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Lopez-Labrador FX, Huber M, Sidorov IA, Brown JR, Cuypers L, Laenen L, Vanmechelen B, Maes P, Fischer N, Pichler I, Storey N, Atkinson L, Schmutz S, Kufner V, van Boheemen S, Mulders CE, Grundhoff A, Blümke P, Robitaille A, Cinek O, Hubáčková K, Mourik K, Boers SA, Stauber L, Salmona M, Cappy P, Ramette A, Franze' A, LeGoff J, Claas ECJ, Rodriguez C, de Vries JJC. Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics. J Clin Virol 2024; 173:105695. [PMID: 38823290 DOI: 10.1016/j.jcv.2024.105695] [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: 01/13/2024] [Revised: 04/10/2024] [Accepted: 05/18/2024] [Indexed: 06/03/2024]
Abstract
Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons for viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark of metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS). A mock viral reference panel was designed to mimic low biomass clinical specimens. The panel was used to assess the performance of twelve metagenomic wet lab protocols currently in use in the diagnostic laboratories of participating ENNGS member institutions. Both Illumina and Nanopore, shotgun and targeted capture probe protocols were included. Performance metrics sensitivity, specificity, and quantitative potential were assessed using a central bioinformatics pipeline. Overall, viral pathogens with loads down to 104 copies/ml (corresponding to CT values of 31 in our PCR assays) were detected by all the evaluated metagenomic wet lab protocols. In contrast, lower abundant mixed viruses of CT values of 35 and higher were detected only by a minority of the protocols. Considering the reference panel as the gold standard, optimal thresholds to define a positive result were determined per protocol, based on the horizontal genome coverage. Implementing these thresholds, sensitivity and specificity of the protocols ranged from 67 to 100 % and 87 to 100 %, respectively. A variety of metagenomic protocols are currently in use in clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implying the need for standardization of metagenomic analysis for use in clinical settings.
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Affiliation(s)
- F Xavier Lopez-Labrador
- Virology Laboratory, Genomics and Health Area, Center for Public Health Research (FISABIO-Public Health), Generalitat Valenciana, Valencia, Spain; Microbiology & Ecology Department, Medical School, University of Valencia, Spain; and CIBERESP, Instituto de Salud Carlos III, Spain
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Igor A Sidorov
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Julianne R Brown
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Lize Cuypers
- Department of Laboratory Medicine, University Hospitals Leuven, and Laboratory of Clinical Microbiology, KU, Leuven, Belgium
| | - Lies Laenen
- Department of Laboratory Medicine, University Hospitals Leuven, and Laboratory of Clinical Microbiology, KU, Leuven, Belgium
| | - Bert Vanmechelen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Nicole Fischer
- University Medical Center Hamburg-Eppendorf, UKE Institute for Medical Microbiology, Virology and Hygiene, Germany
| | - Ian Pichler
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Nathaniel Storey
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Laura Atkinson
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Switzerland
| | | | | | | | | | | | - Ondrej Cinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czech Republic
| | - Klára Hubáčková
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czech Republic
| | - Kees Mourik
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Stefan A Boers
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lea Stauber
- Institute for Infectious Diseases, University of Bern, Switzerland
| | - Maud Salmona
- Virology Department, AP-HP, Hôpital Saint Louis, F-75010 Paris, France
| | | | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Switzerland
| | - Alessandra Franze'
- Virology Laboratory, Genomics and Health Area, Center for Public Health Research (FISABIO-Public Health), Generalitat Valenciana, Valencia, Spain
| | - Jerome LeGoff
- Virology Department, AP-HP, Hôpital Saint Louis, F-75010 Paris, France
| | - Eric C J Claas
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Jutte J C de Vries
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
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van Ackeren V, Schmutz S, Pichler I, Ziltener G, Zaheri M, Kufner V, Huber M. Retrospective Genotyping of Enteroviruses Using a Diagnostic Nanopore Sequencing Workflow. Pathogens 2024; 13:390. [PMID: 38787241 PMCID: PMC11124337 DOI: 10.3390/pathogens13050390] [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: 03/21/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
Enteroviruses are among the most common viruses pathogenic to humans. They are associated with various forms of disease, ranging from mild respiratory illness to severe neurological diseases. In recent years, an increasing number of isolated cases of children developing meningitis or encephalitis as a result of enterovirus infection have been reported, as well as discrete enterovirus D68 outbreaks in North America in 2014 and 2016. We developed an assay to rapidly genotype enteroviruses by sequencing a region within the VP1 gene using nanopore Flongles. We retrospectively analyzed enterovirus-/rhinovirus-positive clinical samples from the Zurich, Switzerland area mainly collected during two seasons in 2019/2020 and 2021/2022. Respiratory, cerebrospinal fluid, and stool samples were analyzed. Whole-genome sequencing was performed on samples with ambiguous genotyping results and enterovirus D68-positive samples. Out of 255 isolates, a total of 95 different genotypes were found. A difference in the prevalence of enterovirus and rhinovirus infections was observed for both sample type and age group. In particular, children aged 0-4 years showed a higher frequency of enterovirus infections. Comparing the respiratory seasons, a higher prevalence was found, especially for enterovirus A and rhinovirus A after the SARS-CoV-2 pandemic. The enterovirus genotyping workflow provides a rapid diagnostic tool for individual analysis and continuous enterovirus surveillance.
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Affiliation(s)
| | | | | | | | | | | | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (V.v.A.); (S.S.); (I.P.); (G.Z.); (M.Z.); (V.K.)
