 110001, China
| | - Hui Cao
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Breast Medicine, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Mingxi Jing
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Breast Medicine, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Tao Sun
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Breast Medicine, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Junnan Xu
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Pharmacology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Breast Medicine, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Medical Oncology, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital and Institute, No. 44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning110042, P. R. China
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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] [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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Thomas J, Nguyen NV, Fashina T, Huang Y, Yeh S, Conrady CD. An update on immunological and molecular tests and their impact in infectious uveitis. FRONTIERS IN OPHTHALMOLOGY 2023; 3:1132131. [PMID: 38983089 PMCID: PMC11182284 DOI: 10.3389/fopht.2023.1132131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/06/2023] [Indexed: 07/11/2024]
Abstract
Early diagnosis of infectious uveitis can lead to prompt initiation of treatment to minimize vision-threatening sequelae. As various infectious etiologies of uveitis share similar clinical features, advancements in polymerase chain reaction (PCR) and metagenomic next-generation sequencing (MDS) have shown significant promise in improving diagnostic capabilities. Various techniques of PCR, including real-time, multiplex, comprehensive, and broad-range, have increased the armamentarium for infectious uveitis diagnosis. Additionally, metagenomic deep sequencing technology has provided a methodology to identify causative pathogens as well as novel etiologies of uveitis. This review discusses the diagnostic tools available for infectious uveitis and highlights the advantages and disadvantages of the techniques.
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Affiliation(s)
- Joanne Thomas
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Nam V. Nguyen
- College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Tolulope Fashina
- Department of Ophthalmology and Visual Sciences, Stanley M. Truhlsen Eye Institute, University of Nebraska Medical Center, Omaha, NE, United States
| | - Ye Huang
- College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Steven Yeh
- Department of Ophthalmology and Visual Sciences, Stanley M. Truhlsen Eye Institute, University of Nebraska Medical Center, Omaha, NE, United States
| | - Christopher D. Conrady
- Department of Ophthalmology and Visual Sciences, Stanley M. Truhlsen Eye Institute, University of Nebraska Medical Center, Omaha, NE, United States
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
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Liang Y, Feng Q, Wei K, Hou X, Song X, Li Y. Potential of metagenomic next-generation sequencing in detecting infections of ICU patients. Mol Cell Probes 2023; 68:101898. [PMID: 36764622 DOI: 10.1016/j.mcp.2023.101898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023]
Abstract
BACKGROUND Due to the limitations of traditional microbiological detection techniques in evaluating complicated infections in ICU patients, it is necessary to explore novel and effective methods to improve the clinical detection of ICU patients' infections. OBJECTIVE This study aimed to evaluate the efficiency and specificity of mNGS in screening pathogens in the blood, deep phlegm, urine, and other sample types of ICU patients exploring an effective method for infection detection. METHODS A total of 56 ICU patients with 131 samples were included in this study. The sample types included blood, deep phlegm, urine, drainage, anal swabs, and other types. Samples were analyzed by both conventional detection method and mNGS tests. The diagnosis efficiency and consistency of the two methods were compared. The distribution of the identified pathogens was analyzed. Moreover, the clinical features of patients with mNGS-positive or mNGS-negative results were compared. RESULTS The positive rate of mNGS was 81.7% (107/131) including 3.1% (4/131) weakly positive, while the positive rate of traditional detection was only 30.5%, including 29 strong positive results and 11 weak positive results. Additionally, there were 41 patients chose to adjust anti-infection strategies according to the results of mNGS, which significantly saved treatment costs. The mNGS-positive patients showed a shorter ICU hospitalization and higher intention to adjust anti-infection strategies than the mNGS-negative patients. CONCLUSION mNGS is of great potential for the pathogen detection of ICU patients, and has a higher detection rate than traditional detection methods. Further clinical application investigations can be carried out to expand the application of mNGS.
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Affiliation(s)
- Yanxu Liang
- Department of Critical Care Medicine, The Fifth Central Hospital of Tianjin, Tianjin, 300450, China
| | - Qingguo Feng
- Department of Critical Care Medicine, The Fifth Central Hospital of Tianjin, Tianjin, 300450, China.
| | - Kai Wei
- Department of Critical Care Medicine, The Fifth Central Hospital of Tianjin, Tianjin, 300450, China
| | - Xiaoming Hou
- Department of Critical Care Medicine, The Fifth Central Hospital of Tianjin, Tianjin, 300450, China
| | - Xiaotao Song
- Department of Critical Care Medicine, The Fifth Central Hospital of Tianjin, Tianjin, 300450, China
| | - Yuantao Li
- Department of Critical Care Medicine, The Fifth Central Hospital of Tianjin, Tianjin, 300450, China
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Ye Z, Yang Y, Ke W, Li Y, Wang K, Chen M. Overview and update on cytomegalovirus-associated anterior uveitis and glaucoma. Front Public Health 2023; 11:1117412. [PMID: 36935679 PMCID: PMC10014866 DOI: 10.3389/fpubh.2023.1117412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/08/2023] [Indexed: 03/06/2023] Open
Abstract
Cytomegalovirus anterior uveitis is the most common ocular inflammatory disease caused by cytomegalovirus infection. It mainly occurs in middle-aged males with competent immunologic function, and the incidence is higher in Asia. The clinical manifestations vary from Posner-Schlossman syndrome and corneal endotheliitis to Fuchs uveitis syndrome, and are often accompanied by intraocular hypertension. Secondary glaucoma is a potentially blinding ocular complication with a pathogenesis that includes complicated immunological factors, intraocular inflammation, different types of angle abnormalities, and the administration of steroids, which may result in physical discomfort and visual impairment. Diagnostic tests, such as the polymerase chain reaction, optical coherence tomography, ocular microscopy, and confocal microscopy, might help in identifying anterior uveitis caused by other viruses. Combinations of antiviral medications and anti-inflammatory agents are effective treatments. If pharmacological therapy cannot reduce intraocular pressure or slow the progression of glaucomatous optic neuropathy, surgical intervention is required as a last resort.
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Affiliation(s)
- Zifan Ye
- Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Yumei Yang
- Shangyu People's Hospital of Shaoxing, Shaoxing, China
| | - Weishaer Ke
- Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Yuhang Li
- Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Kaijun Wang
- Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
- Kaijun Wang
| | - Min Chen
- Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
- *Correspondence: Min Chen
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Qian Z, Zhang Y, Wang L, Li Z, Wang H, Kang H, Feng J, Hu X, Tao Y. Application of metagenomic next-generation sequencing in suspected intraocular infections. Eur J Ophthalmol 2023; 33:391-397. [PMID: 35712966 DOI: 10.1177/11206721221107311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
PURPOSE To evaluate the efficacy of metagenomic next-generation sequencing (mNGS) and to explore its value in the diagnosis of intraocular infection. METHODS A retrospective case-series study of patients with suspected intraocular infection was performed. Intraocular fluid samples were collected from all the patients and sent for mNGS. Detailed clinical data, the results of mNGS and other laboratory examinations, the sequencing data of mNGS, and the final diagnosis were recorded. RESULTS Fifteen eyes of 15 patients were included in the study. Eight samples were identified as positive for different kinds of pathogens by mNGS, which were all confirmed by other laboratory examinations or effective diagnostic treatment. The mNGS results were negative in seven samples. The final diagnosis was still intraocular infection in four of the seven negative results. Of these, one patient was diagnosed with fungal endophthalmitis according to the clinical characteristics and good treatment response to the anti-fungal therapy, one patient underwent vitrectomy and the bacterial culture of the vitreous sample was positive for Brucella melitensis, and two patients were diagnosed with ocular tuberculosis according to the positive T-SPOT test and effective anti-tuberculous treatments. CONCLUSIONS mNGS could be helpful in determining pathogens in cases of suspected intraocular infection. The mNGS protocols should be optimized for the detection of intracellular bacterial and fungal pathogens.
