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Askari A, Benson J, Felipe Bastos Horta L, Daneshmand A, Dasenbrock H, Cervantes-Arslanian AM. Candida Dublinensis Meningitis in an Immunocompetent Host: A Case Report and Review of the Literature. Neurol Clin Pract 2024; 14:e200279. [PMID: 38808026 PMCID: PMC11129330 DOI: 10.1212/cpj.0000000000200279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 03/11/2024] [Indexed: 05/30/2024]
Abstract
Objectives This study presents a case of Candida dubliniensis meningitis in an immunocompetent injection drug user and provides a literature review of CNS infections related to C dubliniensis. Methods A 32-year-old man with a history of opioid use disorder presented with seizures and underwent extensive diagnostic evaluations, including imaging, lumbar puncture, and tissue biopsies. Treatment consisted of antifungal therapy and placement of ventriculoperitoneal shunt (VPS). Results C dublinensis meningitis was identified on culture from a posterior fossa arachnoid sample. The patient demonstrated leptomeningeal enhancement on imaging, which resolved following 20 weeks of fluconazole. The development of hydrocephalus necessitated placement of VPS. Additional published cases of C dublinensis meningitis revealed varying presentations, diagnostic methods, and treatment regimens. Discussion C dublinensis meningitis is a rare condition affecting both immunocompromised and immunocompetent individuals, particularly those with intravenous drug use. The diagnosis can be challenging, often requiring repeat lumbar punctures, extensive CSF sampling, or meningeal biopsy. Treatment involves a combination of antifungal agents, such as amphotericin B and fluconazole. Intracranial hypertension and hydrocephalus may necessitate surgical intervention. In conclusion, C dublinensis meningitis should be considered as a potential etiology of meningitis, particularly in those with a history of injection drug use.
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Affiliation(s)
- Asra Askari
- Department of Neurosurgery (AA, HD, AMC-A); Department of Infectious Disease (JB); and Department of Neurology (LFBH, AD, AMC-A), Boston University School of Medicine and Boston Medical Center, MA
| | - Jemma Benson
- Department of Neurosurgery (AA, HD, AMC-A); Department of Infectious Disease (JB); and Department of Neurology (LFBH, AD, AMC-A), Boston University School of Medicine and Boston Medical Center, MA
| | - Lucas Felipe Bastos Horta
- Department of Neurosurgery (AA, HD, AMC-A); Department of Infectious Disease (JB); and Department of Neurology (LFBH, AD, AMC-A), Boston University School of Medicine and Boston Medical Center, MA
| | - Ali Daneshmand
- Department of Neurosurgery (AA, HD, AMC-A); Department of Infectious Disease (JB); and Department of Neurology (LFBH, AD, AMC-A), Boston University School of Medicine and Boston Medical Center, MA
| | - Hormuzdiyar Dasenbrock
- Department of Neurosurgery (AA, HD, AMC-A); Department of Infectious Disease (JB); and Department of Neurology (LFBH, AD, AMC-A), Boston University School of Medicine and Boston Medical Center, MA
| | - Anna M Cervantes-Arslanian
- Department of Neurosurgery (AA, HD, AMC-A); Department of Infectious Disease (JB); and Department of Neurology (LFBH, AD, AMC-A), Boston University School of Medicine and Boston Medical Center, MA
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2
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Liu Y, Ma Y. Clinical applications of metagenomics next-generation sequencing in infectious diseases. J Zhejiang Univ Sci B 2024:1-14. [PMID: 38772736 DOI: 10.1631/jzus.b2300029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/06/2023] [Indexed: 05/23/2024]
Abstract
Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.
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Affiliation(s)
- Ying Liu
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Yongjun Ma
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China.
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3
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Chen W, Liu G, Cui L, Tian F, Zhang J, Zhao J, Lv Y, Du J, Huan X, Wu Y, Zhang Y. Evaluation of metagenomic and pathogen-targeted next-generation sequencing for diagnosis of meningitis and encephalitis in adults: A multicenter prospective observational cohort study in China. J Infect 2024; 88:106143. [PMID: 38548243 DOI: 10.1016/j.jinf.2024.106143] [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: 11/26/2023] [Revised: 02/17/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Next-generation sequencing (NGS) might aid in the identification of causal pathogens. However, the optimal approaches applied to cerebrospinal fluid (CSF) for detection are unclear, and studies evaluating the application of different NGS workflows for the diagnosis of intracranial infections are limited. METHODS In this multicenter, prospective observational cohort study, we described the diagnostic efficacy of pathogen-targeted NGS (ptNGS) and metagenomic NGS (mNGS) compared to that of composite microbiologic assays, for infectious meningitis/encephalitis (M/E). RESULTS In total, 152 patients diagnosed with clinically suspected M/E at four tertiary hospitals were enrolled; ptNGS and mNGS were used in parallel for pathogen detection in CSF. Among the 89 patients who were diagnosed with definite infectious M/E, 57 and 39 patients had causal microbial detection via ptNGS and mNGS, respectively. The overall accuracy of ptNGS was 65.1%, with a positive percent agreement (PPA) of 64% and a negative percent agreement (NPA) of 66.7%; and the overall accuracy of mNGS was 47.4%, with a PPA of 43.8% and an NPA of 52.4% after discrepancy analysis. There was a significant difference in the detection efficiency between these two methods both for PPA (sensitivity) and overall accuracy for pathogen detection (P < 0.05). CONCLUSIONS NGS tests have provided new information in addition to conventional microbiologic tests. ptNGS seems to have superior performance over mNGS for common causative pathogen detection in CSF for infectious M/E.
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Affiliation(s)
- Weibi Chen
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Gang Liu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Lili Cui
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Fei Tian
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jiatang Zhang
- Department of Neurology, the First Medical Center of People's Liberation Army General Hospital, Beijing, China
| | - Jiahua Zhao
- Department of Neurology, the First Medical Center of People's Liberation Army General Hospital, Beijing, China
| | - Ying Lv
- Department of Neurology & Psychiatry, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jianxin Du
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery, Beijing Fengtai Youanmen Hospital, Beijing, China
| | - Xinyu Huan
- Department of Neurosurgery, Beijing Fengtai Youanmen Hospital, Beijing, China
| | - Yingfeng Wu
- Department of Vascular Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China.
| | - Yan Zhang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China; Department of Sleep and Consciousness Disorders, Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China.
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4
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Beatty NL, Kaur H, Schlaffer K, Thompson K, Manavalan P, Rijos ZR, Raman AA, Droghini HR, O’Connell EM. Subarachnoid Neurocysticercosis Case Series Reveals a Significant Delay in Diagnosis-Requiring a High Index of Suspicion Among Those at Risk. Open Forum Infect Dis 2024; 11:ofae176. [PMID: 38680612 PMCID: PMC11055394 DOI: 10.1093/ofid/ofae176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/20/2024] [Indexed: 05/01/2024] Open
Abstract
Subarachnoid neurocysticercosis can be challenging to recognize, which often leads to a delay in diagnosis. We report 3 cases presenting as chronic headache disorders that highlight the unique manifestations seen with this form of neurocysticercosis and the role that the infectious diseases consultant can play in ensuring a timely diagnosis.
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Affiliation(s)
- Norman L Beatty
- Division of Infectious Diseases and Global Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Harpreet Kaur
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Kathryn Schlaffer
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Kathryn Thompson
- Division of Infectious Diseases and Global Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Preeti Manavalan
- Division of Infectious Diseases and Global Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Zulmarie R Rijos
- Division of Infectious Diseases and Global Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Abhinandan A Raman
- Division of Infectious Diseases and Global Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - H Richard Droghini
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Elise M O’Connell
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
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5
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Li C, Xiao NS, Ke BY, Li S, Lin Y. Application of Metagenomic Next-Generation Sequencing in Suspected Spinal Infectious Diseases. World Neurosurg 2024; 185:e542-e548. [PMID: 38401756 DOI: 10.1016/j.wneu.2024.02.071] [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: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 02/26/2024]
Abstract
OBJECTIVE This study aimed to explore the clinical efficacy of metagenomic next-generation sequencing (mNGS) in diagnosing and treating suspected spinal infectious diseases. METHODS Between October 2022 to December 2023, a retrospective analysis was performed on patient records within the Department of Spinal Surgery at Guilin People's Hospital. The analysis included comprehensive data on patients with presumed spinal infectious diseases, incorporating results from mNGS tests conducted externally, conventional pathogen detection results, laboratory examination results, and imaging findings. The study aimed to assess the applicability of mNGS in the context of suspected spinal infectious lesions. RESULTS Twenty-seven patients were included in the final analysis. Pathogenic microorganisms were identified in 23 cases. The included cases encompassed 1 case of tuberculous spondylitis, 1 case of fungal infection, 3 cases of Brucella spondylitis, 3 cases of viral infection, 9 cases of bacterial infection, and 6 cases of mixed infections. Pathogenic microorganisms remained elusive in 4 cases. The application of the mNGS method demonstrated a significantly elevated positive detection rate compared to conventional methods (85.19% vs. 48.15%, P < 0.05). Moreover, the mNGS method detected a greater variety of pathogen species than traditional methods (Z = 10.69, P < 0.05). Additionally, the mNGS method exhibited a shorter detection time. CONCLUSIONS mNGS demonstrated significantly higher detection rates for bacterial, fungal, viral, and mixed infections in cases of suspected spinal infectious diseases. The clinical implementation of mNGS could further enhance the efficiency of diagnosing and treating suspected spinal infectious diseases.
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Affiliation(s)
- Cheng Li
- Department of Orthopaedics, Guilin People's Hospital, Guilin, Guangxi Province, China
| | - Nian-Su Xiao
- Department of Orthopaedics, Guilin People's Hospital, Guilin, Guangxi Province, China
| | - Bao-Yi Ke
- Department of Orthopaedics, Guilin People's Hospital, Guilin, Guangxi Province, China
| | - Sen Li
- Department of Orthopaedics, Guilin People's Hospital, Guilin, Guangxi Province, China
| | - Yang Lin
- Department of Orthopaedics, Guilin People's Hospital, Guilin, Guangxi Province, China.
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6
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Shirazinia M, Sheybani F, Naderi H, Haddad M, Hajipour P, Khoroushi F. Chronic meningitis in adults: a comparison between neurotuberculosis and neurobrucellosis. BMC Infect Dis 2024; 24:441. [PMID: 38664652 PMCID: PMC11046744 DOI: 10.1186/s12879-024-09345-6] [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: 02/08/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND In regions endemic for tuberculosis and brucellosis, distinguishing between tuberculous meningitis (TBM) and brucella meningitis (BM) poses a substantial challenge. This study investigates the clinical and paraclinical characteristics of patients with TBM and BM. METHODS Adult patients diagnosed with either TBM or BM who were admitted to two referral hospitals between March 2015 and October 2022, were included, and the characteristics of the patients were analyzed. RESULTS Seventy patients formed the study group, 28 with TBM and 42 with BM, were included. TBM patients had a 2.06-fold (95% CI: 1.26 to 3.37, P-value: 0.003) higher risk of altered consciousness and a 4.80-fold (95% CI: 1.98 to 11.61, P-value: < 0.001) higher risk of extra-neural involvement as compared to BM patients. Cerebrospinal fluid (CSF) analysis revealed a significantly higher percentage of polymorphonuclear leukocytes (PMN) in TBM compared to BM (Standardized mean difference: 0.69, 95% CI: 0.18 to 1.20, P-value: 0.008). Neuroimaging findings indicated higher risks of hydrocephalus (P-value: 0.002), infarction (P-value: 0.029), and meningeal enhancement (P-value: 0.012) in TBM compared to BM. Moreover, TBM patients had a 67% (95% CI: 21% to 131%, P-value:0.002) longer median length of hospital stay and a significantly higher risk of unfavorable outcomes (Risk ratio: 6.96, 95% CI: 2.65 to 18.26, p < 0.001). CONCLUSIONS Our study emphasizes that TBM patients displayed increased frequencies of altered consciousness, PMN dominance in CSF, extra-neural involvement, hydrocephalus, meningeal enhancement, and brain infarction. The findings emphasize the diagnostic difficulties and underscore the importance of cautious differentiation between these two conditions to guide appropriate treatment strategies.
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Affiliation(s)
- Matin Shirazinia
- Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fereshte Sheybani
- Department of Infectious Diseases and Tropical Medicine, Imam Reza Teaching Hospital, Faculty of Medicine, Mashhad University of Medical Sciences, Daneshgah Street, Mashhad, Iran.
| | - HamidReza Naderi
- Department of Infectious Diseases and Tropical Medicine, Imam Reza Teaching Hospital, Faculty of Medicine, Mashhad University of Medical Sciences, Daneshgah Street, Mashhad, Iran
| | - Mahboubeh Haddad
- Department of Infectious Diseases and Tropical Medicine, Imam Reza Teaching Hospital, Faculty of Medicine, Mashhad University of Medical Sciences, Daneshgah Street, Mashhad, Iran
| | - Pouria Hajipour
- Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzaneh Khoroushi
- Department of Radiology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Kuenzli AB, Müller MD, Z`Graggen WJ, Walti LN, Martin Y, Lazarevic V, Schrenzel J, Oberli A. Case report: Chronic Candida albicans meningitis: a rare entity diagnosed by metagenomic next-generation sequencing. Front Cell Infect Microbiol 2024; 14:1322847. [PMID: 38707513 PMCID: PMC11066203 DOI: 10.3389/fcimb.2024.1322847] [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: 10/16/2023] [Accepted: 02/07/2024] [Indexed: 05/07/2024] Open
Abstract
The aetiology of chronic aseptic meningitis is difficult to establish. Candida meningitis in particular is often diagnosed late, as cerebrospinal fluid (CSF) work-up and imaging findings are nonspecific. A 35-year-old patient with chronic aseptic meningitis, for which repeated microbiological testing of CSF was unrevealing, was finally diagnosed with Candida albicans (C. albicans) meningitis with cauda equina involvement using metagenomic next-generation sequencing (mNGS). This report highlights the diagnostic challenges and the difficulties of treating shunt-associated fungal meningitis.