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3
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Kufner V, Frey AC, Burkhard SH, Schmutz S, Ziltener G, Zaheri M, Wiedmer CV, Plate A, Trkola A, Huber M, Mueller NJ. Exploring viral aetiology in upper respiratory tract infections: insights from metagenomic next-generation sequencing in Swiss outpatients before and during the SARS-CoV-2 pandemic. Swiss Med Wkly 2024; 154:3797. [PMID: 38587784 DOI: 10.57187/s.3797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
AIMS OF THE STUDY Upper respiratory tract infections are among the most common reasons for primary care consultations. They are diagnosed predominantly based on clinical assessment. Here, we investigated the benefit of viral metagenomic next-generation sequencing (mNGS) in an outpatient setting. METHODS This prospective cross-sectional study included immunocompetent patients with acute upper respiratory tract infections. General practitioners collected pharyngeal swabs and demographic and clinical data. Specimens were analysed using viral mNGS and conventional tests. RESULTS Two hundred seventy-seven patients were recruited by 21 general practitioners between 10/2019 and 12/2020, of which 91% had a suspected viral aetiology. For 138 patients (49.8%), mNGS identified one or more respiratory viruses. The mNGS showed a high overall agreement with conventional routine diagnostic tests. Rhinoviruses were the most frequently detected respiratory viruses (20.2% of patients). Viral mNGS reflected the influenza wave in early 2020 and the SARS-CoV-2 pandemic outbreak in Switzerland in March 2020. Notably, rhinoviruses continued to circulate despite non-pharmaceutical hygiene measures. CONCLUSIONS Viral mNGS allowed the initial diagnosis to be retrospectively re-evaluated. Assuming reduced turnaround times, mNGS has the potential to directly guide the treatment of upper respiratory tract infections. On an epidemiological level, our study highlights the utility of mNGS in respiratory infection surveillance, allowing early detection of epidemics and providing information crucial for prevention.
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Affiliation(s)
- Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Andrea C Frey
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Sara H Burkhard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Gabriela Ziltener
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Caroline V Wiedmer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Andreas Plate
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Nicolas J Mueller
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
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Nafea AM, Wang Y, Wang D, Salama AM, Aziz MA, Xu S, Tong Y. Application of next-generation sequencing to identify different pathogens. Front Microbiol 2024; 14:1329330. [PMID: 38348304 PMCID: PMC10859930 DOI: 10.3389/fmicb.2023.1329330] [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: 10/28/2023] [Accepted: 12/18/2023] [Indexed: 02/15/2024] Open
Abstract
Early and precise detection and identification of various pathogens are essential for epidemiological monitoring, disease management, and reducing the prevalence of clinical infectious diseases. Traditional pathogen detection techniques, which include mass spectrometry, biochemical tests, molecular testing, and culture-based methods, are limited in application and are time-consuming. Next generation sequencing (NGS) has emerged as an essential technology for identifying pathogens. NGS is a cutting-edge sequencing method with high throughput that can create massive volumes of sequences with a broad application prospects in the field of pathogen identification and diagnosis. In this review, we introduce NGS technology in detail, summarizes the application of NGS in that identification of different pathogens, including bacteria, fungi, and viruses, and analyze the challenges and outlook for using NGS to identify clinical pathogens. Thus, this work provides a theoretical basis for NGS studies and provides evidence to support the application of NGS in distinguishing various clinical pathogens.
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Affiliation(s)
- Aljuboori M. Nafea
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- College of Medicine, Department of Microbiology, Ibn Sina University of Medical and Pharmaceutical Science, Baghdad, Iraq
| | - Yuer Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Duanyang Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Ahmed M. Salama
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, China
- Medical Laboratory at Sharkia Health Directorate, Ministry of Health, Sharkia, Egypt
| | - Manal A. Aziz
- College of Medicine, Department of Microbiology, Ibn Sina University of Medical and Pharmaceutical Science, Baghdad, Iraq
| | - Shan Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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Fourgeaud J, Regnault B, Ok V, Da Rocha N, Sitterlé É, Mekouar M, Faury H, Milliancourt-Seels C, Jagorel F, Chrétien D, Bigot T, Troadec É, Marques I, Serris A, Seilhean D, Neven B, Frange P, Ferroni A, Lecuit M, Nassif X, Lortholary O, Leruez-Ville M, Pérot P, Eloit M, Jamet A. Performance of clinical metagenomics in France: a prospective observational study. THE LANCET. MICROBE 2024; 5:e52-e61. [PMID: 38048804 DOI: 10.1016/s2666-5247(23)00244-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) allows untargeted identification of a broad range of pathogens, including rare or novel microorganisms. Despite the recognition of mNGS as a valuable diagnostic tool for infections, the most relevant indications for this innovative strategy remain poorly defined. We aimed to assess the determinants of positivity and clinical utility of mNGS. METHODS In this observational study, we prospectively performed short-read shotgun metagenomics analysis as a second-line test (in cases of negative first-line test or when the symptoms were not fully explained by initial positive results) or as a first-line test in life-threatening situations requiring urgent non-targeted pathogen identification at the Necker-Enfants Malades Hospital (Paris, France). All sample types, clinical indications, and patient populations were included. Samples were accompanied by a mandatory form completed by the senior clinician or pathologist, on which the clinical level of suspected infection (defined as high or low) was indicated. We assessed the variables (gender, age, immune status, initial suspicion of infection, indication, and sample type) associated with mNGS pathogen detection using odds ratios (ORs) from multivariate logistic regression. Additional investigations were carried out using specific PCR or culture techniques, to confirm positive mNGS results, or when infectious suspicion was particularly high despite a negative mNGS result. FINDINGS Between Oct 29, 2019, and