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Affiliation(s)
- Zhuyun Qian
- Beijing GIANTMED medical diagnostics Lab, Beijing, China
| | - Yankun Zhang
- Department of Ophthalmology, Hebei Chest Hospital, Hebei, China
| | - Lu Wang
- Beijing GIANTMED medical diagnostics Lab, Beijing, China
| | - Ziqiang Li
- Beijing GIANTMED medical diagnostics Lab, Beijing, China
| | - Hui Wang
- Department of Ophthalmology, 74639Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Hao Kang
- Department of Ophthalmology, 74639Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Jing Feng
- Department of Ophthalmology, 74639Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Xiaofeng Hu
- Department of Ophthalmology, 74639Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yong Tao
- Department of Ophthalmology, 74639Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
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Chiquet C, Bron AM, Lundström M, Maurin M. Acute postoperative endophthalmitis: Microbiology from the laboratory to the bedside. Surv Ophthalmol 2022; 67:1698-1710. [PMID: 35843367 DOI: 10.1016/j.survophthal.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 11/26/2022]
Abstract
Postoperative endophthalmitis is a dreaded complication of intraocular surgery. Acute presentations need prompt management and good knowledge of differential diagnoses. In the last 10 years, progress in direct microbial detection and identification from intraocular samples included the use of blood culture systems and, more recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, improving the rate of bacterial identification. Whatever the method used, diagnostic sensitivity is better for vitreous samples than for aqueous humor samples. Besides, molecular biology techniques have further improved the identification rate of infectious agents in intraocular samples. They also provide faster results compared to culture-based techniques. Quantitative real-time PCR (qPCR) can also determine the bacterial load in intraocular samples. Several studies have shown that intraocular bacterial loads in endophthalmitis patients are usually high, which helps differentiating infection from contamination. The prognostic value of qPCR remains to be validated. Whole genome DNA sequencing technologies facilitate direct and sequencing of single DNA molecules. They have the potential to increase the rate of microbiological identification. Some antibiotic resistance markers (e.g., methicillin resistance in staphylococci and vancomycin resistance in enterococci) may be detected earlier using molecular techniques (usually real-time PCR tests). Early determination of the involved microorganism and their antibiotic resistances can help establishing an earlier therapeutic strategy.
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Affiliation(s)
- Christophe Chiquet
- Department of Ophthalmology, University Hospital of Grenoble, France; Grenoble Alpes University, Grenoble, France; HP2 Laboratory, INSERM U1042, University Grenoble Alpes, Grenoble, France.
| | - Alain M Bron
- Department of Ophthalmology, University Hospital, Dijon, France; Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Mats Lundström
- Department of Clinical Sciences, Ophthalmology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Max Maurin
- Laboratoire de Bactériologie, Institut de Biologie et Pathologie, CHU, Grenoble, Alpes; University Grenoble Alpes, CNRS, Grenoble, INP; CHU Grenoble Alpes, TIMC-IMAG, 38000, Grenoble, France
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14
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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] [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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15
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Evidence-based Management of Culture-negative Microbial Keratitis. Int Ophthalmol Clin 2022; 62:111-124. [PMID: 35325914 DOI: 10.1097/iio.0000000000000411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Li Y, Yang Q, Ding J. Metagenomic Next-generation Sequencing: Application in Infectious Diseases. EXPLORATORY RESEARCH AND HYPOTHESIS IN MEDICINE 2022; 7:19-24. [DOI: 10.14218/erhm.2021.00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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An N, Wang C, Dou X, Liu X, Wu J, Cheng Y. Comparison of 16S rDNA Amplicon Sequencing With the Culture Method for Diagnosing Causative Pathogens in Bacterial Corneal Infections. Transl Vis Sci Technol 2022; 11:29. [PMID: 35179557 PMCID: PMC8859490 DOI: 10.1167/tvst.11.2.29] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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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Steptoe PJ, Pearce I, Beare NAV, Sreekantam S, Mohammed BR, Barry RJ, Steeples LR, Denniston AK, Murray PI. Proposing a Neurotropic Etiology for Acute Posterior Multifocal Placoid Pigment Epitheliopathy and Relentless Placoid Chorioretinitis. FRONTIERS IN OPHTHALMOLOGY 2022; 1:802962. [PMID: 38983970 PMCID: PMC11182168 DOI: 10.3389/fopht.2021.802962] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/20/2021] [Indexed: 07/11/2024]
Abstract
Purpose To reassess the underlying pathophysiology of acute posterior multifocal placoid pigment epitheliopathy (APMPPE) and relentless placoid chorioretinitis (RPC) through comparison with the non-inoculated eye of the von Szily animal model of neurotropic viral retinal infection. Methods Narrative review. Results Literature reports of isolated neurotropic viral entities and rising serological viral titers in APMPPE after presentation support a potential direct infective etiology. In general, viral transport along axons results in mitochondrial stasis and disruption of axoplasmic flow. Clinical manifestations of axoplasmic flow disruption in APMPPE/RPC may signify the passage of virus along the neuronal pathway. From a case series of 11 patients, we demonstrate a timely, spatial, and proportional association of optic disc swelling with APMPPE lesion occurrence. Signs within the inner retina appear to precede outer retinal lesions; and acute areas of outer nuclear layer (ONL) hyperreflectivity appear to be the result of coalescence of multiple hyperreflective foci resembling axonal spheroids (which occur as a consequence of axoplasmic disruption) and follow the Henle fiber layer neurons. Underlying areas of retinal pigment epithelium (RPE) hyper-autofluorescence follow ONL hyperreflectivity and may signify localized infection. Areas of apparent choriocapillaris hypoperfusion mirror areas of RPE/Bruch's membrane separation and appear secondary to tractional forces above. Increases in choroidal thickness with lesion occurrence and focal areas of choriocapillaris hypoperfusion are observed in both APMPPE/RPC and the von Szily model. Conclusions The neurotrophic infection model provides significant advantages over the existing primary choriocapillaris ischemia hypothesis to account for the range of imaging signs observed in APMPPE and RPC.