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Affiliation(s)
- Andrea B. Kuenzli
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Service d’Infectiologie, Department of Internal Medicine, Neuchâtel Hospital Network, Neuchâtel, Switzerland
| | - Mandy D. Müller
- Department of Neurosurgery, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Werner J. Z`Graggen
- Department of Neurosurgery, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Laura N. Walti
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Yonas Martin
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of General Internal Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Vladimir Lazarevic
- Genomic Research Laboratory, Geneva University Hospitals (HUG) and University of Geneva, Geneva, Switzerland
| | - Jacques Schrenzel
- Genomic Research Laboratory, Geneva University Hospitals (HUG) and University of Geneva, Geneva, Switzerland
| | - Alexander Oberli
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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8
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Lass-Flörl C, Kanj SS, Govender NP, Thompson GR, Ostrosky-Zeichner L, Govrins MA. Invasive candidiasis. Nat Rev Dis Primers 2024; 10:20. [PMID: 38514673 DOI: 10.1038/s41572-024-00503-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/15/2024] [Indexed: 03/23/2024]
Abstract
Invasive candidiasis is an important fungal disease caused by Candida albicans and, increasingly, non-albicans Candida pathogens. Invasive Candida infections originate most frequently from endogenous human reservoirs and are triggered by impaired host defences. Signs and symptoms of invasive candidiasis are non-specific; candidaemia is the most diagnosed manifestation, with disseminated candidiasis affecting single or multiple organs. Diagnosis poses many challenges, and conventional culture techniques are frequently supplemented by non-culture-based assays. The attributable mortality from candidaemia and disseminated infections is ~30%. Fluconazole resistance is a concern for Nakaseomyces glabratus, Candida parapsilosis, and Candida auris and less so in Candida tropicalis infection; acquired echinocandin resistance remains uncommon. The epidemiology of invasive candidiasis varies in different geographical areas and within various patient populations. Risk factors include intensive care unit stay, central venous catheter use, broad-spectrum antibiotics use, abdominal surgery and immune suppression. Early antifungal treatment and central venous catheter removal form the cornerstones to decrease mortality. The landscape of novel therapeutics is growing; however, the application of new drugs requires careful selection of eligible patients as the spectrum of activity is limited to a few fungal species. Unanswered questions and knowledge gaps define future research priorities and a personalized approach to diagnosis and treatment of invasive candidiasis is of paramount importance.
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Affiliation(s)
- Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, ECMM Excellence Centres of Medical Mycology, Medical University of Innsbruck, Innsbruck, Austria.
| | - Souha S Kanj
- Infectious Diseases Division, and Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
| | - Nelesh P Govender
- Faculty of Health Sciences, University of the Witwatersrand and National Institute for Communicable Diseases, Johannesburg, South Africa
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - George R Thompson
- UC Davis Health Medical Center, Division of Infectious Diseases, Sacramento, CA, USA
| | | | - Miriam Alisa Govrins
- Institute of Hygiene and Medical Microbiology, ECMM Excellence Centres of Medical Mycology, Medical University of Innsbruck, Innsbruck, Austria
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Downie DL, Rao P, David-Ferdon C, Courtney S, Lee JS, Kugley S, MacDonald PDM, Barnes K, Fisher S, Andreadis JL, Chaitram J, Mauldin MR, Salerno RM, Schiffer J, Gundlapalli AV. Literature Review of Pathogen Agnostic Molecular Testing of Clinical Specimens From Difficult-to-Diagnose Patients: Implications for Public Health. Health Secur 2024; 22:93-107. [PMID: 38608237 PMCID: PMC11044852 DOI: 10.1089/hs.2023.0100] [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: 05/22/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 04/14/2024] Open
Abstract
To better identify emerging or reemerging pathogens in patients with difficult-to-diagnose infections, it is important to improve access to advanced molecular testing methods. This is particularly relevant for cases where conventional microbiologic testing has been unable to detect the pathogen and the patient's specimens test negative. To assess the availability and utility of such testing for human clinical specimens, a literature review of published biomedical literature was conducted. From a corpus of more than 4,000 articles, a set of 34 reports was reviewed in detail for data on where the testing was being performed, types of clinical specimens tested, pathogen agnostic techniques and methods used, and results in terms of potential pathogens identified. This review assessed the frequency of advanced molecular testing, such as metagenomic next generation sequencing that has been applied to clinical specimens for supporting clinicians in caring for difficult-to-diagnose patients. Specimen types tested were from cerebrospinal fluid, respiratory secretions, and other body tissues and fluids. Publications included case reports and series, and there were several that involved clinical trials, surveillance studies, research programs, or outbreak situations. Testing identified both known human pathogens (sometimes in new sites) and previously unknown human pathogens. During this review, there were no apparent coordinated efforts identified to develop regional or national reports on emerging or reemerging pathogens. Therefore, development of a coordinated sentinel surveillance system that applies advanced molecular methods to clinical specimens which are negative by conventional microbiological diagnostic testing would provide a foundation for systematic characterization of emerging and underdiagnosed pathogens and contribute to national biodefense strategy goals.
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Affiliation(s)
- Diane L. Downie
- Diane L. Downie, PhD, MPH, is Deputy Associate Director for Science, Office of Readiness and Response; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Preetika Rao
- Preetika Rao, MPH, is a Health Scientist; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Corinne David-Ferdon
- Corinne David-Ferdon, PhD, is Associate Director of Science, Office of Public Health Data, Surveillance, and Technology; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Sean Courtney
- Sean Courtney, PhD, is a Health Scientist, at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Justin S. Lee
- Justin Lee, DVM, PhD, is a Health Scientist, Division of Global Health Protection; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Shannon Kugley
- Shannon Kugley, MLIS, is a Research Public Health Analyst; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Pia D. M. MacDonald
- Pia D. M. MacDonald, PhD, MPH, is a Senior Infectious Disease Epidemiologist; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Keegan Barnes
- Keegan Barnes is a Public Health Analyst; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Shelby Fisher
- Shelby Fisher, MPH, is an Epidemiologist; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Joanne L. Andreadis
- Joanne L. Andreadis, PhD, is Associate Director for Science, at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Jasmine Chaitram
- Jasmine Chaitram, MPH, is Branch Chief, at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Matthew R. Mauldin
- Matthew R. Mauldin, PhD, is Health Scientists, Office of Readiness and Response; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Reynolds M. Salerno
- Reynolds M. Salerno, PhD, is Director, Division of Laboratory Systems; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Jarad Schiffer
- Jarad Schiffer, MS, is Health Scientists, Office of Readiness and Response; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Adi V. Gundlapalli
- Adi V. Gundlapalli, MD, PhD, is a Senior Advisor, Data Readiness and Response, Office of Public Health Data, Surveillance, and Technology; at the US Centers for Disease Control and Prevention, Atlanta, GA
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10
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Costales C, Dien Bard J. The Report Says What?: How the Medical Microbiologist can aid in the Interpretation of Next-Generation Sequencing Results. Clin Lab Med 2024; 44:75-84. [PMID: 38280799 DOI: 10.1016/j.cll.2023.10.006] [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] [Indexed: 01/29/2024]
Abstract
The applications of next-generation sequencing (NGS) in the clinical microbiology laboratory are expanding at a rapid pace. The medical microbiologist thus plays a key role in translating the results of these emerging technologies to the practicing clinician. Here we discuss the factors to consider to successfully develop standardized reporting for microbial targeted or metagenomic NGS testing in the clinical laboratory.
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Affiliation(s)
- Cristina Costales
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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11
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Meng D, Zou Y, Li J, Zhai J, Guo R, Jin X. Invasive pulmonary and central nervous system aspergillosis in a child: A case report and literature review. Medicine (Baltimore) 2024; 103:e37160. [PMID: 38335438 PMCID: PMC10861009 DOI: 10.1097/md.0000000000037160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/12/2024] [Indexed: 02/12/2024] Open
Abstract
RATIONALE Children with haematological malignancies have a higher risk of developing aggressive pulmonary aspergillosis and a higher mortality rate. The most common site of extrapulmonary aspergillosis in children is the central nervous system (CNS), and the death rate is higher when CNS is affected. Therefore, early diagnosis and treatment of invasive aspergillosis are essential for reducing mortality. PATIENT CONCERNS We report a case of an 8-year-old girl with acute lymphoblastic leukaemia who developed invasive pulmonary aspergillosis complicated by CNS aspergillosis. Aspergillus was confirmed by metagenomic sequencing of pathogenic microorganisms. DIAGNOSES Invasive pulmonary and central nervous system aspergillosis. INTERVENTIONS The patient was treated with combined systemic antifungal agents (voriconazole and liposomal amphotericin B) and intrathecal injection of amphotericin B. OUTCOMES The treatment was well tolerated and resulted in remarkable clinical and radiological head improvements. LESSONS Invasive aspergillosis has a high mortality rate and requires early diagnosis and treatment. Pathogenic microbial metagenomic sequencing is a convenient method to assist in the early diagnosis of aspergillosis. Voriconazole is the drug of choice for the treatment of invasive aspergillosis. When CNS aspergillosis occurs, it can be combined with other systemic antifungal drugs and intrathecal injection of amphotericin B.
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Affiliation(s)
- Dongmei Meng
- Department of Pneumology, Tianjin Children’s Hospital/Tianjin University Children’s Hospital, Tianjin, China
| | - Yingxue Zou
- Department of Pneumology, Tianjin Children’s Hospital/Tianjin University Children’s Hospital, Tianjin, China
- Department of Infectious Disease, Tianjin Children’s Hospital/Tianjin University Children’s Hospital, Tianjin, China
| | - Jiao Li
- Department of Pneumology, Tianjin Children’s Hospital/Tianjin University Children’s Hospital, Tianjin, China
| | - Jia Zhai
- Department of Pneumology, Tianjin Children’s Hospital/Tianjin University Children’s Hospital, Tianjin, China
| | - Run Guo
- Department of Pneumology, Tianjin Children’s Hospital/Tianjin University Children’s Hospital, Tianjin, China
| | - Xingnan Jin
- Department of Infectious Disease, Tianjin Children’s Hospital/Tianjin University Children’s Hospital, Tianjin, China
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12
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Zhang M, Chen L, Zhao H, Qiao T, Jiang L, Wang C, Zhong X, Li X, Xu Y. Metagenomic next-generation sequencing for diagnosis of infectious encephalitis and meningitis: a retrospective study of 90 patients. Neurol Res 2024; 46:187-194. [PMID: 37931016 DOI: 10.1080/01616412.2023.2265243] [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: 12/23/2022] [Accepted: 09/24/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND Infections of the central nervous system (CNS) are potentially life-threatening and can cause serious morbidity. We evaluated the clinical value of metagenomic next-generation sequencing (mNGS) in the diagnosis of infectious encephalitis and meningitis and explored the factors affecting the results of mNGS. METHODS Patients with suspected cases of encephalitis or meningitis who presented in Northern Jiangsu People's Hospital from 1 March 2018 to 30 September 2022 were collected. Demographic, historical, and clinical information were obtained, and cerebrospinal fluid (CSF) samples were treated with mNGS. The pathogen was identified using National Center for Biotechnology Information (NCBI) GenBank sequence data. RESULTS Ninety-six patients were screened and finally 90 subjects enrolled. Of the 90 enrolled cases, 67 (74.4%) were diagnosed with central nervous system infections, which included 48 cases (71.6%) of viral infection, 11 (12.2%) of bacterial infection, 5 (7.5%) of mycobacterium tuberculosis, 2 (3.0%) of fungal infection, and 1 (1.5%) of rickettsia infection. From these cases, mNGS identified 40 (44.4%) true-positive cases, 3 (3.3%) false-positive case, 22 (24.4%) true-negative cases, and 25 (27.8%) false-negative cases. The sensitivity and specificity of mNGS were 61.5% and 88%, respectively. mNGS of CSF could show a higher positive rate in patients with marked CSF abnormalities, including elevated protein concentrations and monocyte counts. CONCLUSION mNGS of CSF is an effective method for detecting infectious encephalitis and meningitis, and the results should be analyzed combined with conventional microbiological testing results.
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Affiliation(s)
- Mengling Zhang
- Department of Neurology, Northern Jiangsu People's Hospital, Clinical Medical College of Yangzhou University, Yangzhou, China
| | - Lanlan Chen
- Department of Neurology, Northern Jiangsu People's Hospital, Clinical Medical College of Yangzhou University, Yangzhou, China
| | - Haina Zhao
- Department of Neurology, Northern Jiangsu People's Hospital, Clinical Medical College of Yangzhou University, Yangzhou, China
| | - Tingting Qiao
- Department of Neurology, Northern Jiangsu People's Hospital, Clinical Medical College of Yangzhou University, Yangzhou, China
| | - Li Jiang
- Department of Gerontology Northern Jiangsu People's Hospital, Clinical Medical School of Yangzhou University, Yangzhou, China
| | - Chenxin Wang
- Department of Neurology, Northern Jiangsu People's Hospital, The Yangzhou School of Clinical Medicine of Dalian Medical University, Yangzhou, China
| | - Xingxing Zhong
- Department of Neurology, Northern Jiangsu People's Hospital, Clinical Medical College of Yangzhou University, Yangzhou, China
| | - Xiaobo Li
- Department of Neurology, Northern Jiangsu People's Hospital, Clinical Medical College of Yangzhou University, Yangzhou, China
| | - Yao Xu
- Department of Neurology, Northern Jiangsu People's Hospital, Clinical Medical College of Yangzhou University, Yangzhou, China
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13
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Xiao G, Shu M. Massive neurocysticercosis in a ten-year-old girl: a case report. BMC Pediatr 2024; 24:79. [PMID: 38267910 PMCID: PMC10807077 DOI: 10.1186/s12887-024-04530-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 01/02/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Massive neurocysticercosis is a rare form of neurocysticercosis, and can lead to serious conditions and even death. CASE PRESENTATION Here we present a case of ten-year-old Tibetan girl who developed headache and vomiting. Her brain magnetic resonance imaging (MRI) illustrated lots of intracranial cystic lesions, and no obvious extracranial lesions were found. Serum immunoglobulin G antibodies against cysticerci were positive by the use of an enzyme-linked immunosorbent assay (ELISA). These results in combination with her medical history were in line with massive neurocysticercosis. The patients recovered well after supportive management and antiparasitic treatment. CONCLUSIONS This case provides insights on the diagnosis and treatment of massive neurocysticercosis. The treatment of patients with massive neurocysticercosis should be in an individualized fashion, and the use of antiparasitic drugs in these patients must be decided after carefully weighing the risks and benefits.
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Affiliation(s)
- Guoguang Xiao
- Department of Pediatrics, West China Second Hospital, Sichuan University, No. 20, Section 3, Renmin South Road, Chengdu, 610041, Sichuan Province, P. R. China
- West China Xiamen Hospital of Sichuan University, Xiamen, 361022, China
| | - Min Shu
- Department of Pediatrics, West China Second Hospital, Sichuan University, No. 20, Section 3, Renmin South Road, Chengdu, 610041, Sichuan Province, P. R. China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, 610041, China.