Nov 7, 2022, we analysed 742 samples collected from 523 patients. The initial suspicion of infection was either high (n=470, 63%) or low (n=272, 37%). Causative or possibly causative pathogens were detected in 117 (25%) samples from patients with high initial suspicion of infection, versus nine (3%) samples analysed to rule out infection (OR 9·1, 95% CI 4·6-20·4; p<0·0001). We showed that mNGS had higher odds of detecting a causative or possibly causative pathogenic virus on CNS biopsies than CSF samples (4·1, 1·7-10·7; p=0·0025) and in samples from immunodeficient compared with immunocompetent individuals (2·4, 1·4-4·1; p=0·0013). Concordance with conventional confirmatory tests results was 103 (97%) of 106, when mNGS detected causative or possibly causative pathogens. Altogether, among 231 samples investigated by both mNGS and subsequent specific tests, discordant results were found in 69 (30%) samples, of which 58 (84%) were mNGS positive and specific tests negative, and 11 (16%) mNGS negative and specific tests positive. INTERPRETATION Major determinants of pathogen detection by mNGS are immune status and initial level of suspicion of infection. These findings will contribute, along with future studies, to refining the positioning of mNGS in diagnostic and treatment decision-making algorithms. FUNDING Necker-Enfants Malades Hospital and Institut Pasteur. TRANSLATION For the French translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Jacques Fourgeaud
- Université Paris Cité, FETUS, Paris, France; Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | - Béatrice Regnault
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France; Bioinformatics and Biostatistics Hub, Computational Biology Department, Institut Pasteur, Paris, France
| | - Vichita Ok
- Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | - Nicolas Da Rocha
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France
| | - Émilie Sitterlé
- Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | - Meryem Mekouar
- Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | - Hélène Faury
- Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | | | - Florence Jagorel
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France
| | - Delphine Chrétien
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France
| | - Thomas Bigot
- Bioinformatics and Biostatistics Hub, Computational Biology Department, Institut Pasteur, Paris, France
| | - Éric Troadec
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France
| | | | - Alexandra Serris
- Université Paris Cité, Centre d'Infectiologie Necker-Pasteur, IHU Imagine, Hôpital Necker, Paris, France
| | - Danielle Seilhean
- Département de Neuropathologie Raymond Escourolle, AP-HP-Sorbonne, Groupe Hospitalier Pitié-Salpêtrière, Paris, France; Institut du Cerveau-Paris Brain Institute-ICM, INSERM U1127, CNRS UMR7225, AP-HP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Bénédicte Neven
- Pediatric Hematology Immunology and Rheumatology Unit, AP-HP, Hôpital Necker, Paris, France; Université Paris Cité, INSERM, Institut Imagine, Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Paris, France
| | - Pierre Frange
- Université Paris Cité, FETUS, Paris, France; Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | - Agnès Ferroni
- Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | - Marc Lecuit
- Université Paris Cité, Centre d'Infectiologie Necker-Pasteur, IHU Imagine, Hôpital Necker, Paris, France; Institut Pasteur, Université de Paris, INSERM U1117, Biology of Infection Unit, Paris, France; Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, Paris, France
| | - Xavier Nassif
- Université Paris Cité, CNRS, INSERM, Institut Necker-Enfants Malades, Team Pathogenesis of Systemic Infection, Paris, France
| | - Olivier Lortholary
- Université Paris Cité, Centre d'Infectiologie Necker-Pasteur, IHU Imagine, Hôpital Necker, Paris, France; Institut Pasteur, Centre National de Référence Mycoses Invasives et Antifongiques, Département de Mycologie, Labex IBEID, Paris, France
| | - Marianne Leruez-Ville
- Université Paris Cité, FETUS, Paris, France; Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | - Philippe Pérot
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France; Institut Pasteur, Centre National de Référence Mycoses Invasives et Antifongiques, Département de Mycologie, Labex IBEID, Paris, France
| | - Marc Eloit
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France; Institut Pasteur, Université Paris Cité, The WOAH Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Paris, France; École Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - Anne Jamet
- Microbiology Department, AP-HP, Hôpital Necker, Paris, France; Université Paris Cité, CNRS, INSERM, Institut Necker-Enfants Malades, Team Pathogenesis of Systemic Infection, Paris, France.
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Okoh GR, Ariel E, Whitmore D, Horwood PF. Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies. ECOHEALTH 2023; 20:427-440. [PMID: 38091182 DOI: 10.1007/s10393-023-01659-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 10/26/2023] [Indexed: 02/21/2024]
Abstract
The agile wallaby (Notamacropus agilis) is one of the most abundant marsupial species in northern Queensland and a competent host for the zoonotic Ross River virus. Despite their increased proximity and interactions with humans, little is known about the viruses carried by these animals, and whether any are of conservation or zoonotic importance. Metagenomics and molecular techniques were used in a complementary manner to identify and characterize novel viruses in the fecal samples of free-ranging agile wallabies. We detected a variety of novel marsupial-related viral species including agile wallaby atadenovirus 1, agile wallaby chaphamaparvovirus 1-2, agile wallaby polyomavirus 1-2, agile wallaby associated picobirnavirus 1-9, and a known macropod gammaherpesvirus 3. Phylogenetic analyses indicate that most of these novel viruses would have co-evolved with their hosts (agile wallabies). Additionally, non-marsupial viruses that infect bacteria (phages), plants, insects, and other eukaryotes were identified. This study highlighted the utility of non-invasive sampling as well as the integration of broad-based molecular assays (consensus PCR and next generation sequencing) for monitoring the emergence of potential pathogenic viruses in wildlife species. Furthermore, the novel marsupial viruses identified in this study will enrich the diversity of knowledge about marsupial viruses, and may be useful for developing diagnostics and vaccines.
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Affiliation(s)
- God'spower Richard Okoh
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia.
| | - Ellen Ariel
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - David Whitmore
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - Paul F Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia.