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Affiliation(s)
- Paul J Steptoe
- Princess Alexandra Eye Pavilion, Edinburgh, United Kingdom
| | - Ian Pearce
- St. Paul's Eye Unit, Liverpool University Hospitals National Health Service (NHS) Foundation Trust, Liverpool, United Kingdom
| | - Nicholas A V Beare
- St. Paul's Eye Unit, Liverpool University Hospitals National Health Service (NHS) Foundation Trust, Liverpool, United Kingdom
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | | | - Robert J Barry
- Birmingham and Midland Eye Centre, Birmingham, United Kingdom
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Laura R Steeples
- Manchester Royal Eye Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, United Kingdom
| | - Alastair K Denniston
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Ophthalmology Department, University Hospital Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Centre for Rare Diseases, University Hospital Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Philip I Murray
- Birmingham and Midland Eye Centre, Birmingham, United Kingdom
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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Metagenomic Sequencing as a Pathogen-Agnostic Clinical Diagnostic Tool for Infectious Diseases: a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies. J Clin Microbiol 2021; 59:e0291620. [PMID: 33910965 DOI: 10.1128/jcm.02916-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Metagenomic sequencing is frequently claimed to have the potential to revolutionize microbiology through rapid species identification and antimicrobial resistance (AMR) prediction. We assess the progress toward these developments. We perform a systematic review and meta-analysis of all published literature on culture-independent metagenomic sequencing for pathogen-agnostic infectious disease diagnostics up to 12 August 2020. Methodologic bias and applicability were assessed using the tool Quadas-2. (Prospero CRD42020163777). A total of 2,023 clinical samples from 13/21 eligible diagnostic test accuracy studies were included in the meta-analysis. Reference standards were culture, molecular testing, clinical decision, or a composite measure. Sensitivity and specificity in the most widely investigated sample types were 90% (95% confidence interval [CI], 78% to 96%) and 86% (45% to 98%) for blood, 75% (54% to 89%) and 96% (72% to 100%) for cerebrospinal fluid (CSF), and 84% (79% to 88%) and 67% (38% to 87%) for orthopedic samples, respectively. We identified a limited use of controls, especially negative controls which were used in only 62% (13/21) of studies. AMR prediction and comparison to phenotypic results were undertaken in four studies; categorical agreement was 88%(80% to 97%), and very major and major error rates were 24% (8% to 40%) and 5% (0% to 12%), respectively. Better human DNA depletion methods are required; a median 91% (interquartile range [IQR], 82% to 98%; range, 76% to 98%) of sequences was classified as human. The median (IQR; range) time from sample to result was 29 hours (24 to 94; 4 to 144 hours). The reported consumable cost per sample ranged from $130 to $685. There is scope for improving the quality of reporting in clinical metagenomic studies. Although our results are limited by the heterogeneity displayed, our results reflect a promising outlook for clinical metagenomics. Methodological improvements and convergence around protocols and best practices may improve performance in the future.
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Metagenomic Shotgun Sequencing Analysis of Canalicular Concretions in Lacrimal Canaliculitis Cases. Curr Issues Mol Biol 2021; 43:676-686. [PMID: 34287258 PMCID: PMC8928969 DOI: 10.3390/cimb43020049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [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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Babu K, Konana VK, Ganesh SK, Patnaik G, Chan NSW, Chee SP, Sobolewska B, Zierhut M. Viral anterior uveitis. Indian J Ophthalmol 2021; 68:1764-1773. [PMID: 32823392 PMCID: PMC7690545 DOI: 10.4103/ijo.ijo_928_20] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Viral anterior uveitis (VAU) needs to be suspected in anterior uveitis (AU) associated with elevated intraocular pressure, corneal involvement, and iris atrophic changes. Common etiologies of VAU include herpes simplex, varicella-zoster, cytomegalovirus, and rubella virus. Clinical presentations can vary from granulomatous AU with corneal involvement, Posner-Schlossman syndrome, Fuchs uveitis syndrome, and endothelitis. Due to overlapping clinical manifestations between the different viruses, diagnostic tests like polymerase chain reaction and Goldmann-Witmer coefficient analysis on the aqueous humor may help in identifying etiology to plan and monitor treatment.
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Affiliation(s)
- Kalpana Babu
- Department of Uveitis and Ocular inflammation, Vittala International Institute of Ophthalmology and Prabha Eye Clinic and Research Centre, Bangalore, Karnataka, India
| | - Vinaya Kumar Konana
- Department of Uveitis and Ocular inflammation, Vittala International Institute of Ophthalmology and Prabha Eye Clinic and Research Centre, Bangalore, Karnataka, India
| | - Sudha K Ganesh
- Department of Uveitis and Ocular Inflammation, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Gazal Patnaik
- Department of Uveitis and Ocular Inflammation, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Nicole S W Chan
- Department of Ophthalmology, National University Hospital, Singapore
| | - Soon-Phaik Chee
- Singapore National Eye Centre; Singapore Eye Research Institute; Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore; Duke-NUS Graduate Medical School Singapore, Singapore
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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: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [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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Targeted metagenomics using next generation sequencing in laboratory diagnosis of culture negative endophthalmitis. Heliyon 2021; 7:e06780. [PMID: 33997374 PMCID: PMC8099753 DOI: 10.1016/j.heliyon.2021.e06780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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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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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Doan T, Sahoo MK, Ruder K, Huang C, Zhong L, Chen C, Hinterwirth A, Lin C, Gonzales JA, Pinsky BA, Acharya NR. Comprehensive pathogen detection for ocular infections. J Clin Virol 2021; 136:104759. [PMID: 33609933 DOI: 10.1016/j.jcv.2021.104759] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND Molecular diagnostics such as pathogen-directed PCRs have transformed testing for ocular infections since the late 1990s. Although these assays remain important diagnostic tools for samples with low biomass, the lack of diagnostic range motivates alternative molecular approaches for ocular infections. The aim of this study was to determine the performance of a high-throughput RNA sequencing approach, RNA-seq, to detect infectious agents in ocular samples from patients with presumed ocular infections. METHODS We compared the performance of RNA-seq to pathogen-directed PCRs using remnant nucleic acids from 41 aqueous or vitreous samples of patients with presumed ocular infections. Pathogen-directed PCRs were performed at the CLIA-certified Stanford Clinical Virology Laboratory. RNA-seq was performed in a masked manner at the Proctor Foundation at the University of California San Francisco. Percent positive and negative agreement between the two testing approaches were calculated. Discordant results were subjected to orthogonal testing. RESULTS The positive percent agreement between RNA-seq and pathogen-directed PCRs was 100% (95% confidence interval (CI): 78.5%-100%). The negative percent agreement was 92.6% (95% CI: 76.6%-97.9%). RNA-seq identified pathogens not on the differential diagnosis for 9.7% (4/41) of the samples. Two pathogens solely identified with RNA-seq were confirmed with orthogonal testing. CONCLUSIONS RNA-seq can accurately identify common and rare pathogens in aqueous and vitreous samples of patients with presumed ocular infections. Such an unbiased approach to testing has the potential to improve diagnostics although practical clinical utility warrants additional studies.
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Affiliation(s)
- Thuy Doan
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA; Department of Ophthalmology, University of California, San Francisco, CA, USA.
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kevin Ruder
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lina Zhong
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA
| | - Cindi Chen
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA
| | - Armin Hinterwirth
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA
| | - Charles Lin
- Byers Eye Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - John A Gonzales
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA; Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nisha R Acharya
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA; Department of Ophthalmology, University of California, San Francisco, CA, USA
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26
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Zhong Y, Xu F, Wu J, Schubert J, Li MM. Application of Next Generation Sequencing in Laboratory Medicine. Ann Lab Med 2021; 41:25-43. [PMID: 32829577 PMCID: PMC7443516 DOI: 10.3343/alm.2021.41.1.25] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.
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Affiliation(s)
- Yiming Zhong
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
| | - Feng Xu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jinhua Wu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jeffrey Schubert
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Marilyn M. Li
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
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27
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Sabapathypillai SL, James HR, Lyerla RRL, Hassman L. The Next Generation of Ocular Pathogen Detection. Asia Pac J Ophthalmol (Phila) 2021; 10:109-113. [PMID: 33512832 DOI: 10.1097/apo.0000000000000366] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
ABSTRACT Metagenomic next-generation sequencing is a powerful method for pathogen detection that combines advanced genome sequencing technology with cutting-edge bioinformatics to analyze microbial populations. Metagenomic next-generation sequencing has the potential to identify uncommon, unculturable, and even previously unidentified pathogens from a clinical isolate. Of particular interest to ophthalmology, this robust data extraction can occur from very small volume clinical samples. Here we discuss the opportunities and limitations of this technique and their current and future application to ophthalmic diagnostics.