- West China Xiamen Hospital of Sichuan University, Xiamen, 361022, China.
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14
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Yan M, Zou X, Wang Y, Wang C, Wang Y, Liu Z, Shang L, Cui X, Cao B. Impact of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluid on Antimicrobial Stewardship in Patients With Lower Respiratory Tract Infections: A Retrospective Cohort Study. J Infect Dis 2024; 229:223-231. [PMID: 37506257 DOI: 10.1093/infdis/jiad296] [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: 03/19/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND The impact of metagenomic next-generation sequencing (mNGS) on antimicrobial stewardship in patients with lower respiratory tract infections (LRTIs) is still unknown. METHODS This retrospective cohort study included patients who had LRTIs diagnosed and underwent bronchoalveolar lavage between September 2019 and December 2020. Patients who underwent both mNGS and conventional microbiologic tests were classified as the mNGS group, while those with conventional tests only were included as a control group. A 1:1 propensity score match for baseline variables was conducted, after which changes in antimicrobial stewardship between the 2 groups were assessed. RESULTS A total of 681 patients who had an initial diagnosis of LRTIs and underwent bronchoalveolar lavage were evaluated; 306 patients were finally included, with 153 in each group. mNGS was associated with lower rates of antibiotic escalation than in the control group (adjusted odds ratio, 0.466 [95% confidence interval, .237-.919]; P = .02), but there was no association with antibiotic de-escalation. Compared with the control group, more patients discontinued the use of antivirals in the mNGS group. CONCLUSIONS The use of mNGS was associated with lower rates of antibiotic escalation and may facilitate the cessation of antivirals, but not contribute to antibiotic de-escalation in patients with LRTIs.
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Affiliation(s)
- Mengwei Yan
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Xiaohui Zou
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Yeming Wang
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Chenhui Wang
- Department of Anesthesiology, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yimin Wang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Zhibo Liu
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Lianhan Shang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Xiaojing Cui
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Tsinghua University School of Medicine, Beijing, China
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15
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Tian Y, Gao R, Wang Y, Zhou Y, Xu S, Duan Y, Lv W, Wang S, Hou M, Chen Y, Li F, Gao W, Zhang L, Zhou JX. Economic impact of metagenomic next-generation sequencing versus traditional bacterial culture for postoperative central nervous system infections using a decision analysis mode: study protocol for a randomized controlled trial. mSystems 2023; 8:e0058123. [PMID: 37937972 PMCID: PMC10734456 DOI: 10.1128/msystems.00581-23] [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: 06/20/2023] [Accepted: 09/26/2023] [Indexed: 11/09/2023] Open
Abstract
IMPORTANCE Diagnosing and treating postoperative central nervous system infections (PCNSIs) remains challenging due to the low detection rate and time-consuming nature of traditional methods for identifying microorganisms in cerebrospinal fluid. Metagenomic next-generation sequencing (mNGS) technology provides a rapid and comprehensive understanding of microbial composition in PCNSIs by swiftly sequencing and analyzing the microbial genome. The current study aimed to assess the economic impact of using mNGS versus traditional bacterial culture-directed PCNSIs diagnosis and therapy in post-neurosurgical patients from Beijing Tiantan Hospital. mNGS is a relatively expensive test item, and whether it has the corresponding health-economic significance in the clinical application of diagnosing intracranial infection has not been studied clearly. Therefore, the investigators hope to explore the clinical application value of mNGS detection in PCNSIs after neurosurgery.
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Affiliation(s)
- Ying Tian
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ran Gao
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yumei Wang
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yimin Zhou
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shanshan Xu
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuqing Duan
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wenyi Lv
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shuya Wang
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Mengxue Hou
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuqing Chen
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fangqiang Li
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wei Gao
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Linlin Zhang
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Beijing Engineering Research Center of Digital Healthcare for Neurological Diseases, Beijing, China
| | - Jian-Xin Zhou
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Beijing Engineering Research Center of Digital Healthcare for Neurological Diseases, Beijing, China
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
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16
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Wang Q, Cheng S, Wang Y, Li F, Chen J, Du W, Kang H, Wang Z. Global characteristics and trends in research on Candida auris. Front Microbiol 2023; 14:1287003. [PMID: 38125576 PMCID: PMC10731253 DOI: 10.3389/fmicb.2023.1287003] [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: 09/01/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction Candida auris, a fungal pathogen first reported in 2009, has shown strong resistance to azole antifungal drugs and has caused severe nosocomial outbreaks. It can also form biofilms, which can colonize patients' skin and transmit to others. Despite numerous reports of C. auris isolation in various countries, many studies have reported contradictory results. Method A bibliometric analysis was conducted using VOSviewer to summarize research trends and provide guidance for future research on controlling C. auris infection. The analysis revealed that the United States and the US CDC were the most influential countries and research institutions, respectively. For the researchers, Jacques F. Meis published the highest amount of related articles, and Anastasia P. Litvintseva's articles with the highest average citation rate. The most cited publications focused on clade classification, accurate identification technologies, nosocomial outbreaks, drug resistance, and biofilm formation. Keyword co-occurrence analysis revealed that the top five highest frequencies were for 'drug resistance,' 'antifungal susceptibility test,' 'infection,' 'Candida auris,' and 'identification.' The high-frequency keywords clustered into four groups: rapid and precise identification, drug resistance research, pathogenicity, and nosocomial transmission epidemiology studies. These clusters represent different study fields and current research hotspots of C. auris. Conclusion The bibliometric analysis identified the most influential country, research institution, and researcher, indicating current research trends and hotspots for controlling C. auris.
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Affiliation(s)
- Qihui Wang
- Laboratory of Microbiology, Department of Clinical Laboratory, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Shitong Cheng
- Laboratory of Microbiology, Department of Clinical Laboratory, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yinling Wang
- Laboratory of Microbiology, Department of Clinical Laboratory, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Fushun Li
- Laboratory of Microbiology, Department of Clinical Laboratory, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jingjing Chen
- Laboratory of Microbiology, Department of Clinical Laboratory, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wei Du
- National Clinical Research Center for Laboratory Medicine, Department of Clinical Laboratory, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Hui Kang
- Laboratory of Microbiology, Department of Clinical Laboratory, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhongqing Wang
- Department of Information Centre, The First Hospital of China Medical University, Shenyang, Liaoning, China
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17
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Boruah AP, Kroopnick A, Thakkar R, Wapniarski AE, Kim C, Dugue R, Harrigan E, Lipkin WI, Mishra N, Thakur KT. Application of VirCapSeq-VERT and BacCapSeq in the diagnosis of presumed and definitive neuroinfectious diseases. J Neurovirol 2023; 29:678-691. [PMID: 37851324 DOI: 10.1007/s13365-023-01172-w] [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: 03/09/2023] [Revised: 03/09/2023] [Accepted: 08/28/2023] [Indexed: 10/19/2023]
Abstract
Unbiased high-throughput sequencing (HTS) has enabled new insights into the diversity of agents implicated in central nervous system (CNS) infections. The addition of positive selection capture methods to HTS has enhanced the sensitivity while reducing sequencing costs and the complexity of bioinformatic analysis. Here we report the use of virus capture-based sequencing for vertebrate viruses (VirCapSeq-VERT) and bacterial capture sequencing (BacCapSeq) in investigating CNS infections. Thirty-four samples were categorized: (1) patients with definitive CNS infection by routine testing; (2) patients meeting clinically the Brighton criteria (BC) for meningoencephalitis; (3) patients with presumptive infectious etiology highest on the differential. RNA extracts from cerebrospinal fluid (CSF) were used for VirCapSeq-VERT, and DNA extracts were used for BacCapSeq analysis. Among 8 samples from known CNS infections in group 1, VirCapSeq and BacCapSeq confirmed 3 expected diagnoses (42.8%), were negative in 2 (25%), yielded an alternative result in 1 (11.1%), and did not detect 2 expected negative pathogens. The confirmed cases identified HHV-6, HSV-2, and VZV while the negative samples included JCV and HSV-2. In groups 2 and 3, 11/26 samples (42%) were positive for at least one pathogen; however, 27% of the total samples (7/26) were positive for commensal organisms. No microbial nucleic acids were detected in negative control samples. HTS showed limited promise for pathogen identification in presumed CNS infectious diseases in our small sample. Before conducting larger-scale prospective studies to assess the clinical value of this novel technique, clinicians should understand the benefits and limitations of using this modality.
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Affiliation(s)
- Abhilasha P Boruah
- Department of Neurology, Columbia University Irving Medical Center/New York Presbyterian Hospital (CUIMC/NYP), New York, NY, USA
- Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Adam Kroopnick
- Department of Neurology, Columbia University Irving Medical Center/New York Presbyterian Hospital (CUIMC/NYP), New York, NY, USA
| | - Riddhi Thakkar
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Anne E Wapniarski
- Department of Neurology, Columbia University Irving Medical Center/New York Presbyterian Hospital (CUIMC/NYP), New York, NY, USA
| | - Carla Kim
- Department of Neurology, Columbia University Irving Medical Center/New York Presbyterian Hospital (CUIMC/NYP), New York, NY, USA
| | - Rachelle Dugue
- Department of Neurology, Columbia University Irving Medical Center/New York Presbyterian Hospital (CUIMC/NYP), New York, NY, USA
| | - Eileen Harrigan
- Department of Neurology, Columbia University Irving Medical Center/New York Presbyterian Hospital (CUIMC/NYP), New York, NY, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Kiran T Thakur
- Department of Neurology, Columbia University Irving Medical Center/New York Presbyterian Hospital (CUIMC/NYP), New York, NY, USA.
- Division of Critical Care and Hospitalist Neurology, Department of Neurology, Milstein Hospital, 177 Fort Washington Avenue, New York, NY, 8GS-39910032, USA.
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18
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Son H, Moon J, Ha EJ, Kim N, Kim EY, Lee HS, Koh EJ, Phi JH, Park CK, Kim JE, Kim SK, Lee ST, Jung KH, Lee SK, Cho WS, Chu K. Identification of bacterial pathogens in brain abscesses by metagenomic approach using nanopore 16S amplicon sequencing. Diagn Microbiol Infect Dis 2023; 107:116041. [PMID: 37741170 DOI: 10.1016/j.diagmicrobio.2023.116041] [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: 03/09/2023] [Revised: 06/30/2023] [Accepted: 07/22/2023] [Indexed: 09/25/2023]
Abstract
Brain abscess is medically challenging. In this study, we applied nanopore sequencing for 16S rRNA analysis and investigated its efficacy and diagnostic value for patients with brain abscesses. Genomic DNA was extracted from the pus samples (n = 27) of brain abscess, and 16S rRNA genes were amplified by PCR. Sequencing libraries were generated using a rapid barcoding kit, and the generated reads were analyzed using the EPI2ME16S workflow. A conventional culture study was performed. More sensitive identification of pathogens was made by 16S sequencing, faster than the culture study. The proportion of anaerobic bacteria identified by 16S sequencing was higher (75%) than that obtained by culturing (32%). Polymicrobial infections were identified in 10 cases (40%) by 16S sequencing, while the culture study identified multiple bacteria in only 2 cases (8%). 16S sequencing was useful for identifying the composition of polymicrobial infections, including rare pathogens, and for the initial diagnosis of space-occupying lesions.
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Affiliation(s)
- Hyoshin Son
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea; Department of Neurology, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea
| | - Jangsup Moon
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea; Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Eun Jin Ha
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Narae Kim
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea
| | - Eun-Young Kim
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea; Department of Neurology, Chungnam National University Sejong Hospital, Sejong, Korea
| | - Han Sang Lee
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea; Center of Hospital Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Eun Jung Koh
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea; Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, South Korea; Center of Hospital Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Ji Hoon Phi
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea; Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, South Korea
| | - Chul-Kee Park
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Jeong Eun Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Seung-Ki Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea; Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, South Korea
| | - Soon-Tae Lee
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea
| | - Keun-Hwa Jung
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea
| | - Sang Kun Lee
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea
| | - Won-Sang Cho
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Kon Chu
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea.
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Pedrosa DA, Bruniera Peres Fernandes G, Filipe de Souza Godoy L, C Felício A, Pinho JR, Mário Doi A, de Araújo Gleizer R. Neurocysticercosis: diagnosis via metagenomic next-generation sequencing. Pract Neurol 2023; 23:509-511. [PMID: 37468299 DOI: 10.1136/pn-2023-003795] [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] [Accepted: 06/20/2023] [Indexed: 07/21/2023]
Abstract
A 68-year-old Brazilian woman had 3 months of progressive fatigue, difficulty walking and 18 kg weight loss. On examination, there was gait apraxia and executive dysfunction. MR scan of brain showed communicating hydrocephalus and a cerebrospinal fluid showed 105 white cells/µL (≤5), predominantly lymphocytes, protein of 1.35 g/L (0.15-0.45) and the glucose content of 0.06 mmol/L (3.3-4.4). We suspected an infective cause and used of metagenomic next-generation sequencing to diagnose neurocysticercosis. This case highlights the challenge of diagnosing chronic meningitis and the relevance of genetic approaches in diagnosing neurological infections.
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Affiliation(s)
- Denison Alves Pedrosa
- General Neurology Division, Albert Einstein Israeli Institute of Education and Research, São Paulo, Brazil
| | - Gustavo Bruniera Peres Fernandes
- Research and Development Sector, Clinical Laboratory, Albert Einstein Israeli Institute of Education and Research, São Paulo, Brazil
| | | | - André C Felício
- General Neurology Division, Albert Einstein Israeli Institute of Education and Research, São Paulo, Brazil
| | - João Rebello Pinho
- Research and Development Sector, Clinical Laboratory, Albert Einstein Israeli Institute of Education and Research, São Paulo, Brazil
| | - André Mário Doi
- Research and Development Sector, Clinical Laboratory, Albert Einstein Israeli Institute of Education and Research, São Paulo, Brazil
| | - René de Araújo Gleizer
- General Neurology Division, Albert Einstein Israeli Institute of Education and Research, São Paulo, Brazil
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20
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Lathe R, Schultek NM, Balin BJ, Ehrlich GD, Auber LA, Perry G, Breitschwerdt EB, Corry DB, Doty RL, Rissman RA, Nara PL, Itzhaki R, Eimer WA, Tanzi RE. Establishment of a consensus protocol to explore the brain pathobiome in patients with mild cognitive impairment and Alzheimer's disease: Research outline and call for collaboration. Alzheimers Dement 2023; 19:5209-5231. [PMID: 37283269 PMCID: PMC10918877 DOI: 10.1002/alz.13076] [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: 02/08/2023] [Accepted: 03/06/2023] [Indexed: 06/08/2023]
Abstract
Microbial infections of the brain can lead to dementia, and for many decades microbial infections have been implicated in Alzheimer's disease (AD) pathology. However, a causal role for infection in AD remains contentious, and the lack of standardized detection methodologies has led to inconsistent detection/identification of microbes in AD brains. There is a need for a consensus methodology; the Alzheimer's Pathobiome Initiative aims to perform comparative molecular analyses of microbes in post mortem brains versus cerebrospinal fluid, blood, olfactory neuroepithelium, oral/nasopharyngeal tissue, bronchoalveolar, urinary, and gut/stool samples. Diverse extraction methodologies, polymerase chain reaction and sequencing techniques, and bioinformatic tools will be evaluated, in addition to direct microbial culture and metabolomic techniques. The goal is to provide a roadmap for detecting infectious agents in patients with mild cognitive impairment or AD. Positive findings would then prompt tailoring of antimicrobial treatments that might attenuate or remit mounting clinical deficits in a subset of patients.