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Perlejewski K, Radkowski M, Pawełczyk A, Rydzanicz M, Dzieciątkowski T, Makowiecki M, Paciorek M, Welc-Falęciak R, Horban A, Laskus T. Enteroviral central nervous system infections in patients with Lyme neuroborreliosis. Ticks Tick Borne Dis 2023; 14:102253. [PMID: 37729847 DOI: 10.1016/j.ttbdis.2023.102253] [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: 04/12/2023] [Revised: 08/21/2023] [Accepted: 09/10/2023] [Indexed: 09/22/2023]
Abstract
Patients with Lyme neuroborreliosis (LNB) are rarely tested for the presence of neurovirulent viruses other than tick-borne encephalitis virus (TBEV); however, such coinfections could be of clinical importance. The aim of the study was to search for the presence of neurotropic viruses in a LNB patients. Fourteen patients admitted with signs and symptoms of neuroinfection who were eventually diagnosed to have LNB (according to the guidelines of the European Federation of Neurological Societies) were subjects of the study. Sera and cerebrospinal fluid (CSF) collected at the time of initial presentation were tested for viral pathogens most common in our geographical area: human enteroviruses (EV), herpes simplex virus type 1 and 2, varicella-zoster virus, Epstein-Barr virus, cytomegalovirus, human herpesvirus type 6, human adenoviruses, and TBEV using PCR/RT-PCR and serological assays. RNA and DNA-based metagenomic next-generation sequencing (mNGS) was used to detect other viral pathogens. EV was detected in CSF from two (14 %) LNB patients and viral loads were similar (220 and 270 copies/ml). The mMGS analysis were performed on CSFs from 10 patients and generated a total 213,750,885 NGS reads, 0.05 % of which were viral. However, none of potential pathogens fulfilled the criteria for positive viral detection by mNGS. Using a number of PCR/RT-PCR assays and mNGS we identified EV infection in two out of 14 LNB patients. The possible co-occurrence of enterovirus and Lyme neuroborreliosis infections may warrant further research.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Pawińskiego 3c, Warsaw 02-106, Poland.
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Pawińskiego 3c, Warsaw 02-106, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Pawińskiego 3c, Warsaw 02-106, Poland
| | - Małgorzata Rydzanicz
- Department of the Medical Genetics, Medical University of Warsaw, Pawińskiego 3c, Warsaw 02-106, Poland
| | - Tomasz Dzieciątkowski
- Department of Microbiology, Medical University of Warsaw, Chalubińskiego 5, Warsaw 02-004, Poland
| | - Michał Makowiecki
- Department of Adults Infectious Diseases, Medical University of Warsaw, Wolska 37, Warsaw 01-201, Poland
| | - Marcin Paciorek
- Department of Adults Infectious Diseases, Medical University of Warsaw, Wolska 37, Warsaw 01-201, Poland
| | - Renata Welc-Falęciak
- Department of Parasitology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw 02-096, Poland
| | - Andrzej Horban
- Department of Adults Infectious Diseases, Medical University of Warsaw, Wolska 37, Warsaw 01-201, Poland
| | - Tomasz Laskus
- Department of Adults Infectious Diseases, Medical University of Warsaw, Wolska 37, Warsaw 01-201, Poland
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8
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Vlad B, Jelcic I, Balint B. Parkinsonism due to Coxsackie B Virus Infection-Case Report and Literature Review. Mov Disord Clin Pract 2023; 10:S24-S28. [PMID: 37636219 PMCID: PMC10448620 DOI: 10.1002/mdc3.13773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/15/2023] [Accepted: 05/03/2023] [Indexed: 08/29/2023] Open
Affiliation(s)
- Benjamin Vlad
- Department of NeurologyUniversity Hospital ZurichZurichSwitzerland
| | - Ilijas Jelcic
- Department of NeurologyUniversity Hospital ZurichZurichSwitzerland
| | - Bettina Balint
- Department of NeurologyUniversity Hospital ZurichZurichSwitzerland
- University of ZurichZurichSwitzerland
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9
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Piralla A, Borghesi A, Di Comite A, Giardina F, Ferrari G, Zanette S, Figar TA, Angelini M, Pisoni C, Pitrolo AMG, Paolucci S, Rovida F, Pellicioli I, Bonanomi E, Baldanti F, Ghirardello S. Fulminant echovirus 11 hepatitis in male non-identical twins in northern Italy, April 2023. Euro Surveill 2023; 28:2300289. [PMID: 37318763 PMCID: PMC10318938 DOI: 10.2807/1560-7917.es.2023.28.24.2300289] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 06/14/2023] [Indexed: 06/16/2023] Open
Abstract
Echovirus 11 (E11) has recently been associated with a series of nine neonatal cases of severe hepatitis in France. Here, we present severe hepatitis caused by E11 in a pair of twins. In one of the neonates, the clinical picture evolved to fulminant hepatitis. The E11 genome showed 99% nucleotide identity with E11 strains reported in the cases in France. Rapid genome characterisation using next generation sequencing is essential to identify new and more pathogenetic variants.