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Affiliation(s)
- Sharon L Sabapathypillai
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO
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28
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Doan T, Worden L, Hinterwirth A, Arzika AM, Maliki R, Abdou A, Zhong L, Chen C, Cook C, Lebas E, O’Brien KS, Oldenburg CE, Chow ED, Porco TC, Lipsitch M, Keenan JD, Lietman TM. Macrolide and Nonmacrolide Resistance with Mass Azithromycin Distribution. N Engl J Med 2020; 383:1941-1950. [PMID: 33176084 PMCID: PMC7492079 DOI: 10.1056/nejmoa2002606] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Mass distribution of azithromycin to preschool children twice yearly for 2 years has been shown to reduce childhood mortality in sub-Saharan Africa but at the cost of amplifying macrolide resistance. The effects on the gut resistome, a reservoir of antimicrobial resistance genes in the body, of twice-yearly administration of azithromycin for a longer period are unclear. METHODS We investigated the gut resistome of children after they received twice-yearly distributions of azithromycin for 4 years. In the Niger site of the MORDOR trial, we enrolled 30 villages in a concurrent trial in which they were randomly assigned to receive mass distribution of either azithromycin or placebo, offered to all children 1 to 59 months of age every 6 months for 4 years. Rectal swabs were collected at baseline, 36 months, and 48 months for analysis of the participants' gut resistome. The primary outcome was the ratio of macrolide-resistance determinants in the azithromycin group to those in the placebo group at 48 months. RESULTS Over the entire 48-month period, the mean (±SD) coverage was 86.6±12% in the villages that received placebo and 83.2±16.4% in the villages that received azithromycin. A total of 3232 samples were collected during the entire trial period; of the samples obtained at the 48-month monitoring visit, 546 samples from 15 villages that received placebo and 504 from 14 villages that received azithromycin were analyzed. Determinants of macrolide resistance were higher in the azithromycin group than in the placebo group: 7.4 times as high (95% confidence interval [CI], 4.0 to 16.7) at 36 months and 7.5 times as high (95% CI, 3.8 to 23.1) at 48 months. Continued mass azithromycin distributions also selected for determinants of nonmacrolide resistance, including resistance to beta-lactam antibiotics, an antibiotic class prescribed frequently in this region of Africa. CONCLUSIONS Among villages assigned to receive mass distributions of azithromycin or placebo twice yearly for 4 years, antibiotic resistance was more common in the villages that received azithromycin than in those that received placebo. This trial showed that mass azithromycin distributions may propagate antibiotic resistance. (Funded by the Bill and Melinda Gates Foundation and others; ClinicalTrials.gov number, NCT02047981.).
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Affiliation(s)
- Thuy Doan
- Francis I Proctor Foundation, University of California San
Francisco, USA
- Department of Ophthalmology, University of California San
Francisco, USA
| | - Lee Worden
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Armin Hinterwirth
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | | | | | - Amza Abdou
- Ministry of Health, Niger
- Programme National de Santé Oculaire, Niger
| | - Lina Zhong
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Cindi Chen
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Catherine Cook
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Elodie Lebas
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Kieran S. O’Brien
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Catherine E. Oldenburg
- Francis I Proctor Foundation, University of California San
Francisco, USA
- Department of Ophthalmology, University of California San
Francisco, USA
- Department of Epidemiology and Biostatistics, University
of California San Francisco, USA
| | - Eric D. Chow
- Department of Biochemistry and Biophysics, University of
California San Francisco, USA
| | - Travis C. Porco
- Francis I Proctor Foundation, University of California San
Francisco, USA
- Department of Ophthalmology, University of California San
Francisco, USA
- Department of Epidemiology and Biostatistics, University
of California San Francisco, USA
| | - Marc Lipsitch
- Department of Epidemiology, Harvard T.H. Chan School of
Public Health, Harvard University, MA, USA
| | - Jeremy D. Keenan
- Francis I Proctor Foundation, University of California San
Francisco, USA
- Department of Ophthalmology, University of California San
Francisco, USA
| | - Thomas M. Lietman
- Francis I Proctor Foundation, University of California San
Francisco, USA
- Department of Ophthalmology, University of California San
Francisco, USA
- Department of Epidemiology and Biostatistics, University
of California San Francisco, USA
- Institute for Global Health Sciences, University of
California San Francisco, USA
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29
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Abstract
Purpose: to summarize the origin and very recent history of the use of metagenomic sequencing for the diagnosis of infectious uveitis, convey the technique as described by one of the primary institutions experimenting with the technology, and present recent successful applications of the technology as well as potential advantages and pitfalls compared to other current diagnostic tools.Methods: review of peer-reviewed literature concerning metagenomic sequencing for the diagnosis of infectious uveitis.Conclusion: compared to existing diagnostic methods, metagenomic deep sequencing is a sensitive, unbiased, and comprehensive technique with great potential for diagnosing the causative pathogens of cases of infectious uveitis. However, many issues remain to be addressed in the process of developing this technology, including but not limited to the potentially overwhelming amount of information generated, definition of diagnostic thresholds, demonstration of validity, contamination, and cost.
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Affiliation(s)
- Lianna Valdes
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School , Boston, MA, USA
| | - Paulo Bispo
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School , Boston, MA, USA
| | - Lucia Sobrin
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School , Boston, MA, USA
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30
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Affiliation(s)
- Narsing A Rao
- Department of Ophthalmology, Keck School of Medicine of USC, San Marino, California, USA
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31
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Wang L, Wang Z, Ma J, Li Q, Chen X, Chen Y, Sun X. Comparison of Intraocular Antibody Measurement, Quantitative Pathogen PCR, and Metagenomic Deep Sequencing of Aqueous Humor in Secondary Glaucoma Associated with Anterior Segment Uveitis. Ocul Immunol Inflamm 2020; 30:153-159. [PMID: 32809886 DOI: 10.1080/09273948.2020.1776883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE To identify viral pathogens in patients with secondary glaucoma associated with anterior segment uveitis and compare metagenomic deep sequencing (MDS) with enzyme-linked immunosorbent assay (ELISA) combined with Witmer-Desmonts coefficient (WDC) evaluation and real-time quantitative polymerase chain reaction (qPCR) on investigating pathogens in aqueous humor. METHODS Aqueous humor from 31 patients, including 22 Posner-Schlossman Syndrome and 9 other anterior uveitis, was assessed pathogens by ELISA combined with WDC evaluation, virus deoxyribonucleic acid (DNA) detection by real-time qPCR and MDS. RESULTS Viral pathogens (HCMV or VZV or RV) were detected in 19 out of 31 eyes (61.3%) by real-time qPCR or WDC evaluation. MDS revealed the presence of HCMV DNA sequences in three PSS patients. CONCLUSION Virus is an important pathogen in secondary glaucoma associated with anterior segment uveitis. MDS is a potential etiologic diagnosis tool to seek intraocular viral pathogens for secondary glaucoma associated anterior segment uveitis.