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Affiliation(s)
- Richard Lathe
- Division of Infection Medicine, Chancellor's Building, University of Edinburgh Medical School, Edinburgh, UK
| | | | - Brian J. Balin
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA 19131, USA
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | | | - George Perry
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Edward B. Breitschwerdt
- Intracellular Pathogens Research Laboratory, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - David B. Corry
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Richard L. Doty
- Smell and Taste Center, Department of Otorhinolaryngology: Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert A. Rissman
- Department of Neurosciences, University of California, San Diego and VA San Diego Healthcare System, La Jolla, CA
| | | | - Ruth Itzhaki
- Institute of Population Ageing, University of Oxford, Oxford, UK
| | - William A. Eimer
- Genetics and Aging Research Unit, Mass General Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
- McCance Cancer Center for Brain Health, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rudolph E. Tanzi
- Genetics and Aging Research Unit, Mass General Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
- McCance Cancer Center for Brain Health, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Intracell Research Group Consortium Collaborators
- David L. Hahn (Intracell Research Group, USA), Benedict C. Albensi (Nova Southeastern, USA), James St John (Griffith University, Australia), Jenny Ekberg (Griffith University, Australia), Mark L. Nelson (Intracell Research Group, USA), Gerald McLaughlin (National Institutes of Health, USA), Christine Hammond (Philadelphia College of Osteopathic Medicine, USA), Judith Whittum-Hudson (Wayne State University, USA), Alan P. Hudson (Wayne State University, USA), Guillaume Sacco (Université Cote d’Azur, Centre Hospitalier Universitaire de Nice, CoBTek, France), Alexandra Konig (Université Cote d’Azur and CoBTek, France), Bruno Pietro Imbimbo (Chiesi Farmaceutici, Parma, Italy), Nicklas Linz (Ki Elements Ltd, Saarbrücken, Germany), Nicole Danielle Bell (Author, 'What Lurks in the Woods'), Shima T. Moein (Smell and Taste Center, Department of Otorhinolaryngology, Perelman School of Medicine, University of Philadelphia, USA), Jürgen G. Haas (Infection Medicine, University of Edinburgh Medical School, UK)
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21
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Ramachandran PS, Williamson DA. The transformative potential of metagenomics in microbiology: advancements and implications. Intern Med J 2023; 53:1520-1523. [PMID: 37743240 DOI: 10.1111/imj.16228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/20/2023] [Indexed: 09/26/2023]
Affiliation(s)
- Prashanth S Ramachandran
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Melbourne, Australia
- Department of Neurology, Royal Melbourne Hospital, Victoria, Melbourne, Australia
- Department of Neurology, St. Vincent's Hospital, Victoria, Melbourne, Australia
| | - Deborah A Williamson
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Melbourne, Australia
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Victoria, Melbourne, Australia
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22
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Fan J, Tang R, Zhang L, Hoang PT, Ayoade F, Diaz-Perez JA, Moss HE, Jiang H. Atypical Presentations of Extraparenchymal Neurocysticercosis. J Neuroophthalmol 2023; 43:370-375. [PMID: 36637411 PMCID: PMC10318114 DOI: 10.1097/wno.0000000000001782] [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] [Indexed: 01/14/2023]
Abstract
BACKGROUND Neurocysticercosis (NCC) is the most common parasitic infection of the central nervous system and is typically diagnosed through visualization of the cysts in the cerebral parenchyma by neuro-imaging. However, neuro-imaging may not detect extraparenchymal neurocysticercosis (EPNCC), which is a rare manifestation of the disease involving the subarachnoid, meningeal, and intraventricular spaces. We report 2 cases of extraparenchymal neurocysticercosis, and discuss the diagnostic challenges and management of this entity. METHODS Two cases were identified through clinical records. RESULTS Both patients had an insidious onset with slow progression of disease, and presented with papilledema and cerebrospinal fluid (CSF) eosinophilia. One case was diagnosed with spinal cord biopsy. The other was diagnosed with CSF serology and next-generation sequencing-based pathogen analysis. Both patients were treated with ventriculoperitoneal shunt, systemic antiparasitic agents, and immunosuppression. CONCLUSIONS EPNCC is less common than parenchymal NCC. A high level of clinical suspicion is required given its rarity, long incubation period, and slow progression. Diagnosis and treatment can be challenging and requires a multidisciplinary approach.
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Affiliation(s)
- Jason Fan
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL
| | - Rui Tang
- Texas Tech University Health Sciences Center, Paul L. Foster School of Medicine, El Paso, TX
| | - Lily Zhang
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL
| | - Phuong T. Hoang
- Department of Neurology & Neurological Sciences, Stanford University, Palo Alto, CA
| | - Folusakin Ayoade
- Division of Infectious Disease, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL
| | - Julio A. Diaz-Perez
- Department of Pathology & Laboratory Medicine, University of Miami, Miami, FL
- Department of Dermatology, University of Tennessee, Memphis, TN
| | - Heather E. Moss
- Department of Neurology & Neurological Sciences, Stanford University, Palo Alto, CA
- Department of Ophthalmology, Stanford University, Palo Alto, CA
| | - Hong Jiang
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL
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23
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Zhou S, Bao Z, Ma S, Ou C, Hu H, Yang Y, Feng X, Pan Y, Gong S, Fan F, Chen P, Chu Q. A local dark tea - Liubao tea - extract exhibits remarkable performance in oral tissue regeneration, inflammation relief and oral microbiota reconstruction. Food Funct 2023; 14:7400-7412. [PMID: 37475617 DOI: 10.1039/d3fo02277c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The prevalence of oral health problems is ubiquitous in contemporary society, with particular emphasis placed on the central role of oral flora in mitigating this issue. Both ancient literature and modern research have highlighted the promising application of tea with substantial bioactive properties, particularly dark tea, in preserving and promoting oral health. Liubao tea, a widely consumed dark tea with increasing popularity in recent years, has been reported to possess abundant bioactive constituents, exhibit remarkable antioxidant and anti-inflammatory effects, modulate the flora structure and so on. It may be a promising candidate for addressing oral health problems. In this study, Liubao tea was meticulously extracted, purified and identified, followed by an investigation of its potential to modulate oral microecology by virtue of an acetic acid-induced oral disorder murine model. The results revealed that Liubao tea extract (LTE) application commendably reconstructed the oral mucosal barrier, promoted tissue regeneration and mitigated micro-inflammation. Furthermore, LTE treatment could also ameliorate the oral flora composition by decreasing the abundance of Proteobacteria and increasing the abundance of Firmicutes and Actinobacteria at the phylum level, as well as inhibiting pernicious bacteria such as Streptococcus and Delftia acidovorans. So, it could promote the generation of a beneficial microenvironment and regulate the immune process. Overall, LTE demonstrated remarkable potential in regulating the balance of oral microecology, suggesting that it may represent a promising therapeutic strategy for oral health concerns.
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Affiliation(s)
- Su Zhou
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Zhelu Bao
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
| | - Shicheng Ma
- Wuzhou Liubao Tea Research Association, Wuzhou, 543000, P. R. China
| | - Cansong Ou
- Wuzhou Tea Industry Development Service Center, Wuzhou, 543000, P. R. China
| | - Hao Hu
- College of Agriculture and Food Science, Zhejiang Agriculture & Forest University, Hangzhou 310058, P. R. China
| | - Yunyun Yang
- College of Standardization, China Jiliang University, Hangzhou 310018, P. R. China
| | - Xinyu Feng
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Yani Pan
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
| | - Shuying Gong
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
| | - Fangyuan Fan
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
| | - Ping Chen
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
| | - Qiang Chu
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
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24
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Amin M, Uchino K, Hajj-Ali RA. Central Nervous System Vasculitis: Primary Angiitis of the Central Nervous System and Central Nervous System Manifestations of Systemic Vasculitis. Rheum Dis Clin North Am 2023; 49:603-616. [PMID: 37331735 DOI: 10.1016/j.rdc.2023.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Central nervous system vasculitis (CNSV) is a group of disorders leading to inflammatory vasculopathy within the brain, spinal cord, and leptomeninges. CNSV is divided into primary angiitis of the central nervous system (PACNS) and secondary CNSV based on the underlying etiology. PACNS is a rare inflammatory disorder with poorly understood pathophysiology and heterogeneous and highly variable clinical features. The diagnosis depends on a combination of clinical and laboratory variables, multimodal imaging, and histopathological examination as well as exclusion of mimics. Several systemic vasculitides, infectious etiologies and connective tissue disorders have been shown to cause secondary CNSV and require prompt recognition.
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Affiliation(s)
- Moein Amin
- Mellen Center for Multiple Sclerosis Treatment and Research, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ken Uchino
- Cerebrovascular Center, Cleveland Clinic, Cleveland, OH, USA
| | - Rula A Hajj-Ali
- Cleveland Clinic Center for Vasculitis Care and Research, Cleveland Clinic, 9500 Euclid Avenue, A50, Cleveland, OH 44195, USA.
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25
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Mathias MB, Menezes FG, Fernandes GBP, Paes VR, Silva GS, Braga-Neto P, Barbosa AA, De Oliveira ACP, Baccin CE, Dutra LA. Neurobrucellosis Mimicking Primary CNS Vasculitis-Should We Perform CSF Metagenomics Before Brain Biopsy?: A Case Report. Neurol Clin Pract 2023; 13:e200167. [PMID: 37188245 PMCID: PMC10173873 DOI: 10.1212/cpj.0000000000200167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 03/22/2023] [Indexed: 05/17/2023]
Abstract
Objective To report a patient with neurobrucellosis mimicking primary CNS vasculitis (PCNSV) diagnosed by CSF metagenomic next-generation sequencing (mNGS). Methods A 32-year-old male patient with a prior stroke developed headache, dizziness, fever, and memory complaints in the past 30 days. Physical examination was unremarkable except for slight apathy. He was investigated with brain MRI, cerebral digital angiography, CSF analysis with mNGS, and brain biopsy. Results An examination of the brain MRI showed a left nucleocapsular gliosis compatible with prior stroke; MR angiogram showed circular enhancement of distal branches of the middle cerebral arteries. Digital angiogram revealed stenosis of intracranial carotid arteries and the left middle cerebral artery. The CSF disclosed 42 cells/mm3, 46 mg/dL of glucose, and 82 mg/dL of protein. Brain biopsy showed a chronic leptomeningeal inflammatory process, not fulfilling criteria for PCNSV. mNGS revealed the presence of Brucella sp. genetic material. He was treated with antibiotics with full remission of systemic and neurologic symptoms. Discussion Brucellosis is an endemic disease in developing countries and may mimic PCNSV. Our patient fulfilled the criteria for possible PCNSV; however, brain biopsy was inconsistent with PCNSV, and CSF mNGS disclosed neurobrucellosis. This case illustrates the importance of CSF mNGS in the differential diagnosis of CNS vasculitis.