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Affiliation(s)
- Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- These authors contributed equally to this work and share first authorship
| | - Alessandro Borghesi
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- These authors contributed equally to this work and share first authorship
| | - Amelia Di Comite
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Federica Giardina
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Guglielmo Ferrari
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Simona Zanette
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | | | - Micol Angelini
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Camilla Pisoni
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | | | - Stefania Paolucci
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Francesca Rovida
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Isabella Pellicioli
- Paediatric Intensive Care Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Ezio Bonanomi
- Paediatric Intensive Care Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
- These authors contributed equally to the work and share the last authorship
| | - Stefano Ghirardello
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- These authors contributed equally to the work and share the last authorship
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10
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Everhart J, Henshaw NG. Updates in Molecular Diagnostics in Solid Organ Transplantation Recipients. Infect Dis Clin North Am 2023:S0891-5520(23)00038-7. [PMID: 37244805 DOI: 10.1016/j.idc.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Advances in molecular diagnostics have the potential to improve patient care among solid organ transplant recipients by reducing time to pathogen identification and informing directed therapy. Although cultures remain the cornerstone of traditional microbiology, advanced molecular diagnostics, such as metagenomic next-generation sequencing (mNGS), may increase detection of pathogens. This is particularly true in the settings of prior antibiotic exposure, and when causative organisms are fastidious. mNGS also offers a hypothesis-free diagnostic method of testing. This is useful in situations whereby the differential is broad or when the infectious agent is unlikely to be detected by routine methods.
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Affiliation(s)
- James Everhart
- Duke University Medical Center, 2351 Erwin Road, Wadsworth Building, Room 0170, Durham, NC 27705, USA.
| | - Nancy G Henshaw
- Duke University Medical Center, 2351 Erwin Road, Wadsworth Building, Room 0170, Durham, NC 27705, USA
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11
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Fu Y, Zhu X, Cao P, Shen C, Qian X, Miao H, Yu Y, Wang H, Zhai X. Metagenomic Next-Generation Sequencing in the Diagnosis of Infectious Fever During Myelosuppression Among Pediatric Patients with Hematological and Neoplastic Diseases. Infect Drug Resist 2022; 15:5425-5434. [PMID: 36124109 PMCID: PMC9482462 DOI: 10.2147/idr.s379582] [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] [Received: 07/07/2022] [Accepted: 09/03/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose To analyze the contribution of metagenomic next-generation sequencing (mNGS) in the guidance of clinical treatment and outcomes of infection during myelosuppression among children with hematological and neoplastic diseases. Patients and Methods The clinical data and results of mNGS assay of febrile patients suspected of infection were retrospectively collected. The characteristics of pathogenic microorganisms and clinical course of myelosuppressed children with hematological diseases were summarized. Results Our study included 70 patients (45 males) with a median age of 5 years (range: 0.5 to 13 y). During the study period, there were 96 events of suspected infection. According to comprehensive clinical diagnosis, 73 blood infections, 43 pneumonia and 2 urinary tract infections occurred. The positive rate of mNGS was significantly higher than that of traditional microbial detection (83.3% vs 17.7%). The main pathogens detected by mNGS were Pseudomonas aeruginosa, Acinetobacter, human herpesvirus, Candida and Aspergillus. The average duration of fever was 4.9 days and 11.6 days (P < 0.05), and the average cost of anti-infection treatment was RMB ¥28,077 and 39,898 (P < 0.05) among children received mNGS within 48 hours and more than 48 hours after the onset of infection symptoms. Conclusion mNGS contributes to clinical management of children with infection during myelosuppression, especially among patients with negative traditional microbial detection. Early implementation of mNGS in children with symptoms has a tendency to reduce the time of infection, fever and the cost of treatment.
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Affiliation(s)
- Yang Fu
- Department of Hematology, National Children's Medical Center Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Xiaohua Zhu
- Department of Hematology, National Children's Medical Center Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Ping Cao
- Department of Hematology, National Children's Medical Center Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Chen Shen
- Department of Hematology, National Children's Medical Center Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Xiaowen Qian
- Department of Hematology, National Children's Medical Center Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Hui Miao
- Department of Hematology, National Children's Medical Center Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Yi Yu
- Department of Hematology, National Children's Medical Center Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Hongsheng Wang
- Department of Hematology, National Children's Medical Center Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Xiaowen Zhai
- Department of Hematology, National Children's Medical Center Children's Hospital of Fudan University, Shanghai, People's Republic of China
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12
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13
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Jurasz H, Pawłowski T, Perlejewski K. Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives. Front Microbiol 2021; 12:745076. [PMID: 34745046 PMCID: PMC8564396 DOI: 10.3389/fmicb.2021.745076] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
We describe the most common internal and external sources and types of contamination encountered in viral metagenomic studies and discuss their negative impact on sequencing results, particularly for low-biomass samples and clinical applications. We also propose some basic recommendations for reducing the background noise in viral shotgun metagenomic (SM) studies, which would limit the bias introduced by various classes of contaminants. Regardless of the specific viral SM protocol, contamination cannot be totally avoided; in particular, the issue of reagent contamination should always be addressed with high priority. There is an urgent need for the development and validation of standards for viral metagenomic studies especially if viral SM protocols will be more widely applied in diagnostics.
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Affiliation(s)
- Henryk Jurasz
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Pawłowski
- Division of Psychotherapy and Psychosomatic Medicine, Department of Psychiatry, Wrocław Medical University, Wrocław, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
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14
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Casto AM, Fredricks DN, Hill JA. Diagnosis of infectious diseases in immunocompromised hosts using metagenomic next generation sequencing-based diagnostics. Blood Rev 2021; 53:100906. [PMID: 34802773 DOI: 10.1016/j.blre.2021.100906] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 02/07/2023]
Abstract
The diagnosis of infectious diseases in immunocompromised hosts presents unique challenges for the clinician. Metagenomic next generation sequencing (mNGS) based diagnostics that identify microbial nucleic acids in clinical samples (mNGS for pathogen identification or mNGSpi) may be a useful tool in addressing some of these challenges. Studies of mNGSpi in immunocompromised hosts have demonstrated that these diagnostics are capable of identifying causative organisms in a subset of patients for whom conventional testing has been negative. While these studies provide proof of concept for mNGSpi utility, they have a number of limitations, which make it difficult to confidently assess test performance and clinical impact based on current data. Future studies will likely feature larger cohort sizes and controlled interventional study designs that assess the impact of mNGSpi on clinical endpoints. They will also likely include assessments of the clinical value of data generated by mNGS beyond pathogen identification.