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Affiliation(s)
- Li Wang
- Department of Ophthalmology & Vision Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China.,NHC Key Laboratory of Myopia, Key Laboratory of Myopia, Chinese Academy of Medical Sciences, and Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai, China
| | - Zhujian Wang
- Clinical Laboratory, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jinmin Ma
- Infection Disease Department, BGI-Shenzhen, Shenzhen, China
| | - Qiongfang Li
- Infection Disease Department, BGI-Shenzhen, Shenzhen, China
| | - Xueli Chen
- Department of Ophthalmology & Vision Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China.,NHC Key Laboratory of Myopia, Key Laboratory of Myopia, Chinese Academy of Medical Sciences, and Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai, China
| | - Yuhong Chen
- Department of Ophthalmology & Vision Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China.,NHC Key Laboratory of Myopia, Key Laboratory of Myopia, Chinese Academy of Medical Sciences, and Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai, China
| | - Xinghuai Sun
- Department of Ophthalmology & Vision Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China.,NHC Key Laboratory of Myopia, Key Laboratory of Myopia, Chinese Academy of Medical Sciences, and Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
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32
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Hinterwirth A, Sié A, Coulibaly B, Ouermi L, Dah C, Tapsoba C, Zhong L, Chen C, Lietman TM, Keenan JD, Doan T, Oldenburg CE. Rapid Reduction of Campylobacter Species in the Gut Microbiome of Preschool Children after Oral Azithromycin: A Randomized Controlled Trial. Am J Trop Med Hyg 2020; 103:1266-1269. [PMID: 32524948 DOI: 10.4269/ajtmh.19-0940] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Campylobacter has emerged as a potential important cause of childhood morbidity in sub-Saharan Africa. Biannual mass azithromycin distribution has previously been shown to reduce all-cause child mortality in sub-Saharan Africa. We conducted a randomized controlled trial in Burkina Faso in which children were randomized in a 1:1 fashion to a 5-day course of azithromycin or placebo to investigate the effect of oral antibiotics on the gut microbiome. We evaluated the changes in the gut microbiome of preschool children treated with azithromycin using metagenomic DNA sequencing. We found that three Campylobacter species were reduced with azithromycin treatment compared with placebo. These results were consistent with other studies that have shown decreases in Campylobacter species after azithromycin treatment, generating the hypothesis that a decrease in Campylobacter may contribute to observations of reduction in mortality following azithromycin distribution.
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Affiliation(s)
- Armin Hinterwirth
- Francis I. Proctor Foundation, University of California, San Francisco, San Francisco, California
| | - Ali Sié
- Centre de Recherche en Santé de Nouna, Nouna, Burkina Faso
| | | | | | - Clarisse Dah
- Centre de Recherche en Santé de Nouna, Nouna, Burkina Faso
| | | | - Lina Zhong
- Francis I. Proctor Foundation, University of California, San Francisco, San Francisco, California
| | - Cindi Chen
- Francis I. Proctor Foundation, University of California, San Francisco, San Francisco, California
| | - Thomas M Lietman
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, California.,Department of Ophthalmology, University of California, San Francisco, San Francisco, California.,Francis I. Proctor Foundation, University of California, San Francisco, San Francisco, California
| | - Jeremy D Keenan
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California.,Francis I. Proctor Foundation, University of California, San Francisco, San Francisco, California
| | - Thuy Doan
- Francis I. Proctor Foundation, University of California, San Francisco, San Francisco, California.,Department of Ophthalmology, University of California, San Francisco, San Francisco, California
| | - Catherine E Oldenburg
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, California.,Department of Ophthalmology, University of California, San Francisco, San Francisco, California.,Francis I. Proctor Foundation, University of California, San Francisco, San Francisco, California
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33
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Conrady CD, Feist RM, Vitale AT, Shakoor A. Long-term visual outcomes of endophthalmitis and the role of systemic steroids in addition to intravitreal dexamethasone. BMC Ophthalmol 2020; 20:181. [PMID: 32375683 PMCID: PMC7201644 DOI: 10.1186/s12886-020-01449-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 04/23/2020] [Indexed: 11/18/2022] Open
Abstract
Background The purpose of this study was to evaluate the role of systemic steroids in post-procedural endophthalmitis as the role of intravitreal steroids in treatment algorithms of endophthalmitis remain controversial. Methods This is a retrospective analysis from a single tertiary referral center of all patients older than 18 years old that developed presumed post-procedure endophthalmitis and were treated at our center from 2009 to 2018. Results Eighty-three patients were followed after being treated for post-procedural endophthalmitis that either received systemic steroids or did not around the time of diagnosis. Almost 30 % of all patients regained a final visual acuity of 20/40 or better, while 31.2% had poor visual outcomes of count fingers or worse. Non-clearing debris was the most significant long-term complication. Visual improvement plateaued in 67.7% by 1 month after diagnosis and initial treatment in both groups. There was no difference in visual outcomes when comparing the sixteen patients that received systemic steroids and the sixty-seven that did not; however, no enucleation or evisceration was required in patients receiving systemic steroids. Five patients that did not receive systemic steroids required an enucleation or evisceration due to a blind, painful eye. Conclusions The use of systemic steroids does not seem to worsen long-term outcomes of endophthalmitis compared to those patients that did not receive them and they may prove beneficial in the most severe cases by reducing the risk of losing the globe altogether.
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Affiliation(s)
- Christopher D Conrady
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA. .,Department of Ophthalmology and Visual Sciences, University of Michigan, 1000 Wall St, Ann Arbor, MI, 48103, USA.
| | - Richard M Feist
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA
| | - Albert T Vitale
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA
| | - Akbar Shakoor
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA
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34
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Phadke VK, Shantha JG, O’Keefe G. Relapsing Uveitis due to Human T-lymphotropic Virus Type 1 in a Patient Living With HIV Diagnosed by Metagenomic Deep Sequencing. Open Forum Infect Dis 2020; 7:ofaa078. [PMID: 32206676 PMCID: PMC7081385 DOI: 10.1093/ofid/ofaa078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/06/2020] [Indexed: 12/17/2022] Open
Abstract
HIV infection can result in vision loss from different causes, including HIV retinopathy and uveitis secondary to other infections, such as toxoplasmosis and viral retinitis. It is imperative to identify any infectious causes of uveitis to successfully treat the condition and prevent further vision loss. Metagenomic deep sequencing (MDS) is an emerging technology that presents an unbiased approach to the evaluation of clinical syndromes, including uveitis, that have not been diagnosed by pathogen-specific testing. Herein we present a case of a woman living with HIV with 11 years of relapsing bilateral uveitis refractory to systemic corticosteroid therapy who was diagnosed with human T-lymphotropic virus type 1 (HTLV-1)–associated uveitis by this technology. We also briefly review the literature of MDS as a diagnostic tool and the epidemiology, pathogenesis, and diagnosis of HTLV-1-associated uveitis.
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Affiliation(s)
- Varun K Phadke
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jessica G Shantha
- Emory Eye Center, Department of Ophthalmology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ghazala O’Keefe
- Emory Eye Center, Department of Ophthalmology, Emory University School of Medicine, Atlanta, Georgia, USA
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35
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Yang CH, Sahoo MK, Fitzpatrick M, Lau AH, Pinsky BA, Martinez OM. Evaluating for Human Herpesvirus 6 in the Liver Explants of Children With Liver Failure of Unknown Etiology. J Infect Dis 2020; 220:361-369. [PMID: 30418598 DOI: 10.1093/infdis/jiy644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/05/2018] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Liver failure of unknown etiology (LFUE) has a transplant-free survival rate <25%. Human herpesvirus 6 (HHV-6) may be associated with LFUE, but studies are limited by small sample size. METHODS We identified all children who underwent liver transplant for LFUE at a single quaternary children's hospital; 51/65 cases could be age matched with controls (children who underwent liver transplant for metabolic liver disease). Quantitative polymerase chain reaction for HHV-6 was performed on DNA from formalin-fixed paraffin-embedded liver explant tissue. RESULTS HHV-6 was detected in 34/51 cases (66.7%) and 19/51 controls (37.3%) (P = .005). Average HHV-6 viral load was 213207 copies/106 cells in positive cases (range: 7293-1102030) and 38115 copies/106 cells in positive controls (range: 1382-122375) (P = .0008). HHV-6 was present significantly more often in cases compared to controls in patients younger than 6 years. In particular, in patients younger than 3 years, HHV-6 was present in 13/27 cases (48.1%) and 2/27 controls (7.4%) (P = .0009). CONCLUSIONS HHV-6 was detected in liver explants significantly more often and in higher quantities in children transplanted for LFUE compared to controls, suggesting HHV-6 should be evaluated in young children who present with LFUE.