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Affiliation(s)
- Marina Barrionuevo Mathias
- Hospital Israelita Albert Einstein (MBM, FGM, GBPF, VRP, GSS, AAB, ACPDO, CEB, LAD), São Paulo; Department of Neurology and Neurosurgery (GSS), Universidade Federal de São Paulo, UNIFESP; Neurology Section (PB-N), Department of Clinical Medicine, Faculty of Medicine; and Center of Health Sciences (PB-N), Universidade Estadual Do Ceará, Fortaleza, Brazil
| | - Fernando Gatti Menezes
- Hospital Israelita Albert Einstein (MBM, FGM, GBPF, VRP, GSS, AAB, ACPDO, CEB, LAD), São Paulo; Department of Neurology and Neurosurgery (GSS), Universidade Federal de São Paulo, UNIFESP; Neurology Section (PB-N), Department of Clinical Medicine, Faculty of Medicine; and Center of Health Sciences (PB-N), Universidade Estadual Do Ceará, Fortaleza, Brazil
| | - Gustavo Bruniera Peres Fernandes
- Hospital Israelita Albert Einstein (MBM, FGM, GBPF, VRP, GSS, AAB, ACPDO, CEB, LAD), São Paulo; Department of Neurology and Neurosurgery (GSS), Universidade Federal de São Paulo, UNIFESP; Neurology Section (PB-N), Department of Clinical Medicine, Faculty of Medicine; and Center of Health Sciences (PB-N), Universidade Estadual Do Ceará, Fortaleza, Brazil
| | - Vitor Ribeiro Paes
- Hospital Israelita Albert Einstein (MBM, FGM, GBPF, VRP, GSS, AAB, ACPDO, CEB, LAD), São Paulo; Department of Neurology and Neurosurgery (GSS), Universidade Federal de São Paulo, UNIFESP; Neurology Section (PB-N), Department of Clinical Medicine, Faculty of Medicine; and Center of Health Sciences (PB-N), Universidade Estadual Do Ceará, Fortaleza, Brazil
| | - Gisele Sampaio Silva
- Hospital Israelita Albert Einstein (MBM, FGM, GBPF, VRP, GSS, AAB, ACPDO, CEB, LAD), São Paulo; Department of Neurology and Neurosurgery (GSS), Universidade Federal de São Paulo, UNIFESP; Neurology Section (PB-N), Department of Clinical Medicine, Faculty of Medicine; and Center of Health Sciences (PB-N), Universidade Estadual Do Ceará, Fortaleza, Brazil
| | - Pedro Braga-Neto
- Hospital Israelita Albert Einstein (MBM, FGM, GBPF, VRP, GSS, AAB, ACPDO, CEB, LAD), São Paulo; Department of Neurology and Neurosurgery (GSS), Universidade Federal de São Paulo, UNIFESP; Neurology Section (PB-N), Department of Clinical Medicine, Faculty of Medicine; and Center of Health Sciences (PB-N), Universidade Estadual Do Ceará, Fortaleza, Brazil
| | - Alcino Alves Barbosa
- Hospital Israelita Albert Einstein (MBM, FGM, GBPF, VRP, GSS, AAB, ACPDO, CEB, LAD), São Paulo; Department of Neurology and Neurosurgery (GSS), Universidade Federal de São Paulo, UNIFESP; Neurology Section (PB-N), Department of Clinical Medicine, Faculty of Medicine; and Center of Health Sciences (PB-N), Universidade Estadual Do Ceará, Fortaleza, Brazil
| | - Augusto César Penalva De Oliveira
- Hospital Israelita Albert Einstein (MBM, FGM, GBPF, VRP, GSS, AAB, ACPDO, CEB, LAD), São Paulo; Department of Neurology and Neurosurgery (GSS), Universidade Federal de São Paulo, UNIFESP; Neurology Section (PB-N), Department of Clinical Medicine, Faculty of Medicine; and Center of Health Sciences (PB-N), Universidade Estadual Do Ceará, Fortaleza, Brazil
| | - Carlos Eduardo Baccin
- Hospital Israelita Albert Einstein (MBM, FGM, GBPF, VRP, GSS, AAB, ACPDO, CEB, LAD), São Paulo; Department of Neurology and Neurosurgery (GSS), Universidade Federal de São Paulo, UNIFESP; Neurology Section (PB-N), Department of Clinical Medicine, Faculty of Medicine; and Center of Health Sciences (PB-N), Universidade Estadual Do Ceará, Fortaleza, Brazil
| | - Lívia Almeida Dutra
- Hospital Israelita Albert Einstein (MBM, FGM, GBPF, VRP, GSS, AAB, ACPDO, CEB, LAD), São Paulo; Department of Neurology and Neurosurgery (GSS), Universidade Federal de São Paulo, UNIFESP; Neurology Section (PB-N), Department of Clinical Medicine, Faculty of Medicine; and Center of Health Sciences (PB-N), Universidade Estadual Do Ceará, Fortaleza, Brazil
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26
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Boruah AP, Kroopnick A, Thakkar R, Wapniarski AE, Kim C, Dugue R, Harrigan E, Lipkin WI, Mishra N, Thakur KT. Application of VirCapSeq-VERT and BacCapSeq In the Diagnosis of Presumed and Definitive Neuroinfectious Diseases. RESEARCH SQUARE 2023:rs.3.rs-2675665. [PMID: 37502953 PMCID: PMC10371130 DOI: 10.21203/rs.3.rs-2675665/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background Unbiased high-throughput sequencing (HTS) has enabled new insights into the diversity of agents implicated in central nervous system (CNS) infections. The addition of positive selection capture methods to HTS has enhanced the sensitivity while reducing sequencing costs and complexity of bioinformatic analysis. Here we report the use of virus capture based sequencing for vertebrate viruses (VirCapSeq-VERT) and bacterial capture sequencing (BacCapSeq) in investigating CNS infections. Design/Methods Thirty-four samples were categorized: (1) Patients with definitive CNS infection by routine testing; (2) Patients meeting clinically Brighton Criteria (BC) for meningoencephalitis (3) Patients with presumptive infectious etiology highest on the differential. RNA extracts from cerebrospinal fluid (CSF) were used for VirCapSeq-VERT and DNA extracts were used for BacCapSeq analysis. Results Among 8 samples from known CNS infections in group 1, VirCapSeq and BacCapSeq confirmed 3 expected diagnoses (42.8%), were negative in 2 (25%), yielded an alternative result in 1 (11.1%), and did not detect 2 expected negative pathogens. The confirmed cases identified HHV-6, HSV-2, and VZV while the negative samples included JCV and HSV-2. In groups 2 and 3,11/26 samples (42%) were positive for at least one pathogen, however 27% of the total samples (7/26) were positive for commensal organisms. No microbial nucleic acids were detected in negative control samples. Conclusions HTS showed limited promise for pathogen identification in presumed CNS infectious diseases in our small sample. Before conducting larger-scale prospective studies to assess clinical value of this novel technique, clinicians should understand benefits and limitations of using this modality.
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Affiliation(s)
| | | | | | | | | | | | | | - W Ian Lipkin
- Columbia University Mailman School of Public Health
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27
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Diray-Arce J, Fourati S, Doni Jayavelu N, Patel R, Maguire C, Chang AC, Dandekar R, Qi J, Lee BH, van Zalm P, Schroeder A, Chen E, Konstorum A, Brito A, Gygi JP, Kho A, Chen J, Pawar S, Gonzalez-Reiche AS, Hoch A, Milliren CE, Overton JA, Westendorf K, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen L, Grubaugh ND, van Bakel H, Wilson M, Rajan J, Steen H, Eckalbar W, Cotsapas C, Langelier CR, Levy O, Altman MC, Maecker H, Montgomery RR, Haddad EK, Sekaly RP, Esserman D, Ozonoff A, Becker PM, Augustine AD, Guan L, Peters B, Kleinstein SH. Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients. Cell Rep Med 2023; 4:101079. [PMID: 37327781 PMCID: PMC10203880 DOI: 10.1016/j.xcrm.2023.101079] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/31/2023] [Accepted: 05/16/2023] [Indexed: 06/18/2023]
Abstract
The IMPACC cohort, composed of >1,000 hospitalized COVID-19 participants, contains five illness trajectory groups (TGs) during acute infection (first 28 days), ranging from milder (TG1-3) to more severe disease course (TG4) and death (TG5). Here, we report deep immunophenotyping, profiling of >15,000 longitudinal blood and nasal samples from 540 participants of the IMPACC cohort, using 14 distinct assays. These unbiased analyses identify cellular and molecular signatures present within 72 h of hospital admission that distinguish moderate from severe and fatal COVID-19 disease. Importantly, cellular and molecular states also distinguish participants with more severe disease that recover or stabilize within 28 days from those that progress to fatal outcomes (TG4 vs. TG5). Furthermore, our longitudinal design reveals that these biologic states display distinct temporal patterns associated with clinical outcomes. Characterizing host immune responses in relation to heterogeneity in disease course may inform clinical prognosis and opportunities for intervention.
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Affiliation(s)
- Joann Diray-Arce
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Slim Fourati
- Emory School of Medicine, Atlanta, GA 30322, USA
| | | | - Ravi Patel
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Cole Maguire
- The University of Texas at Austin, Austin, TX 78712, USA
| | - Ana C Chang
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Ravi Dandekar
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Jingjing Qi
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brian H Lee
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrick van Zalm
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew Schroeder
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Ernie Chen
- Yale School of Medicine, New Haven, CT 06510, USA
| | | | | | | | - Alvin Kho
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jing Chen
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Annmarie Hoch
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Carly E Milliren
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA
| | | | | | - Charles B Cairns
- Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA
| | | | | | | | - Florian Krammer
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lindsey Rosen
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20814, USA
| | | | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Wilson
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Jayant Rajan
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Hanno Steen
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Walter Eckalbar
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Chris Cotsapas
- Yale School of Medicine, New Haven, CT 06510, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | | | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | - Matthew C Altman
- Benaroya Research Institute, University of Washington, Seattle, WA 98101, USA
| | - Holden Maecker
- Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | | | - Elias K Haddad
- Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA
| | | | | | - Al Ozonoff
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20814, USA
| | - Alison D Augustine
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20814, USA
| | - Leying Guan
- Yale School of Public Health, New Haven, CT 06510, USA
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
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28
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Fan Z, Mei Y, Xing J, Chen T, Hu D, Liu H, Li Y, Liu D, Liu Z, Liang Y. Loop-mediated isothermal amplification (LAMP)/Cas12a assay for detection of Ralstonia solanacearum in tomato. Front Bioeng Biotechnol 2023; 11:1188176. [PMID: 37284238 PMCID: PMC10239818 DOI: 10.3389/fbioe.2023.1188176] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/11/2023] [Indexed: 06/08/2023] Open
Abstract
Introduction: Bacterial wilt (BW) caused by the aerobic, Gram-negative pathogenic species Ralstonia solanacearum (RS) is a major disease impacting commercial agriculture worldwide. Asian phylotype I of RS is the cause of tomato bacterial wilt, which has caused severe economic losses in southern China for many years. An urgent priority in control of bacterial wilt is development of rapid, sensitive, effective methods for detection of RS. Methods: We describe here a novel RS detection assay based on combination of loop-mediated isothermal amplification (LAMP) and CRISPR/Cas12a. crRNA1, with high trans-cleavage activity targeting hrpB gene, was selected out of four candidate crRNAs. Two visual detection techniques, involving naked-eye observation of fluorescence and lateral flow strips, were tested and displayed high sensitivity and strong specificity. Results and Discussion: The LAMP/Cas12a assay accurately detected RS phylotype Ⅰ in 14 test strains, and showed low detection limit (2.0 × 100 copies). RS in tomato stem tissue and soil samples from two field sites with suspected BW infection was identified accurately, suggesting potential application of LAMP/Cas12a assay as point-of-care test (POCT). The overall detection process took less than 2 h and did not require professional lab equipment. Our findings, taken together, indicate that LAMP/Cas12a assay can be developed as an effective, inexpensive technique for field detection and monitoring of RS.
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Affiliation(s)
- Zhiyu Fan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuxia Mei
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiawei Xing
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tian Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Di Hu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hui Liu
- GNSS Research Center, Wuhan University, Wuhan, China
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Derui Liu
- Hubei Jiamachi Ecological Agriculture Co, Ltd, Yichang, China
- Hubei Yishizhuang Agricultural Technology Co, Ltd, Yichang, China
| | - Zufeng Liu
- Hubei Jiamachi Ecological Agriculture Co, Ltd, Yichang, China
- Hubei Yishizhuang Agricultural Technology Co, Ltd, Yichang, China
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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Liu Y, Wang H, Li Y, Yu Z. Clinical application of metagenomic next-generation sequencing in tuberculosis diagnosis. Front Cell Infect Microbiol 2023; 12:984753. [PMID: 37056463 PMCID: PMC10087082 DOI: 10.3389/fcimb.2022.984753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 09/02/2022] [Indexed: 03/30/2023] Open
Abstract
ObjectiveThe purpose of this study was to evaluate the clinical diagnostic value of metagenomic next-generation sequencing (mNGS) for tuberculosis (TB).MethodsThis retrospective study included 52 patients with suspected TB infection. mNGS, targeted PCR, acid-fast staining and, T-SPOT.TB assay were performed on the specimen. The positive rate of mNGS and traditional detection methods was statistically analyzed. Pathological tests were performed when necessary.ResultsIn total, 52 patients with suspected of TB in this study were included in the analysis, and 31 patients were finally diagnosed with TB. Among 52 patients, 14 (26.9%) cases were positive for acid-fast staining. The positive rate of T-SPOT.TB assay in 52 patients was 73.1% (38/52). Among 52 patients, 39 (75%) were detected positive for Mycobacterium tuberculosis (MTB) by mNGS. Regarding the detection rate of MTB, mNGS were as high as 75% (39/52), whereas acid-resistant staining was only 26.9% (14/52), which showed a statistically significant difference (p<0.05). The positive rates of T-SPOT.TB assay and mNGS were not statistically significant (p>0.05). Of the 52 suspected TB patients, 24 had targeted PCR, of which 18 were PCR positive. In 24 patients, the positive rate of PCR was 75%, and the positive rate of mNGS was 100%, with statistical difference between them (p<0.05).ConclusionsThe detection rate of MTB by mNGS was higher than that by conventional acid-fast staining and PCR, but not statistically significant compared with T-SPOT.TB assay. As an adjunctive diagnostic technology, mNGS can be combined with traditional detection methods to play a guiding role in the diagnosis and treatment of TB.
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Affiliation(s)
- Ying Liu
- Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huifen Wang
- Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yaoguang Li
- Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zujiang Yu
- Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Zujiang Yu,
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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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Galardi MM, Sowa GM, Crockett CD, Rudock R, Smith AE, Shwe EE, San T, Linn K, Aye AMM, Ramachandran PS, Zia M, Wapniarski AE, Hawes IA, Hlaing CS, Kyu EH, Thair C, Mar YY, Nway N, Storch GA, Wylie KM, Wylie TN, Dalmau J, Wilson MR, Mar SS. Pathogen and Antibody Identification in Children with Encephalitis in Myanmar. Ann Neurol 2023; 93:615-628. [PMID: 36443898 DOI: 10.1002/ana.26560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/22/2022] [Accepted: 11/20/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Prospective studies of encephalitis are rare in regions where encephalitis is prevalent, such as low middle-income Southeast Asian countries. We compared the diagnostic yield of local and advanced tests in cases of pediatric encephalitis in Myanmar. METHODS Children with suspected subacute or acute encephalitis at Yangon Children's Hospital, Yangon, Myanmar, were prospectively recruited from 2016-2018. Cohort 1 (n = 65) had locally available diagnostic testing, whereas cohort 2 (n = 38) had advanced tests for autoantibodies (ie, cell-based assays, tissue immunostaining, studies with cultured neurons) and infections (ie, BioFire FilmArray multiplex Meningitis/Encephalitis multiplex PCR panel, metagenomic sequencing, and pan-viral serologic testing [VirScan] of cerebrospinal fluid). RESULTS A total of 20 cases (13 in cohort 1 and 7 in cohort 2) were found to have illnesses other than encephalitis. Of the 52 remaining cases in cohort 1, 43 (83%) had presumed infectious encephalitis, of which 2 cases (4%) had a confirmed infectious etiology. Nine cases (17%) had presumed autoimmune encephalitis. Of the 31 cases in cohort 2, 23 (74%) had presumed infectious encephalitis, of which one (3%) had confirmed infectious etiology using local tests only, whereas 8 (26%) had presumed autoimmune encephalitis. Advanced tests confirmed an additional 10 (32%) infections, 4 (13%) possible infections, and 5 (16%) cases of N-methyl-D-aspartate receptor antibody encephalitis. INTERPRETATION Pediatric encephalitis is prevalent in Myanmar, and advanced technologies increase identification of treatable infectious and autoimmune causes. Developing affordable advanced tests to use globally represents a high clinical and research priority to improve the diagnosis and prognosis of encephalitis. ANN NEUROL 2023;93:615-628.