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Affiliation(s)
- Amanda M Casto
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States of America; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America.
| | - David N Fredricks
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States of America; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America.
| | - Joshua A Hill
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States of America; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America.
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15
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Carbo EC, Blankenspoor I, Goeman JJ, Kroes ACM, Claas ECJ, De Vries JJC. Viral metagenomic sequencing in the diagnosis of meningoencephalitis: a review of technical advances and diagnostic yield. Expert Rev Mol Diagn 2021; 21:1139-1146. [PMID: 34607520 DOI: 10.1080/14737159.2021.1985467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Meningoencephalitis patients are often severely impaired and benefit from early etiological diagnosis, though many cases remain without identified cause. Metagenomics as pathogen agnostic approach can result in additional etiological findings; however, the exact diagnostic yield when used as a secondary test remains unknown. AREAS COVERED This review aims to highlight recent advances with regard to wet and dry lab methodologies of metagenomic testing and technical milestones that have been achieved. A selection of procedures currently applied in accredited diagnostic laboratories is described in more detail to illustrate best practices. Furthermore, a meta-analysis was performed to assess the additional diagnostic yield utilizing metagenomic sequencing in meningoencephalitis patients. Finally, the remaining challenges for successful widespread implementation of metagenomic sequencing for the diagnosis of meningoencephalitis are addressed in a future perspective. EXPERT OPINION The last decade has shown major advances in technical possibilities for using mNGS in diagnostic settings including cloud-based analysis. An additional advance may be the current established infrastructure of platforms for bioinformatic analysis of SARS-CoV-2, which may assist to pave the way for global use of clinical metagenomics.
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Affiliation(s)
- Ellen C Carbo
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ivar Blankenspoor
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jelle J Goeman
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Aloys C M Kroes
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric C J Claas
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jutte J C De Vries
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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16
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de Vries JJ, Brown JR, Fischer N, Sidorov IA, Morfopoulou S, Huang J, Munnink BBO, Sayiner A, Bulgurcu A, Rodriguez C, Gricourt G, Keyaerts E, Beller L, Bachofen C, Kubacki J, Cordey S, Laubscher F, Schmitz D, Beer M, Hoeper D, Huber M, Kufner V, Zaheri M, Lebrand A, Papa A, van Boheemen S, Kroes AC, Breuer J, Lopez-Labrador FX, Claas EC. Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples. J Clin Virol 2021; 141:104908. [PMID: 34273858 PMCID: PMC7615111 DOI: 10.1016/j.jcv.2021.104908] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/18/2021] [Accepted: 06/30/2021] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Metagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories. METHODS Metagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analyzed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The pipelines and classification tools were: Centrifuge, DAMIAN, DIAMOND, DNASTAR, FEVIR, Genome Detective, Jovian, MetaMIC, MetaMix, One Codex, RIEMS, VirMet, and Taxonomer. Performance, characteristics, clinical use, and user-friendliness of these pipelines were analyzed. RESULTS Overall, viral pathogens with high loads were detected by all the evaluated metagenomic pipelines. In contrast, lower abundance pathogens and mixed infections were only detected by 3/13 pipelines, namely DNASTAR, FEVIR, and MetaMix. Overall sensitivity ranged from 80% (10/13) to 100% (13/13 datasets). Overall positive predictive value ranged from 71-100%. The majority of the pipelines classified sequences based on nucleotide similarity (8/13), only a minority used amino acid similarity, and 6 of the 13 pipelines assembled sequences de novo. No clear differences in performance were detected that correlated with these classification approaches. Read counts of target viruses varied between the pipelines over a range of 2-3 log, indicating differences in limit of detection. CONCLUSION A wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the need for standardization and validation of metagenomic analysis for clinical diagnostic use. Future studies should address the selective effects due to the choice of different reference viral databases.
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Affiliation(s)
- Jutte J.C. de Vries
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Julianne R. Brown
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Nicole Fischer
- University Medical Center Hamburg-Eppendorf, UKE Institute for Medical Microbiology, Virology and Hygiene, Germany
| | - Igor A. Sidorov
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sofia Morfopoulou
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Jiabin Huang
- University Medical Center Hamburg-Eppendorf, UKE Institute for Medical Microbiology, Virology and Hygiene, Germany
| | | | - Arzu Sayiner
- Dokuz Eylul University, Medical Faculty, Izmir, Turkey
| | | | | | | | - Els Keyaerts
- Laboratory of Clinical and Epidemiological Virology (Rega Institute), KU Leuven, Belgium
| | - Leen Beller
- Laboratory of Clinical and Epidemiological Virology (Rega Institute), KU Leuven, Belgium
| | | | - Jakub Kubacki
- Institute of Virology, University of Zurich, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, University Hospitals of Geneva, Geneva, Switzerland
| | - Florian Laubscher
- Laboratory of Virology, University Hospitals of Geneva, Geneva, Switzerland
| | - Dennis Schmitz
- RIVM National Institute for Public Health and Environment, Bilthoven, the Netherlands
| | - Martin Beer
- Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald, Germany
| | - Dirk Hoeper
- Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald, Germany
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Switzerland
| | | | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece
| | | | - Aloys C.M. Kroes
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Judith Breuer
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - F. Xavier Lopez-Labrador
- Virology Laboratory, Genomics and Health Area, Center for Public Health Research (FISABIO-Public Health), Generalitat Valenciana and Microbiology & Ecology Department, University of Valencia, Spain
- CIBERESP, Instituto de Salud Carlos III, Spain
| | - Eric C.J. Claas
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
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17
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d'Humières C, Salmona M, Dellière S, Leo S, Rodriguez C, Angebault C, Alanio A, Fourati S, Lazarevic V, Woerther PL, Schrenzel J, Ruppé E. The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives. Drugs 2021; 81:1453-1466. [PMID: 34328626 PMCID: PMC8323086 DOI: 10.1007/s40265-021-01572-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2021] [Indexed: 12/24/2022]
Abstract
Clinical metagenomics (CMg) is the process of sequencing nucleic acid of clinical samples to obtain clinically relevant information such as the identification of microorganisms and their susceptibility to antimicrobials. Over the last decades, sequencing and bioinformatic solutions supporting CMg have much evolved and an increasing number of case reports and series covering various infectious diseases have been published. Metagenomics is a new approach to infectious disease diagnosis that is currently being developed and is certainly one of the most promising for the coming years. However, most CMg studies are retrospective, and few address the potential impact CMg could have on patient management, including initiation, adaptation, or cessation of antimicrobials. In this narrative review, we have discussed the potential role of CMg in bacteriology, virology, mycology, and parasitology. Several reports and case-series confirm that CMg is an innovative tool with which one can (i) identify more microorganisms than with conventional methods in a single test, (ii) obtain results within hours, and (iii) tailor the antimicrobial regimen of patients. However, the cost-efficiency of CMg and its real impact on patient management are still to be determined.