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Affiliation(s)
- Christine H Yang
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Lucile Packard Children's Hospital Stanford, Palo Alto, California
| | | | | | | | - Benjamin A Pinsky
- Department of Pathology.,Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, California
| | - Olivia M Martinez
- Department of Surgery, Division of Abdominal Transplantation and Stanford Immunology, Stanford University Medical Center, California
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36
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37
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Conrady CD, Hanson KE, Mehra S, Carey A, Larochelle M, Shakoor A. The First Case of Trypanosoma cruzi-Associated Retinitis in an Immunocompromised Host Diagnosed With Pan-Organism Polymerase Chain Reaction. Clin Infect Dis 2019; 67:141-143. [PMID: 29385482 DOI: 10.1093/cid/ciy058] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/23/2018] [Indexed: 11/14/2022] Open
Abstract
We report the first case of Trypanosoma cruzi-associated retinitis diagnosed using 28s ribosomal DNA sequencing. The case highlights the utility of broad-range molecular diagnostics for detecting rare and unsuspected ocular pathogens. Ocular involvement in Chagas disease is also discussed.
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Affiliation(s)
- Christopher D Conrady
- Department of Ophthalmology, John A. Moran Eye Center, University of Utah, Salt Lake City
| | - Kimberly E Hanson
- Department of Medicine, Division of Adult Infectious Diseases, University of Utah, Salt Lake City
| | - Sonia Mehra
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Utah, Salt Lake City
| | - Adrienne Carey
- Department of Medicine, Division of Adult Infectious Diseases, University of Utah, Salt Lake City
| | - Marissa Larochelle
- Department of Ophthalmology, John A. Moran Eye Center, University of Utah, Salt Lake City
| | - Akbar Shakoor
- Department of Ophthalmology, John A. Moran Eye Center, University of Utah, Salt Lake City
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38
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Doan T, Hinterwirth A, Worden L, Arzika AM, Maliki R, Abdou A, Kane S, Zhong L, Cummings ME, Sakar S, Chen C, Cook C, Lebas E, Chow ED, Nachamkin I, Porco TC, Keenan JD, Lietman TM. Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution. Nat Med 2019; 25:1370-1376. [PMID: 31406349 DOI: 10.1038/s41591-019-0533-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 06/25/2019] [Indexed: 01/25/2023]
Abstract
The MORDOR I trial1, conducted in Niger, Malawi and Tanzania, demonstrated that mass azithromycin distribution to preschool children reduced childhood mortality1. However, the large but simple trial design precluded determination of the mechanisms involved. Here we examined the gut microbiome of preschool children from 30 Nigerien communities randomized to either biannual azithromycin or placebo. Gut microbiome γ-diversity was not significantly altered (P = 0.08), but the relative abundances of two Campylobacter species, along with another 33 gut bacteria, were significantly reduced in children treated with azithromycin at the 24-month follow-up. Metagenomic analysis revealed functional differences in gut bacteria between treatment groups. Resistome analysis showed an increase in macrolide resistance gene expression in gut microbiota in communities treated with azithromycin (P = 0.004). These results suggest that prolonged mass azithromycin distribution to reduce childhood mortality reduces certain gut bacteria, including known pathogens, while selecting for antibiotic resistance.
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Affiliation(s)
- T Doan
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA.
- Department of Ophthalmology, University of California, San Francisco, CA, USA.
| | - A Hinterwirth
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | - L Worden
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | | | - R Maliki
- The Carter Center, Niamey, Niger
| | - A Abdou
- Ministry of Public Health, Niamey, Niger
- Programme National de Soins Oculaires, Niamey, Niger
| | - S Kane
- The Carter Center, Niamey, Niger
| | - L Zhong
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | - M E Cummings
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | - S Sakar
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | - C Chen
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | - C Cook
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | - E Lebas
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | - E D Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - I Nachamkin
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - T C Porco
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
- Department of Ophthalmology, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - J D Keenan
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
- Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - T M Lietman
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
- Department of Ophthalmology, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Institute for Global Health Sciences, University of California, San Francisco, CA, USA
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Lalitha P, Seitzman GD, Kotecha R, Hinterwirth A, Chen C, Zhong L, Cummings ME, Lebas E, Sahoo MK, Pinsky BA, Lietman TM, Doan T. Unbiased Pathogen Detection and Host Gene Profiling for Conjunctivitis. Ophthalmology 2019; 126:1090-1094. [PMID: 30953744 PMCID: PMC6646074 DOI: 10.1016/j.ophtha.2019.03.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/15/2019] [Accepted: 03/26/2019] [Indexed: 12/17/2022] Open
Abstract
PURPOSE The etiology of conjunctivitis is often misdiagnosed. An ideal diagnostic test would identify all possible infectious causes. In this study, we apply unbiased metagenomic RNA deep sequencing (MDS) to identify pathogens causing conjunctivitis. DESIGN Molecular study of prospectively collected conjunctival swabs from patients with presumed infectious conjunctivitis. PARTICIPANTS Patients with presumed acute infectious conjunctivitis. METHODS Conjunctival swabs were collected from patients presenting with acute conjunctivitis. Swabs were processed for MDS. Pathogens were identified using a rapid computational pipeline to analyze the nonhost sequences obtained from MDS. Differential gene expression analysis was performed to evaluate for host transcriptome signatures for infectious types. Clinical samples were deidentified, and laboratory personnel handling the samples and interpreting the data were masked. MAIN OUTCOME MEASURES Pathogens and differential transcripts identified by MDS. RESULTS Metagenomic RNA deep sequencing detected pathogens in 86% (12/14) of the patients tested. Swabs from 10 of 14 patients were positive for human adenovirus (HAdV) while swabs from 2 of 14 patients were positive for Vittaforma corneae (a parasitic fungal species of the microsporidia group). Samples positive for HAdV by RNA-seq were independently verified in a CLIA-certified laboratory. Pathogen-directed polymerase chain reaction confirmed the presence of V. corneae genome in the samples positive by RNA-seq. Local host transcriptome analysis identified 12 differentially expressed genes that provided distinct expression signatures for patients infected with HAdV compared with V. corneae. CONCLUSIONS Metagenomic RNA deep sequencing can reliably detect and quantify common and rare pathogens causing conjunctivitis, and identify strains. The unbiased nature of metagenomic RNA deep sequencing allowed an expanded scope of pathogen detection, including fungal species not commonly associated with acute conjunctivitis. In addition, the identification of infection type-specific local host transcriptome signatures may allow for pathogen detection even when the pathogen load is too low for direct identification.
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Affiliation(s)
- Prajna Lalitha
- Department of Ocular Microbiology, Aravind Eye Hospital, Madurai, Tamil Nadu, India
| | - Gerami D Seitzman
- Francis I. Proctor Foundation, San Francisco, California; Department of Ophthalmology, University of California, San Francisco, California
| | - Ritesh Kotecha
- Department of Ocular Microbiology, Aravind Eye Hospital, Madurai, Tamil Nadu, India
| | | | - Cindi Chen
- Francis I. Proctor Foundation, San Francisco, California
| | - Lina Zhong
- Francis I. Proctor Foundation, San Francisco, California
| | - M E Cummings
- Francis I. Proctor Foundation, San Francisco, California
| | - Elodie Lebas
- Francis I. Proctor Foundation, San Francisco, California
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California
| | - Thomas M Lietman
- Francis I. Proctor Foundation, San Francisco, California; Department of Ophthalmology, University of California, San Francisco, California
| | - Thuy Doan
- Francis I. Proctor Foundation, San Francisco, California; Department of Ophthalmology, University of California, San Francisco, California.