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Affiliation(s)
- Maria M Galardi
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Gavin M Sowa
- Department of Medicine, McGaw Medical Center of Northwestern University, Chicago, IL
| | - Cameron D Crockett
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Robert Rudock
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Alyssa E Smith
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Ei E Shwe
- Department of Pathology, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Thidar San
- Department of Pathology, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Kyaw Linn
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Aye Mya M Aye
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Prashanth S Ramachandran
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Maham Zia
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Anne E Wapniarski
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Isobel A Hawes
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Chaw S Hlaing
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Ei H Kyu
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Cho Thair
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Yi Y Mar
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Nway Nway
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Gregory A Storch
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | - Kristine M Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | - Todd N Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | - Josep Dalmau
- Neuroimmunology Program, Institut d'Investigacions Biomèdiques August Pi i Sunyer Hospital Clínic, University of Barcelona, Barcelona, Spain.,Department of Neurology, University of Pennsylvania, Philadelphia, PA.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Michael R Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Soe S Mar
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
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Ibañez-Lligoña M, Colomer-Castell S, González-Sánchez A, Gregori J, Campos C, Garcia-Cehic D, Andrés C, Piñana M, Pumarola T, Rodríguez-Frias F, Antón A, Quer J. Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses. Viruses 2023; 15:v15020587. [PMID: 36851800 PMCID: PMC9965957 DOI: 10.3390/v15020587] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Epidemics and pandemics have occurred since the beginning of time, resulting in millions of deaths. Many such disease outbreaks are caused by viruses. Some viruses, particularly RNA viruses, are characterized by their high genetic variability, and this can affect certain phenotypic features: tropism, antigenicity, and susceptibility to antiviral drugs, vaccines, and the host immune response. The best strategy to face the emergence of new infectious genomes is prompt identification. However, currently available diagnostic tests are often limited for detecting new agents. High-throughput next-generation sequencing technologies based on metagenomics may be the solution to detect new infectious genomes and properly diagnose certain diseases. Metagenomic techniques enable the identification and characterization of disease-causing agents, but they require a large amount of genetic material and involve complex bioinformatic analyses. A wide variety of analytical tools can be used in the quality control and pre-processing of metagenomic data, filtering of untargeted sequences, assembly and quality control of reads, and taxonomic profiling of sequences to identify new viruses and ones that have been sequenced and uploaded to dedicated databases. Although there have been huge advances in the field of metagenomics, there is still a lack of consensus about which of the various approaches should be used for specific data analysis tasks. In this review, we provide some background on the study of viral infections, describe the contribution of metagenomics to this field, and place special emphasis on the bioinformatic tools (with their capabilities and limitations) available for use in metagenomic analyses of viral pathogens.
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Affiliation(s)
- Marta Ibañez-Lligoña
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Sergi Colomer-Castell
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Alejandra González-Sánchez
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
| | - Cristina Andrés
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Maria Piñana
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Tomàs Pumarola
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Francisco Rodríguez-Frias
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Department of Basic Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, 08195 Barcelona, Spain
| | - Andrés Antón
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
- Correspondence:
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Wang L, Li S, Qin J, Tang T, Hong J, Tung TH, Xu C, Yu S, Qian J. Clinical Diagnosis Application of Metagenomic Next-Generation Sequencing of Plasma in Suspected Sepsis. Infect Drug Resist 2023; 16:891-901. [PMID: 36820080 PMCID: PMC9938705 DOI: 10.2147/idr.s395700] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
Purpose We analyzed the clinical concordance of mNGS test results from blood samples and improved the clinical efficiency of mNGS in the diagnosis of suspected sepsis pathogens. Patients and Methods In this study, 99 samples of suspected blood flow infection were included for plasma mNGS, and the correlation between mNGS results and blood culture results, serum inflammatory indices, clinical symptoms and antibiotic treatment was analyzed, as well as the comparison with the detection rate of BALF pathogens, as well as the classification of different pathogens in the mNGS results were analyzed. Results The mNGS pathogen detection rate was higher than that of traditional blood culture (83.02% vs 35.82%). The rate of the mNGS results being consistent with the clinical diagnosis was also higher than that of traditional blood culture (58.49% vs 20.75%). This study shows that bacteria and fungi are the main pathogens in sepsis, and viral sepsis is very rare. In this study, 32% of sepsis patients were secondary to pneumonia. Compared with the pathogen detection rate using alveolar lavage fluid, the detection rate from plasma mNGS was 62.5%. Samples were also easy to sample, noninvasive, and more convenient for clinical application. Conclusion This study shows that compared with blood culture, the detection rate of mNGS pathogen that meets the diagnosis of sepsis is higher. We need a combination of multiple indicators to monitor the early diagnosis and treatment of sepsis.
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Affiliation(s)
- Lisha Wang
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Shixiao Li
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Jiajia Qin
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Tianbin Tang
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Jiawen Hong
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Tao-Hsin Tung
- Evidence-Based Medicine Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People’s Republic of China
| | - Chunyan Xu
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Sufei Yu
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China,Correspondence: Sufei Yu; Jiao Qian, Email ;
| | - Jiao Qian
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
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Tamzali Y, Scemla A, Bonduelle T, Garandeau C, Gilbert M, Randhawa S, De Nattes T, Hachad H, Pourcher V, Taupin P, Kaminski H, Hazzan M, Moal V, Matignon M, Fihman V, Levi C, Le Quintrec M, Chemouny JM, Rondeau E, Bertrand D, Thervet E, Tezenas Du Montcel S, Savoye E, Barrou B, Kamar N, Tourret J. Specificities of Meningitis and Meningo-Encephalitis After Kidney Transplantation: A French Retrospective Cohort Study. Transpl Int 2023; 36:10765. [PMID: 36744053 PMCID: PMC9889366 DOI: 10.3389/ti.2023.10765] [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: 07/13/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023]
Abstract
Kidney transplant recipients develop atypical infections in their epidemiology, presentation and outcome. Among these, meningitis and meningoencephalitis require urgent and adapted anti-infectious therapy, but published data is scarce in KTRs. The aim of this study was to describe their epidemiology, presentation and outcome, in order to improve their diagnostic and management. We performed a retrospective, multicentric cohort study in 15 French hospitals that included all 199 cases of M/ME in KTRs between 2007 and 2018 (0.9 case per 1,000 KTRs annually). Epidemiology was different from that in the general population: 20% were due to Cryptococcus neoformans, 13.5% to varicella-zoster virus, 5.5% to Mycobacterium tuberculosis, and 4.5% to Enterobacteria (half of which produced extended spectrum beta-lactamases), and 5% were Post Transplant Lymphoproliferative Disorders. Microorganisms causing M/ME in the general population were infrequent (2%, for Streptococcus pneumoniae) or absent (Neisseria meningitidis). M/ME caused by Enterobacteria, Staphylococci or filamentous fungi were associated with high and early mortality (50%-70% at 1 year). Graft survival was not associated with the etiology of M/ME, nor was impacted by immunosuppression reduction. Based on these results, we suggest international studies to adapt guidelines in order to improve the diagnosis and the probabilistic treatment of M/ME in SOTRs.
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Affiliation(s)
- Y. Tamzali
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié-Salpêtrière Hospital, Medical and Surgical Department of Kidney Transplantation, Paris, France,Sorbonne Université, Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié-Salpêtrière Hospital, Department of Infectious and Tropical Diseases, Paris, France,*Correspondence: Y. Tamzali,
| | - A. Scemla
- Université Paris-Descartes, Assistance Publique-Hôpitaux de Paris (AP-HP), Department of Nephrology and Kidney Transplantation, Hôpital Necker, Paris, France
| | - T. Bonduelle
- Neurology Department, Epilepsy Unit, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - C. Garandeau
- Nephrology Department, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - M. Gilbert
- Nephrology and Transplantation Department, Centre Hospitalier Universitaire de Lille, Lille, France
| | - S. Randhawa
- Aix-Marseille Université, Hôpitaux Universitaires de Marseille, Hôpital Conception, Center of Nephrology and Kidney Transplantation, Marseille, France
| | - T. De Nattes
- Department of Nephrology Dialysis and Kidney Transplantation, Centre Hospitalier Universitaire de Rouen, Rouen, France
| | - H. Hachad
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié-Salpêtrière Hospital, Medical and Surgical Department of Kidney Transplantation, Paris, France
| | - V. Pourcher
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié-Salpêtrière Hospital, Department of Infectious and Tropical Diseases, Paris, France
| | - P. Taupin
- University Paris-Descartes, Assistance Publique-Hôpitaux de Paris (AP-HP), Department of Biostatistics, Necker Hospital, Paris, France
| | - H. Kaminski
- Department of Nephrology, Transplantation, Dialysis and Apheresis, CHU Bordeaux, Bordeaux, France
| | - M. Hazzan
- Nephrology and Transplantation Department, Centre Hospitalier Universitaire de Lille, Lille, France
| | - V. Moal
- Aix-Marseille Université, Hôpitaux Universitaires de Marseille, Hôpital Conception, Center of Nephrology and Kidney Transplantation, Marseille, France
| | - M. Matignon
- Université Paris Est Créteil, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France,Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Henri Mondor, Service de Néphrologie et Transplantation, Fédération Hospitalo-Universitaire, Innovative Therapy for Immune Disorders, Créteil, France
| | - V. Fihman
- Bacteriology and Infection Control Unit, Department of Prevention, Diagnosis, and Treatment of Infections, Henri-Mondor University Hospital, Assistance Publique des Hôpitaux de Paris (AP-HP), Créteil, France,EA 7380 Dynamyc, EnvA, Paris-Est University (UPEC), Créteil, France
| | - C. Levi
- Department of Nephrology Immunology and Kidney Transplantation, Centre Hospitalier Univeristaire Edouard Herriot, Lyon, France
| | - M. Le Quintrec
- Department of Nephrology Dialysis and Kidney Transplantation, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - J. M. Chemouny
- Université de Rennes, CHU Rennes, INSERM, EHESP, IRSET—UMR_S 1085, CIC‐P 1414, Rennes, France
| | - E. Rondeau
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris (AP-HP), Department of Nephrology, SINRA, Hôpital Tenon, GHEP, Paris, France
| | - D. Bertrand
- Department of Nephrology Dialysis and Kidney Transplantation, Centre Hospitalier Universitaire de Rouen, Rouen, France
| | - E. Thervet
- Université Paris-Descartes, Assistance Publique-Hôpitaux de Paris (AP-HP), Department of Nephrology, Hôpital Europeen Georges Pompidou, Paris, France
| | - S. Tezenas Du Montcel
- Sorbonne Université, INSERM, Pierre Louis Epidemiology and Public Health Institute, Assistance Publique-Hopitaux de Paris (AP-HP), Medical Information Department, Pitié Salpêtrière-Charles Foix University Hospital, Paris, France
| | - E. Savoye
- Agence de la Biomédecine, Saint Denis, France
| | - B. Barrou
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié-Salpêtrière Hospital, Medical and Surgical Department of Kidney Transplantation, INSERM, UMR 1082, Paris, France
| | - N. Kamar
- Department of Nephrology and Organ, INFINITY-INSERM U1291-CNRS U5051, Université Paul Sabatier, Toulouse, France
| | - J. Tourret
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié-Salpêtrière Hospital, Medical and Surgical Department of Kidney Transplantation, INSERM, UMR 1138, Paris, France
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Chang Y, Jiang K, Zhang L, Yang F, Huang J. Application of next-generation sequencing technology in the detection of pathogenic bacteria of the periprosthetic joint infection after arthroplasty. Int Wound J 2023. [PMID: 36647902 DOI: 10.1111/iwj.14087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
To investigate the application value of next-generation sequencing (NGS) technology in the detection of pathogenic bacteria in the periprosthetic joint infection after arthroplasty. Twenty-two cases of patients with joint infection after arthroplasty in our hospital from March 2020 to March 2021 were selected, with 11 cases of knee and 11 cases of hip, including 8 cases of male and 14 cases of female, and an average age of 63.55 ± 13.11 years old (range from 28 to 85). Microbiological culture results of synovial fluid and periprosthetic joint tissue and NGS results of periprosthetic joint tissue were collected. The detection rate of NGS and microbiological culture were calculated and statistically analysed by paired χ2 test. Among the 22 patients with joint infection after arthroplasty, the positive rate of NGS was 90.91% (20/22), whereas the positive rate of bacterial culture was 50.00% (11/22). Paired chi-square test showed a statistically significant difference in the detection rate between the two groups (P = .0029). In the detection of pathogenic microorganism, NGS detected 12 kinds of bacteria, Staphylococcus aureus in 3 patients, Staphylococcus epidermidis in 5 cases, Streptococcus 1 case, Streptococcus dysgalactiae 1 case, Xanthomonas campestris 3 cases, Escherichia coli 2 cases, Bacillus cereus 2 cases, Klebsiella pneumoniae 1 case, Finegoldia magna 1 case, Corynebacterium klopensteriella in 1 case, Brucella 1 case, and Aspergillus flavus 1 case. Bacterial culture detected 6 kinds of bacteria, included 5 cases of Staphylococcus epidermis (including 3 cases of Methicillin-resistant coagulase-negative Staphylococcus, (MRSCoN)), 2 cases of Staphylococcus aureus (both Methicillin-resistant Staphylococcus aureus, (MRSA)), 1 case of Klebsiella pneumoniae, 1 case of Staphylococcus hominis (MRSCoN), 1 case of G+ bacillus, and 1 case of Brucella. Compared with bacterial culture, NGS technology has some advantages in the detection efficiency, detection rate, and comprehensiveness, which might be greater diagnostic value in the joint fluid of infection after arthroplasty.
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Affiliation(s)
- Yu Chang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Kai Jiang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Lixin Zhang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Fang Yang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Jing Huang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
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Molecular Diagnosis of Endemic Mycoses. J Fungi (Basel) 2022; 9:jof9010059. [PMID: 36675880 PMCID: PMC9866865 DOI: 10.3390/jof9010059] [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: 11/29/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 01/03/2023] Open
Abstract
Diagnosis of endemic mycoses is still challenging. The moderated availability of reliable diagnostic methods, the lack of clinical suspicion out of endemic areas and the limitations of conventional techniques result in a late diagnosis that, in turn, delays the implementation of the correct antifungal therapy. In recent years, molecular methods have emerged as promising tools for the rapid diagnosis of endemic mycoses. However, the absence of a consensus among laboratories and the reduced availability of commercial tests compromises the diagnostic effectiveness of these methods. In this review, we summarize the advantages and limitations of molecular methods for the diagnosis of endemic mycoses.