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Affiliation(s)
- Camille d'Humières
- Université de Paris, IAME, INSERM, 75018, Paris, France.,AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018, Paris, France
| | - Maud Salmona
- Unité de Paris, INSERM U976, Insight Team, 75010, Paris, France.,AP-HP, Hôpital Saint-Louis, Laboratoire de Virologie, 75010, Paris, France
| | - Sarah Dellière
- AP-HP, Hôpital Saint-Louis, Laboratoire de Parasitologie-Mycologie, 75010, Paris, France.,Molecular Mycology Unit, Institut Pasteur, CNRS UMR2000, 75015, Paris, France
| | - Stefano Leo
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Christophe Rodriguez
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,INSERM U955, Université Paris-Est, 94000, Créteil, France
| | - Cécile Angebault
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,Université Paris Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, EA7380 Dynamic, 94000, Créteil, France
| | - Alexandre Alanio
- AP-HP, Hôpital Saint-Louis, Laboratoire de Parasitologie-Mycologie, 75010, Paris, France.,Molecular Mycology Unit, Institut Pasteur, CNRS UMR2000, 75015, Paris, France
| | - Slim Fourati
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,INSERM U955, Université Paris-Est, 94000, Créteil, France
| | - Vladimir Lazarevic
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Paul-Louis Woerther
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,Université Paris Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, EA7380 Dynamic, 94000, Créteil, France
| | - Jacques Schrenzel
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Etienne Ruppé
- Université de Paris, IAME, INSERM, 75018, Paris, France. .,AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018, Paris, France.
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18
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de Vries JJC, Brown JR, Couto N, Beer M, Le Mercier P, Sidorov I, Papa A, Fischer N, Oude Munnink BB, Rodriquez C, Zaheri M, Sayiner A, Hönemann M, Cataluna AP, Carbo EC, Bachofen C, Kubacki J, Schmitz D, Tsioka K, Matamoros S, Höper D, Hernandez M, Puchhammer-Stöckl E, Lebrand A, Huber M, Simmonds P, Claas ECJ, López-Labrador FX. Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting. J Clin Virol 2021; 138:104812. [PMID: 33819811 DOI: 10.1016/j.jcv.2021.104812] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/20/2021] [Indexed: 12/11/2022]
Abstract
Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety of sample types from patients with infectious syndromes. mNGS is still in its early stages of broader translation into clinical applications. To further support the development, implementation, optimization and standardization of mNGS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mNGS for viral diagnostics to share methodologies and experiences, and to develop application guidelines. Following the ENNGS publication Recommendations for the introduction of mNGS in clinical virology, part I: wet lab procedure in this journal, the current manuscript aims to provide practical recommendations for the bioinformatic analysis of mNGS data and reporting of results to clinicians.
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Affiliation(s)
- Jutte J C de Vries
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Julianne R Brown
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.
| | - Natacha Couto
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.
| | - Martin Beer
- Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald, Germany.
| | | | - Igor Sidorov
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece.
| | - Nicole Fischer
- University Medical Center Hamburg-Eppendorf, UKE Institute for Medical Microbiology, Virology and Hygiene, Germany.
| | | | - Christophe Rodriquez
- Department of Virology, University hospital Henri Mondor, Assistance Public des Hopitaux de Paris, Créteil, France.
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Switzerland.
| | - Arzu Sayiner
- Dokuz Eylul University, Medical Faculty, Department of Medical Microbiology, Izmir, Turkey.
| | - Mario Hönemann
- Institute of Virology, Leipzig University, Leipzig, Germany.
| | - Alba Perez Cataluna
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Paterna, Valencia, Spain.
| | - Ellen C Carbo
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | | | - Jakub Kubacki
- Institute of Virology, University of Zurich, Switzerland.
| | - Dennis Schmitz
- RIVM National Institute for Public Health and Environment, Bilthoven, the Netherlands.
| | - Katerina Tsioka
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece.
| | - Sébastien Matamoros
- Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands.
| | - Dirk Höper
- Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald, Germany.
| | - Marta Hernandez
- Laboratory of Molecular Biology and Microbiology, Instituto Tecnologico Agrario de Castilla y Leon, Valladolid, Spain.
| | | | | | - Michael Huber
- Institute of Medical Virology, University of Zurich, Switzerland.