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Gallon P, Parekh M, Ferrari S, Fasolo A, Ponzin D, Borroni D. Metagenomics in ophthalmology: Hypothesis or real prospective? ACTA ACUST UNITED AC 2019; 23:e00355. [PMID: 31312608 PMCID: PMC6609782 DOI: 10.1016/j.btre.2019.e00355] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/30/2019] [Accepted: 06/22/2019] [Indexed: 12/12/2022]
Abstract
Metagenomic analysis was originally associated with the studies of genetic material from environmental samples. But, with the advent of the Human Microbiome Project, it has now been applied in clinical practices. The ocular surface (OS) is the most exposed part of the eye, colonized by several microbial communities (both, OS and environmental) that contribute to the maintenance of the physiological state. Limited knowledge has been acquired on these microbes due to the limitations of conventional diagnostic methods. Emerging fields of research are focusing on Next Generation Sequencing (NGS) technologies to obtain reliable information on the OS microbiome. Currently only pre-specified pathogens can be detected by conventional culture-based techniques or Polymerase Chain Reaction (PCR), but there are conditions to state whether metagenomics could revolutionize the diagnosis of ocular diseases. The aim of this review is to provide an updated overview of the studies involving NGS technology for OS microbiome.
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Affiliation(s)
- Paola Gallon
- Fondazione Banca degli Occhi del Veneto, Venice, Italy
| | - Mohit Parekh
- Institute of Ophthalmology, University College London, London, UK
| | | | | | - Diego Ponzin
- Fondazione Banca degli Occhi del Veneto, Venice, Italy
| | - Davide Borroni
- Department of Doctoral Studies, Riga Stradins University, Riga, Latvia
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Ma L, Jakobiec FA, Dryja TP. A Review of Next-Generation Sequencing (NGS): Applications to the Diagnosis of Ocular Infectious Diseases. Semin Ophthalmol 2019; 34:223-231. [PMID: 31170015 DOI: 10.1080/08820538.2019.1620800] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Purpose: To review the value of next-generation sequencing (NGS) in identifying the pathogens which cause ocular infections, thereby facilitating prompt initiation of treatment with an optimal anti-microbial regimen. Both contemporary and futuristic approaches to identifying pathogens in ocular infections are covered in this brief overview. Methods: Review of the peer reviewed literature on conventional and advanced methods as applied to the diagnosis of infectious diseases of the eye. Conclusion: NGS is a novel technology for identifying the pathogens responsible for ocular infections with the potential to improve the accuracy and speed of diagnosis and hastening the selection of the best therapy.
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Affiliation(s)
- Lina Ma
- a David G Cogan Laboratory of Ophthalmic Pathology, Massachusetts Eye and Ear Infirmary , Harvard Medical School , Boston , MA , USA
| | - Frederick A Jakobiec
- a David G Cogan Laboratory of Ophthalmic Pathology, Massachusetts Eye and Ear Infirmary , Harvard Medical School , Boston , MA , USA
| | - Thaddeus P Dryja
- a David G Cogan Laboratory of Ophthalmic Pathology, Massachusetts Eye and Ear Infirmary , Harvard Medical School , Boston , MA , USA
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42
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Parekh M, Borroni D, Romano V, Kaye SB, Camposampiero D, Ponzin D, Ferrari S. Next-generation sequencing for the detection of microorganisms present in human donor corneal preservation medium. BMJ Open Ophthalmol 2019; 4:e000246. [PMID: 31179394 PMCID: PMC6528759 DOI: 10.1136/bmjophth-2018-000246] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Objective To detect the presence of microorganisms in the storage media of human donor corneas using next-generation sequencing method. Methods Seven samples from organ culture (OC) group (Cornea Max, Eurobio, Les Ulis, France) with one control (sterile media without any cornea) and seven samples from hypothermic storage group (Cornea Cold, Eurobio) with one control were used for this study. The corneas were placed in the respective storage media for 14 days before collecting the samples. Storage media (2 mL) from each sample were collected in RNAase-free tubes and shipped for ribosomal RNA sequencing of 16 S and 18 S. Simultaneously, another 1 mL of media sample was used for conventional diagnostic method (CDM) using Bactec instruments. Results In both, OC and hypothermic storage and control samples, the most abundant genera were Pseudomonas, Comamonas, Stenotrophomonas, Alcanivorax, Brevundimonas and Nitrobacter. Acidovorax, Acetobacter and Hydrogenophilus were detected mostly in the hypothermic storage group. The most abundant fungal pathogen detected belonged to the genus Malassezia, which was found in both the storage conditions. CDM was negative for microorganisms in all the samples. Conclusion Metagenomics provides full taxonomic profiling of the detected genomic material of the organisms and thus has the potential to deliver a much wider microbiological diagnostic approach than CDM. The costs and turn-around time need to be reduced, and; the detection of viable organisms would help this technology to be introduced into routine clinical practice.
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Affiliation(s)
- Mohit Parekh
- Institute of Ophthalmology, University College London, London, UK.,International Center for Ocular Physiopathology, Fondazione Banca degli Occhi del Veneto Onlus, Venice, Italy
| | - Davide Borroni
- St. Paul's Eye Unit, Royal Liverpool University Hospital, Liverpool, UK
| | - Vito Romano
- St. Paul's Eye Unit, Royal Liverpool University Hospital, Liverpool, UK.,Department of Eye and Vision Science, Institute of Ageing andChronic Disease, University of Liverpool, Liverpool, UK.,Instituto Universitario Fernandez-Vega, Universidad de Oviedo and Fundacion de Investigacion on Oftalmologica, Oviedo, Spain
| | - Stephen B Kaye
- St. Paul's Eye Unit, Royal Liverpool University Hospital, Liverpool, UK
| | - Davide Camposampiero
- International Center for Ocular Physiopathology, Fondazione Banca degli Occhi del Veneto Onlus, Venice, Italy
| | - Diego Ponzin
- International Center for Ocular Physiopathology, Fondazione Banca degli Occhi del Veneto Onlus, Venice, Italy
| | - Stefano Ferrari
- International Center for Ocular Physiopathology, Fondazione Banca degli Occhi del Veneto Onlus, Venice, Italy
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44
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Gu W, Miller S, Chiu CY. Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2018; 14:319-338. [PMID: 30355154 DOI: 10.1146/annurev-pathmechdis-012418-012751] [Citation(s) in RCA: 705] [Impact Index Per Article: 117.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nearly all infectious agents contain DNA or RNA genomes, making sequencing an attractive approach for pathogen detection. The cost of high-throughput or next-generation sequencing has been reduced by several orders of magnitude since its advent in 2004, and it has emerged as an enabling technological platform for the detection and taxonomic characterization of microorganisms in clinical samples from patients. This review focuses on the application of untargeted metagenomic next-generation sequencing to the clinical diagnosis of infectious diseases, particularly in areas in which conventional diagnostic approaches have limitations. The review covers ( a) next-generation sequencing technologies and common platforms, ( b) next-generation sequencing assay workflows in the clinical microbiology laboratory, ( c) bioinformatics analysis of metagenomic next-generation sequencing data, ( d) validation and use of metagenomic next-generation sequencing for diagnosing infectious diseases, and ( e) significant case reports and studies in this area. Next-generation sequencing is a new technology that has the promise to enhance our ability to diagnose, interrogate, and track infectious diseases.