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Hu X, Haas JG, Lathe R. The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data. BMC Microbiol 2022; 22:317. [PMID: 36550399 PMCID: PMC9773549 DOI: 10.1186/s12866-022-02671-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 10/11/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Microbiome analysis generally requires PCR-based or metagenomic shotgun sequencing, sophisticated programs, and large volumes of data. Alternative approaches based on widely available RNA-seq data are constrained because of sequence similarities between the transcriptomes of microbes/viruses and those of the host, compounded by the extreme abundance of host sequences in such libraries. Current approaches are also limited to specific microbial groups. There is a need for alternative methods of microbiome analysis that encompass the entire tree of life. RESULTS We report a method to specifically retrieve non-human sequences in human tissue RNA-seq data. For cellular microbes we used a bioinformatic 'net', based on filtered 64-mer sequences designed from small subunit ribosomal RNA (rRNA) sequences across the Tree of Life (the 'electronic tree of life', eToL), to comprehensively (98%) entrap all non-human rRNA sequences present in the target tissue. Using brain as a model, retrieval of matching reads, re-exclusion of human-related sequences, followed by contig building and species identification, is followed by confirmation of the abundance and identity of the corresponding species groups. We provide methods to automate this analysis. The method reduces the computation time versus metagenomics by a factor of >1000. A variant approach is necessary for viruses. Again, because of significant matches between viral and human sequences, a 'stripping' approach is essential. Contamination during workup is a potential problem, and we discuss strategies to circumvent this issue. To illustrate the versatility of the method we report the use of the eToL methodology to unambiguously identify exogenous microbial and viral sequences in human tissue RNA-seq data across the entire tree of life including Archaea, Bacteria, Chloroplastida, basal Eukaryota, Fungi, and Holozoa/Metazoa, and discuss the technical and bioinformatic challenges involved. CONCLUSIONS This generic methodology is likely to find wide application in microbiome analysis including diagnostics.
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Affiliation(s)
- Xinyue Hu
- Program in Bioinformatics, School of Biological Sciences, King's Buildings, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Jürgen G Haas
- Division of Infection Medicine, University of Edinburgh, Little France, Edinburgh, EH16 4SB, UK
| | - Richard Lathe
- Division of Infection Medicine, University of Edinburgh, Little France, Edinburgh, EH16 4SB, UK.
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Price C, Wilson I, Catchpoole E. Candida dubliniensis chronic meningitis in an immunocompetent patient: Case report and literature review. IDCases 2022; 31:e01665. [PMID: 36589766 PMCID: PMC9801098 DOI: 10.1016/j.idcr.2022.e01665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Chronic meningitis due to Candida species is a rare presentation generally associated with immunocompromise. We present a case of chronic meningitis due to Candida dubliniensis in an immunocompetent systemically well man who presented with 32 months of headache and visual changes. This is the fourth reported case in an immunocompetent patient. Injecting drug use was identified as a risk factor in all cases which presented similarly, with prolonged headache and papilloedema. A significant delay to diagnosis is common to all the reported cases. Candidal chronic meningitis in immunocompetent patients may be underdiagnosed due to lack recognition of risk factors, timely cerebrospinal fluid sampling and appropriate culture.
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Affiliation(s)
- Cody Price
- Correspondence to: P.O. Box 902, Cairns North, Queensland 4870, Australia.
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Wang H, Yan S, Liu Y, Li Y, Cui G, Ma X. Metagenomic next-generation sequencing assists in the diagnosis of Cryptococcus pneumonia: Case series and literature review. Front Public Health 2022; 10:971511. [PMID: 36408040 PMCID: PMC9672815 DOI: 10.3389/fpubh.2022.971511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background Pulmonary cryptococcosis (PC) was once thought to occur only in patients with immune deficiencies, such as tested positive for the Human Immunodeficiency Virus (HIV). However, in recent years, it has been discovered that more than half of the patients with PC in our nation are individuals with normal immune function. As more and more PC cases are recorded, our diagnosis and treatment approaches, as well as our understanding of PC, are gradually improving. In reality, most PC patients still have a high incidence of misdiagnosis on their initial visit. It is primarily linked to the diverse clinical manifestations, atypical imaging findings, and inaccurate diagnostic approaches. Methods The research was conducted from 2019 to 2020. We performed traditional microbiological testing and mNGS on sample from patients with fever of Pulmonary nodules or lung infections. Furthermore, we collected patients' baseline information, clinical features, laboratory and imaging examination results, diagnosis, treatment and outcome. In the end, we confirmed three cases of PC using biopsy and mNGS. Conclusion Our data demonstrates that mNGS can be utilized as an auxiliary method for PC diagnosis. Early mNGS aids in the identification of pathogens, enabling early diagnosis and treatment, as well as a reduction in the rate of misdiagnosis and illness progression.
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Affiliation(s)
- Huifen Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Su Yan
- Health Management Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yaoguang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guangying Cui
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,*Correspondence: Guangying Cui
| | - Xiaoxu Ma
- Department of Respiratory Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Xiaoxu Ma
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Background Filtering of Clinical Metagenomic Sequencing with a Library Concentration-Normalized Model. Microbiol Spectr 2022; 10:e0177922. [PMID: 36135379 PMCID: PMC9603461 DOI: 10.1128/spectrum.01779-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Metagenomic next-generation sequencing (mNGS) can accurately detect pathogens in clinical samples. However, wet-lab contamination constrains mNGS analysis and may result in erroneous interpretation of results. Many existing methods rely on large-scale observational microbiome studies and may not be applicable to clinical mNGS tests. By generation of a pretrained profile of common laboratory contaminants, we developed an mNGS noise-filtering model based on the inverse linear relationship between microbial sequencing reads and sample library concentration, named the background elimination and correction by library concentration-normalized (BECLEAN) model. Its efficacy was evaluated with bacteria- and yeast-spiked samples and 28 cerebrospinal fluid (CSF) specimens. The diagnostic accuracy, precision, sensitivity, and specificity of BECLEAN with reference to conventional methods and diagnosis were 92.9%, 86.7%, 100%, and 86.7%, respectively. BECLEAN led to a dramatic reduction of background noise without affecting the true-positive rate and thus can provide a time-saving and convenient tool in various clinical settings. IMPORTANCE Most of the existing methods to remove wet-lab contamination rely on large-scale observational microbiome studies and may not be applicable to clinical mNGS testing in individual cases. In clinical settings, only a handful of samples might be sequenced in a run. The lab-specific microbiome can complicate existing statistical approaches for removing contamination from small-scale clinical metagenomic sequencing data sets; thus, use of a preliminary lab-specific training set is necessary. Our study provides a rapid and accurate background-filtering tool for clinical metagenomic sequencing by generation of a pretrained profile of common laboratory contaminants. Notably, our work demonstrates that the inverse linear relationship between microbial sequencing reads and library concentration can serve to identify true contaminants and evaluate the relative abundance of a taxon in samples by comparing the observed microbial reads to the model-predicted value. Our findings extend the previously published research and demonstrate confirmatory results in clinical settings.
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Lu H, Ma L, Zhang H, Feng L, Yu Y, Zhao Y, Li L, Zhou Y, Song L, Li W, Zhao J, Liu L. The Comparison of Metagenomic Next-Generation Sequencing with Conventional Microbiological Tests for Identification of Pathogens and Antibiotic Resistance Genes in Infectious Diseases. Infect Drug Resist 2022; 15:6115-6128. [PMID: 36277249 PMCID: PMC9586124 DOI: 10.2147/idr.s370964] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) has been widely studied, due to its ability of detecting all the microbial genetic information unbiasedly in a sample at one time and not relying on traditional culture. However, the application of mNGS in the diagnosis of clinical pathogens remains challenging. Methods From December 2019 to March 2021, 134 specimens including Broncho alveolar lavage fluid (BAFL), blood, sputum, cerebrospinal fluid (CSF), bile, pleural fluid, pus, were continuously collected in The First Hospital of Qinhuangdao, and their retrospective diagnoses were classified into infectious disease (128, 95.5%) and noninfectious disease (6, 4.5%). The pathogen-detection performance of mNGS was compared with conventional microbiological tests (CMT) and culture method. In addition, the antibiotic resistance genes (ARGs) and evolutionary relationship of common drug-resistant A. baumannii were also analyzed. Results Compared with CMT and culture methods, mNGS showed higher sensitivity in pathogen detection (74.2% vs 57.8%; P < 0.001 and 66.3% vs 31.7%; P < 0.001, respectively). Importantly, for cases that mNGS-positive only, 18 (35%) cases result in diagnosis modification, and 7 (23%) cases confirmed the clinical diagnosis. In 17 cases that A. baumannii were both detected in mNGS and culture, ade genes were the most frequently detected ARGs (from 13 cases), followed by sul2 and APH(3”)-Ib (both from 12 cases). High consistency was observed among these ARGs and the related phenotype (100% for ade genes, 91.6% for sul2 and APH(3”)-Ib). A. baumannii strains were classified into three groups, and most were well-clustered. It suggested those strains may be the epidemic strains. Conclusion In our study, mNGS had a higher sensitivity than CMT and culture method. And the result of ARGs frequency and cluster analysis of A. baumannii was of great significance to the anti-infective therapy.
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Affiliation(s)
- Hongzhi Lu
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Li Ma
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Hong Zhang
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Li Feng
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Ying Yu
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Yihan Zhao
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Li Li
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Yujiao Zhou
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Li Song
- Shanghai Biotecan Pharmaceuticals Co., Ltd, Shanghai, 201204, People’s Republic of China,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, People’s Republic of China
| | - Wushuang Li
- Shanghai Biotecan Pharmaceuticals Co., Ltd, Shanghai, 201204, People’s Republic of China,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, People’s Republic of China
| | - Jiangman Zhao
- Shanghai Biotecan Pharmaceuticals Co., Ltd, Shanghai, 201204, People’s Republic of China,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, People’s Republic of China
| | - Lanxiang Liu
- Medical Imaging Center, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China,Correspondence: Lanxiang Liu, Department of Medical Imaging Center, First Hospital of Qinhuangdao, 258 Wenhua Road, Qinhuangdao, 066000, Hebei, People’s Republic of China, Email
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Xu L, Zhou Z, Wang Y, Song C, Tan H. Improved accuracy of etiological diagnosis of spinal infection by metagenomic next-generation sequencing. Front Cell Infect Microbiol 2022; 12:929701. [PMID: 36275025 PMCID: PMC9585211 DOI: 10.3389/fcimb.2022.929701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/15/2022] [Indexed: 11/24/2022] Open
Abstract
Currently, the use of metagenomic next-generation sequencing (mNGS), a new approach to identify organisms in infectious diseases, is rarely reported in the diagnosis of spinal infection. This study aimed to evaluate the potential value of mNGS in etiological diagnosis of spinal infection. In this retrospective study, the clinical data of patients with suspected spinal infection were collected by electronic medical records. Specimens obtained from each patient were tested via mNGS assay and other conventional microbiological tests (CMTs). The sensitivity and specificity of mNGS and CMTs were calculated using the final clinical diagnosis as the golden standard. In total, 108 patients were eligible for the study, with the mean length of stay of 42.8 days. Regarding the overall identification of pathogens, mNGS exhibited a better performance than CMTs, and several nontuberculous mycobacteria, fungi, and bacteria were newly discovered. In the diagnosis of spinal infection, the sensitivity, specificity, and area under the curve of mNGS were 90.72%, 81.82%, and 0.89, respectively, which were all higher than 52.17%, 56.25%, and 0.72 of the CMTs. At hospital discharge, the C-reactive protein, erythrocyte sedimentation rate, and white blood cell count of patients significantly decreased compared with hospitalization (all p < 0.05), and 88.89% showed good outcomes. These findings may suggest that mNGS has a better diagnostic accuracy in pathogenic identification of patients with suspected spinal infection, and patients treated with NGS-guided antimicrobial therapy mostly seem to have good outcomes.
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Affiliation(s)
- Liang Xu
- Department of Spinal Infection, Shandong Public Health Clinical Center, Jinan, China
| | - Zheng Zhou
- Katharine Hsu International Research Institute of Infectious Disease, Shandong Public Health Clinical Center, Jinan, China
| | - Yao Wang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
- Department of Medicine, Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Chao Song
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
- Department of Medicine, Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Hongdong Tan
- Department of Spinal Infection, Shandong Public Health Clinical Center, Jinan, China
- *Correspondence: Hongdong Tan,
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Palackdkharry CS, Wottrich S, Dienes E, Bydon M, Steinmetz MP, Traynelis VC. The leptomeninges as a critical organ for normal CNS development and function: First patient and public involved systematic review of arachnoiditis (chronic meningitis). PLoS One 2022; 17:e0274634. [PMID: 36178925 PMCID: PMC9524710 DOI: 10.1371/journal.pone.0274634] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND & IMPORTANCE This patient and public-involved systematic review originally focused on arachnoiditis, a supposedly rare "iatrogenic chronic meningitis" causing permanent neurologic damage and intractable pain. We sought to prove disease existence, causation, symptoms, and inform future directions. After 63 terms for the same pathology were found, the study was renamed Diseases of the Leptomeninges (DLMs). We present results that nullify traditional clinical thinking about DLMs, answer study questions, and create a unified path forward. METHODS The prospective PRISMA protocol is published at Arcsology.org. We used four platforms, 10 sources, extraction software, and critical review with ≥2 researchers at each phase. All human sources to 12/6/2020 were eligible for qualitative synthesis utilizing R. Weekly updates since cutoff strengthen conclusions. RESULTS Included were 887/14286 sources containing 12721 DLMs patients. Pathology involves the subarachnoid space (SAS) and pia. DLMs occurred in all countries as a contributor to the top 10 causes of disability-adjusted life years lost, with communicable diseases (CDs) predominating. In the USA, the ratio of CDs to iatrogenic causes is 2.4:1, contradicting arachnoiditis literature. Spinal fusion surgery comprised 54.7% of the iatrogenic category, with rhBMP-2 resulting in 2.4x more DLMs than no use (p<0.0001). Spinal injections and neuraxial anesthesia procedures cause 1.1%, and 0.2% permanent DLMs, respectively. Syringomyelia, hydrocephalus, and arachnoid cysts are complications caused by blocked CSF flow. CNS neuron death occurs due to insufficient arterial supply from compromised vasculature and nerves traversing the SAS. Contrast MRI is currently the diagnostic test of choice. Lack of radiologist recognition is problematic. DISCUSSION & CONCLUSION DLMs are common. The LM clinically functions as an organ with critical CNS-sustaining roles involving the SAS-pia structure, enclosed cells, lymphatics, and biologic pathways. Cases involve all specialties. Causes are numerous, symptoms predictable, and outcomes dependent on time to treatment and extent of residual SAS damage. An international disease classification and possible treatment trials are proposed.
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Affiliation(s)
| | - Stephanie Wottrich
- Case Western Reserve School of Medicine, Cleveland, Ohio, United States of America
| | - Erin Dienes
- Arcsology®, Mead, Colorado, United States of America
| | - Mohamad Bydon
- Department of Neurologic Surgery, Orthopedic Surgery, and Health Services Research, Mayo Clinic School of Medicine, Rochester, Minnesota, United States of America
| | - Michael P. Steinmetz
- Department of Neurological Surgery, Cleveland Clinic Lerner College of Medicine Neurologic Institute, Cleveland, Ohio, United States of America
| | - Vincent C. Traynelis
- Department of Neurosurgery, Rush University School of Medicine, Chicago, Illinois, United States of America
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Zhang B, Gui R, Wang Q, Jiao X, Li Z, Wang J, Han L, Zhou L, Wang H, Wang X, Fan X, Lyu X, Song Y, Zhou J. Comparing the application of mNGS after combined pneumonia in hematologic patients receiving hematopoietic stem cell transplantation and chemotherapy: A retrospective analysis. Front Cell Infect Microbiol 2022; 12:969126. [PMID: 36211959 PMCID: PMC9532739 DOI: 10.3389/fcimb.2022.969126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Rapid and accurate pathogen identification is essential for timely and effective treatment of pneumonia. Here, we describe the use of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage (BALF) fluid to identify pathogens in patients with hematologic comorbid respiratory symptoms in a retrospective study with 84 patients. In the transplantation group, 8 cases (19.5%) and 47 cases (97.9%) were positive for BALF by conventional method detection and mNGS detection, respectively, and 6 cases (14.0%) and 41 cases (91.1%) in chemotherapy group, respectively. The detection rate of mNGS in both groups was significantly higher than that of conventional detection methods (all P<0.05). Pseudomonas aeruginosa and Streptococcus pneumoniae were the most common bacterial infections in the transplantation and chemotherapy groups, respectively. Aspergillus was the most common fungal infection in both groups. Human betaherpesvirus 5 (HHV-5), torque teno virus and human betaherpesvirus 7 (HHV-7) were the most common pathogen species in both groups. The most common type of infection in patients in the transplantation and chemotherapy groups was the mixed infection of bacteria-virus. Most patients in the transplantation group had mixed infections based on multiple viruses, with 42 cases of viral infections in the transplantation group and 30 cases of viral infections in the chemotherapy group, which were significantly higher in the transplantation group than in the chemotherapy group (χ2 = 5.766, P=0.016). and the mixed infection of virus-virus in the transplantation group was significantly higher than that in the chemotherapy group (27.1% vs 4.4%, P=0.003). The proportion of death due to pulmonary infection was significantly higher in the transplantation group than in the chemotherapy group (76.9% vs 16.7%, χ2 = 9.077, P=0.003). This study demonstrated the value of mNGS of BALF in improving the diagnosis and prognosis of hematologic comorbid pneumonia, helping patients to obtain timely and effective treatment, and giving guidance on the overall treatment plan for patients, with particular benefit for patients with hematologic chemotherapy comorbid pneumonia.
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Affiliation(s)
- Binglei Zhang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- School of Basic Medical Sciences, Academy of Medical Sciences, Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ruirui Gui
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Qian Wang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Xueli Jiao
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Zhen Li
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Juan Wang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Lu Han
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Ling Zhou
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Huili Wang
- Department of Hematology, The Third People’s Hospital of Zhengzhou, Zhengzhou, China
| | - Xianjing Wang
- Department of Hematology, The Third People’s Hospital of Zhengzhou, Zhengzhou, China
| | - Xinxin Fan
- Department of Hematology, The Third People’s Hospital of Zhengzhou, Zhengzhou, China
| | - Xiaodong Lyu
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- *Correspondence: Xiaodong Lyu, ; Yongping Song, ; Jian Zhou,
| | - Yongping Song
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- *Correspondence: Xiaodong Lyu, ; Yongping Song, ; Jian Zhou,
| | - Jian Zhou
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- *Correspondence: Xiaodong Lyu, ; Yongping Song, ; Jian Zhou,
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Bineshfar N, Rezaei A, Mirahmadi A, Shokouhi S, Gharehbagh FJ, Haghighi M, Harandi AA, Shojaei M, Ramezani M, Zoghi A, Gharagozli K, Lotfollahi L, Darazam IA. Evaluation of the epidemiologic, clinical, radiologic, and treatment methods of patients with subacute and chronic meningitis. BMC Neurol 2022; 22:340. [PMID: 36088290 PMCID: PMC9463760 DOI: 10.1186/s12883-022-02873-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 09/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background Meningitis is known as a meningeal inflammation accompanied by pleocytosis in the cerebrospinal fluid (CSF), and can be classified into acute, subacute, and chronic meningitis based on symptoms duration of ≤ 5 days, ≥ 5 days and ≥ 4 weeks, respectively. Subacute and chronic meningitis are caused mainly by indolent infectious agents and noninfectious causes such as autoimmune, and neoplastic. In this study, we investigated the characteristics, diagnosis, and treatment of subacute and chronic meningitis. Methods We extracted the medical records of patients with chronic and subacute meningitis who were referred to three tertiary centers from Jun 2011 to Jun 2021. Initially, 2050 cases of meningitis were screened, and then 79 patients were included in the study. Results Headache (87.3%), nausea and vomiting (74.7%), fever (56.4%), and visual impairments (55.7%) were the most prevalent symptoms. The most common signs were nuchal rigidity (45.3%), altered mental status (26.9%), and papillary edema (37.5%). Brain computed tomography (CT) was normal in 68.6% of the patients while 22.9% of the cases had hydrocephalus. Brain magnetic resonance imaging (MRI) was normal in 60.0% of the patients. The most common abnormal MRI findings were leptomeningeal enhancement (16.0%) and hydrocephalus (16.0%). We had a 44.3% definite diagnosis with bacterial (n:25, 31.6%) and neoplastic (n:8, 10.1%) being the most prevalent etiologies. Mycobacterium tuberculosis (60%) and Brucella spp. (12%) were the most prevalent bacterial pathogens. Conclusions The most common etiologies include infectious, neoplastic, and immunologic. Due to insidious presentation and uncommon etiologies, establishing a proper diagnosis, and providing timely targeted treatment for patients with subacute and chronic meningitis remains a challenge for clinicians.
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Yang HH, He XJ, Nie JM, Guan SS, Chen YK, Liu M. Central nervous system aspergillosis misdiagnosed as Toxoplasma gondii encephalitis in a patient with AIDS: a case report. AIDS Res Ther 2022; 19:40. [PMID: 36076296 PMCID: PMC9461208 DOI: 10.1186/s12981-022-00468-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 08/17/2022] [Indexed: 11/23/2022] Open
Abstract
Background Patients with acquired immunodeficiency syndrome (AIDS) tend to suffer from several central nervous system (CNS) infections due to hypoimmunity. However, CNS aspergillosis (CNSAG) is extremely rare and difficult to diagnose. Thus, it is easily misdiagnosed. Case presentation We reported a 47-year-old male AIDS patient with ghosting vision and anhidrosis on the left head and face. He was accordingly diagnosed with Toxoplasma gondii encephalitis (TE) at other hospitals, for which he received regular anti-Toxoplasma gondii and anti-human immunodeficiency virus (anti-HIV) treatment. Then, the patient was transferred to our hospital due to a lack of any improvement with the prescribed treatment. The patient's neurological examination revealed no abnormalities at admission, only a slight change in the cerebrospinal fluid. His cranial magnetic resonance imaging (MRI) revealed multiple abnormal signals in the brain parenchyma, and his blood was positive for Toxoplasma gondii IgG antibody. The initial diagnosis at our hospital was also TE. Considering the poor efficacy of anti-TE treatment, cerebrospinal fluid metagenomics next-generation sequencing (mNGS) was performed, but no pathogenic bacteria were detected. However, Aspergillus fumigatus was detected in the cerebrospinal fluid via targeted next-generation sequencing (tNGS) and bronchoalveolar alveolar lavage fluid via mNGS. The diagnosis was accordingly revised to CNSAG combined with his other clinical manifestations. After administering voriconazole antifungal therapy, the patient’s symptoms were relieved, with improved absorption of the intracranial lesions. Conclusions The present case experience indicates the need for clinicians to strengthen their understanding of CNSAG. Moreover, for patients with diagnostic difficulties, early mNGS and tNGS (using biological samples with only a few pathogens) are helpful for early diagnosis and treatment, potentially allowing patients to achieve favorable outcomes.
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Affiliation(s)
- Hong-Hong Yang
- Division of Infectious Diseases, Chongqing Public Health Medical Center, 109 Baoyu Road, Shapingba District, Chongqing, 400036, China
| | - Xue-Jiao He
- Division of Infectious Diseases, Chongqing Public Health Medical Center, 109 Baoyu Road, Shapingba District, Chongqing, 400036, China
| | - Jing-Min Nie
- Division of Infectious Diseases, Chongqing Public Health Medical Center, 109 Baoyu Road, Shapingba District, Chongqing, 400036, China
| | - Shao-Shan Guan
- Hunan Sagene Medical Laboratory Limited, Changsha, 410036, Hunan, China
| | - Yao-Kai Chen
- Division of Infectious Diseases, Chongqing Public Health Medical Center, 109 Baoyu Road, Shapingba District, Chongqing, 400036, China
| | - Min Liu
- Division of Infectious Diseases, Chongqing Public Health Medical Center, 109 Baoyu Road, Shapingba District, Chongqing, 400036, China.
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Ju Y, Pu M, Sun K, Song G, Geng J. Nanopore Electrochemistry for Pathogen Detection. Chem Asian J 2022; 17:e202200774. [PMID: 36069587 DOI: 10.1002/asia.202200774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/06/2022] [Indexed: 11/05/2022]
Abstract
Pathogen infections have seriously threatened human health, and there is an urgent demand for rapid and efficient pathogen identification to provide instructions in clinical diagnosis and therapeutic intervention. Recently, nanopore technology, a rapidly maturing technology which delivers ultrasensitive sensing and high throughput in real-time and at low cost, has achieved success in pathogen detection. Furthermore, the remarkable development of nanopore sequencing, for example, the MinION sequencer from Oxford Nanopore Technologies (ONT) as a competitive sequencing technology, has facilitated the rapid analysis of disease-related microbiomes at the whole-genome level and on a large scale. Here, we highlighted recent advances in nanopore approaches for pathogen detection at the single-molecule level. We also overviewed the applications of nanopore sequencing in pathogenic bacteria identification and diagnosis. In the end, we discussed the challenges and future developments of nanopore technology as promising tools for the management of infections, which may be helpful to aid understanding as well as decision-making.
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Affiliation(s)
- Yuan Ju
- Sichuan University, Sichuan University Library, CHINA
| | - Mengjun Pu
- Sichuan University, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, CHINA
| | - Ke Sun
- Sichuan University, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, CHINA
| | - Guiqin Song
- North Sichuan Medical College [Search North Sichuan Medical College]: North Sichuan Medical University, Shool of Basic Medical Sciences and Forensic Medicine, CHINA
| | - Jia Geng
- Sichuan University, State Key Laboratory of Biotherapy, No 17 Section 3 of South Renmin Rd, 610040, Chengdu, CHINA
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Wang Y, Hu X, Yang L, Chen C, Cheng H, Hu H, Liang W, Tong Y, Wang M, Wang H. Application of High-Throughput Sequencing Technology in the Pathogen Identification of Diverse Infectious Diseases in Nephrology Departments. Diagnostics (Basel) 2022; 12:diagnostics12092128. [PMID: 36140529 PMCID: PMC9497786 DOI: 10.3390/diagnostics12092128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/21/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Objective: The purpose of this study was to explore the clinical applications of high-throughput sequencing (HTS) in the identification of pathogens in patients with urinary tract infection (UTI), peritoneal dialysis-associated peritonitis (PDAP), central venous catheter related blood infections (CRBIs), and lung infections in the nephrology department. Methods: Midstream urine samples from 112 patients with UTI, peritoneal fluid samples from 67 patients with PDAP, blood samples from 15 patients with CRBI, and sputum specimens from 53 patients with lung infection were collected. The HTS and ordinary culture methods were carried out in parallel to identify the pathogens in each sample. Pathogen detection positive rate and efficacy were compared between the two methods. Results: The pathogen positive detection rates of HTS in UTI, PDAP, CRBI, and lung infection were strikingly higher than those of the culture method (84.8% vs. 35.7, 71.6% vs. 23.9%, 75% vs. 46.7%, 84.9% vs. 5.7%, p < 0.05, respectively). HTS was superior to the culture method in the sensitivity of detecting bacteria, fungi, atypical pathogens, and mixed microorganisms in those infections. In patients who had empirically used antibiotics before the test being conducted, HTS still exhibited a considerably higher positive rate than the culture method (81.6% vs. 39.0%, 68.1% vs. 14.9%, 72.7% vs. 36.4%, 83.3% vs. 4.2%, p < 0.05, respectively). Conclusions: HTS is remarkably more efficient than the culture method in detecting pathogens in diverse infectious diseases in nephrology, and is particularly potential in identifying the pathogens that are unable to be identified by the common culture method, such as in cases of complex infection with specific pathogens or subclinical infection due to preemptive use of antibiotics.
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Affiliation(s)
- Yujuan Wang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Xiaoyi Hu
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Lianhua Yang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Cheng Chen
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Hui Cheng
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Haiyun Hu
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Wei Liang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Yongqing Tong
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Ming Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
- Correspondence: (M.W.); (H.W.)
| | - Huiming Wang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
- Correspondence: (M.W.); (H.W.)
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Hilt EE, Ferrieri P. Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases. Genes (Basel) 2022; 13:genes13091566. [PMID: 36140733 PMCID: PMC9498426 DOI: 10.3390/genes13091566] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/03/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years.
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Targeted next generation sequencing is comparable with metagenomic next generation sequencing in adults with pneumonia for pathogenic microorganism detection. J Infect 2022; 85:e127-e129. [PMID: 36031154 DOI: 10.1016/j.jinf.2022.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 08/20/2022] [Indexed: 10/31/2022]
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