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Affiliation(s)
- Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA;
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA;
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA; .,Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, California 94107, USA
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Doan T, Hinterwirth A, Arzika AM, Cotter SY, Ray KJ, O’Brien KS, Zhong L, Chow ED, Zhou Z, Cummings SL, Fry D, Oldenburg CE, Worden L, Porco TC, Keenan JD, Lietman TM. Mass Azithromycin Distribution and Community Microbiome: A Cluster-Randomized Trial. Open Forum Infect Dis 2018; 5:ofy182. [PMID: 30151409 PMCID: PMC6101535 DOI: 10.1093/ofid/ofy182] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/20/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Mass distributions of oral azithromycin have long been used to eliminate trachoma, and they are now being proposed to reduce childhood mortality. The observed benefit appears to be augmented with each additional treatment, suggesting a possible community-level effect. Here, we assess whether 2 biannual mass treatments of preschool children affect the community's gut microbiome at 6 months after the last distribution. METHODS In this cluster-randomized controlled trial, children aged 1-60 months in the Dossa region of Niger were randomized at the village level to receive a single dose of azithromycin or placebo every 6 months. Fecal samples were collected 6 months after the second treatment for metagenomic deep sequencing. The prespecified primary outcome was the Euclidean PERMANOVA of the gut microbiome, or effectively the distance between the genus-level centroid at the community level, with the secondary outcome being the Simpson's α diversity. RESULTS In the azithromycin arm, the gut microbial structures were significantly different than in the placebo arm (Euclidean PERMANOVA, P < .001). Further, the diversity of the gut microbiome in the azithromycin arm was significantly lower than in the placebo arm (inverse Simpson's index, P = .005). CONCLUSIONS Two mass azithromycin administrations, 6 months apart, in preschool children led to long-term alterations of the gut microbiome structure and community diversity. Here, long-term microbial alterations in the community did not imply disease but were associated with an improvement in childhood mortality. CLINICAL TRIALS REGISTRATION NCT02048007.
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Affiliation(s)
- Thuy Doan
- Francis I. Proctor Foundation, San Francisco, California
- Department of Ophthalmology, University of California San Francisco, San Francisco, California
| | | | | | - Sun Y Cotter
- Francis I. Proctor Foundation, San Francisco, California
| | - Kathryn J Ray
- Francis I. Proctor Foundation, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | | | - Lina Zhong
- Francis I. Proctor Foundation, San Francisco, California
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California
| | - Zhaoxia Zhou
- Francis I. Proctor Foundation, San Francisco, California
| | | | - Dionna Fry
- Francis I. Proctor Foundation, San Francisco, California
| | - Catherine E Oldenburg
- Francis I. Proctor Foundation, San Francisco, California
- Department of Ophthalmology, University of California San Francisco, San Francisco, California
| | - Lee Worden
- Francis I. Proctor Foundation, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Travis C Porco
- Francis I. Proctor Foundation, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Jeremy D Keenan
- Francis I. Proctor Foundation, San Francisco, California
- Department of Ophthalmology, University of California San Francisco, San Francisco, California
| | - Thomas M Lietman
- Francis I. Proctor Foundation, San Francisco, California
- Department of Ophthalmology, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
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Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator's Perspective. mSystems 2018; 3:mSystems00153-17. [PMID: 29556537 PMCID: PMC5850077 DOI: 10.1128/msystems.00153-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/14/2017] [Indexed: 12/14/2022] Open
Abstract
Severe bacterial pneumonia is a major global cause of morbidity and mortality, yet current diagnostic approaches rely on identification of causative pathogens by cultures, which require extended incubation periods and often fail to detect relevant pathogens. Consequently, patients are prescribed broad-spectrum antibiotics in a “one-size-fits-all” manner, which may be inappropriate for their individual needs and promote antibiotic resistance. Severe bacterial pneumonia is a major global cause of morbidity and mortality, yet current diagnostic approaches rely on identification of causative pathogens by cultures, which require extended incubation periods and often fail to detect relevant pathogens. Consequently, patients are prescribed broad-spectrum antibiotics in a “one-size-fits-all” manner, which may be inappropriate for their individual needs and promote antibiotic resistance. My research focuses on leveraging next-generation sequencing of microbial DNA directly from patient samples for the development of new, culture-independent definitions of pneumonia. In this perspective article, I discuss the current state of the field and focus on the conceptual and research design challenges for clinical translation. With ongoing technological advancements and application of computational biology methods for assessing clinical validity and utility, I anticipate that sequencing-based diagnostics will soon be able to positively disrupt the way we think about, diagnose, and treat pulmonary infections.
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Forbes JD, Knox NC, Peterson CL, Reimer AR. Highlighting Clinical Metagenomics for Enhanced Diagnostic Decision-making: A Step Towards Wider Implementation. Comput Struct Biotechnol J 2018; 16:108-120. [PMID: 30026887 PMCID: PMC6050174 DOI: 10.1016/j.csbj.2018.02.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/19/2018] [Accepted: 02/25/2018] [Indexed: 12/14/2022] Open
Abstract
Clinical metagenomics (CMg) is the discipline that refers to the sequencing of all nucleic acid material present within a clinical specimen with the intent to recover clinically relevant microbial information. From a diagnostic perspective, next-generation sequencing (NGS) offers the ability to rapidly identify putative pathogens and predict their antimicrobial resistance profiles to optimize targeted treatment regimens. Since the introduction of metagenomics nearly a decade ago, numerous reports have described successful applications in an increasing variety of biological specimens, such as respiratory secretions, cerebrospinal fluid, stool, blood and tissue. Considerable advancements in sequencing and computational technologies in recent years have made CMg a promising tool in clinical microbiology laboratories. Moreover, costs per sample and turnaround time from specimen receipt to clinical management continue to decrease, making the prospect of CMg more feasible. Many difficulties, however, are associated with CMg and warrant further improvements such as the informatics infrastructure and analytical pipelines. Thus, the current review focuses on comprehensively assessing applications of CMg for diagnostic and subtyping purposes.
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Affiliation(s)
- Jessica D. Forbes
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- University of Manitoba IBD Clinical and Research Centre, Winnipeg, Manitoba, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Natalie C. Knox
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Christy-Lynn Peterson
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Aleisha R. Reimer
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
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Abstract
PURPOSE OF REVIEW With the advent of novel massively parallel sequencing technologies and bioinformatic processing capabilities, clinical applications of metagenomic studies are rapidly being integrated into medicine. Through this paper, we hope to introduce this powerful new tool to clinicians caring for children. RECENT FINDINGS Very few studies have looked at metagenomic applications in children. The ability to perform these types of massive sequencing projects was not possible as little as 7 years ago. SUMMARY Metagenomics is defined as the study of all genetic material within a given sample. Novel sequencing and analysis approaches allow for unbiased assays to identify pathogens missed by targeted sequencing and culture methods. Although not widely available yet, metagenomic studies have been used to diagnose pediatric infections, identify resistance genes in clinical samples, and characterize outbreaks. Although cost and turnaround time have limited its application in clinical laboratories to date, novel platforms and increasing comfort with these techniques continue to push diagnostic metagenomics into clinical pediatric medicine. Much work in this field is yet to be done. That being said, we feel that pediatric clinicians will be using metagenomic techniques in the care of children with increasing frequency in the near future.
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