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Eric C J Claas
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - F Xavier López-Labrador
- Virology Laboratory, Genomics and Health Area, Centre for Public Health Research (FISABIO-Public Health), Valencia, Spain; Department of Microbiology, Medical School, University of Valencia, Spain; CIBERESP, Instituto de Salud Carlos III, Madrid, Spain.
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19
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Werner J, Reichen I, Huber M, Abela IA, Weller M, Jelcic I. Subacute cerebellar ataxia following respiratory symptoms of COVID-19: a case report. BMC Infect Dis 2021; 21:298. [PMID: 33761897 PMCID: PMC7988684 DOI: 10.1186/s12879-021-05987-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023] Open
Abstract
Background Severe acute respiratory syndrome virus 2 (SARS-CoV-2) is spreading globally and causes most frequently fever and respiratory symptoms, i.e. Coronavirus disease 2019 (COVID-19), however, distinct neurological syndromes associated with SARS-CoV-2 infection have been described. Among SARS-CoV-2-infections-associated neurological symptoms fatigue, headache, dizziness, impaired consciousness and anosmia/ageusia are most frequent, but less frequent neurological deficits such as seizures, Guillain-Barré syndrome or ataxia may also occur. Case presentation Herein we present a case of a 62-year-old man who developed a subacute cerebellar syndrome with limb-, truncal- and gait ataxia and scanning speech 1 day after clinical resolution of symptomatic SARS-CoV-2 infection of the upper airways. Apart from ataxia, there were no signs indicative of opsoclonus myoclonus ataxia syndrome or Miller Fisher syndrome. Cerebral magnetic resonance imaging showed mild cerebellar atrophy. SARS-CoV-2 infection of the cerebellum was excluded by normal cerebrospinal fluid cell counts and, most importantly, absence of SARS-CoV-2 RNA or intrathecal SARS-CoV-2-specific antibody production. Other causes of ataxia such as other viral infections, other autoimmune and/or paraneoplastic diseases or intoxication were ruled out. The neurological deficits improved rapidly after high-dose methylprednisolone therapy. Conclusions The laboratory and clinical findings as well as the marked improvement after high-dose methylprednisolone therapy suggest a post-infectious, immune-mediated cause of ataxia. This report should make clinicians aware to consider SARS-CoV-2 infection as a potential cause of post-infectious neurological deficits with an atypical clinical presentation and to consider high-dose corticosteroid treatment in case that a post-infectious immune-mediated mechanism is assumed.
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Affiliation(s)
- Jana Werner
- Department of Neurology, University Hospital Zurich, Zurich, Switzerland
| | - Ina Reichen
- Department of Neurology, University Hospital Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Irene A Abela
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Michael Weller
- Department of Neurology, University Hospital Zurich, Zurich, Switzerland
| | - Ilijas Jelcic
- Department of Neurology, University Hospital Zurich, Zurich, Switzerland. .,Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University Hospital Zurich, Zurich, Switzerland.
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20
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Tsamis KI, Sakkas H, Giannakis A, Ryu HS, Gartzonika C, Nikas IP. Evaluating Infectious, Neoplastic, Immunological, and Degenerative Diseases of the Central Nervous System with Cerebrospinal Fluid-Based Next-Generation Sequencing. Mol Diagn Ther 2021; 25:207-229. [PMID: 33646562 PMCID: PMC7917176 DOI: 10.1007/s40291-021-00513-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 12/24/2022]
Abstract
Cerebrospinal fluid (CSF) is a clear and paucicellular fluid that circulates within the ventricular system and the subarachnoid space of the central nervous system (CNS), and diverse CNS disorders can impact its composition, volume, and flow. As conventional CSF testing suffers from suboptimal sensitivity, this review aimed to evaluate the role of next-generation sequencing (NGS) in the work-up of infectious, neoplastic, neuroimmunological, and neurodegenerative CNS diseases. Metagenomic NGS showed improved sensitivity—compared to traditional methods—to detect bacterial, viral, parasitic, and fungal infections, while the overall performance was maximized in some studies when all diagnostic modalities were used. In patients with primary CNS cancer, NGS findings in the CSF were largely concordant with the molecular signatures derived from tissue-based molecular analysis; of interest, additional mutations were identified in the CSF in some glioma studies, reflecting intratumoral heterogeneity. In patients with metastasis to the CNS, NGS facilitated diagnosis, prognosis, therapeutic management, and monitoring, exhibiting higher sensitivity than neuroimaging, cytology, and plasma-based molecular analysis. Although evidence is still rudimentary, NGS could enhance the diagnosis and pathogenetic understanding of multiple sclerosis in addition to Alzheimer and Parkinson disease. To conclude, NGS has shown potential to aid the research, facilitate the diagnostic approach, and improve the management outcomes of all the aforementioned CNS diseases. However, to establish its role in clinical practice, the clinical validity and utility of each NGS protocol should be determined. Lastly, as most evidence has been derived from small and retrospective studies, results from randomized control trials could be of significant value.
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Affiliation(s)
- Konstantinos I Tsamis
- Department of Neurology, University Hospital of Ioannina, 45500, Ioannina, Greece. .,School of Medicine, European University Cyprus, 2404, Nicosia, Cyprus.
| | - Hercules Sakkas
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Alexandros Giannakis
- Department of Neurology, University Hospital of Ioannina, 45500, Ioannina, Greece
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul, 03080, Korea
| | - Constantina Gartzonika
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Ilias P Nikas
- School of Medicine, European University Cyprus, 2404, Nicosia, Cyprus
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21
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Pohl MO, Busnadiego I, Kufner V, Glas I, Karakus U, Schmutz S, Zaheri M, Abela I, Trkola A, Huber M, Stertz S, Hale BG. SARS-CoV-2 variants reveal features critical for replication in primary human cells. PLoS Biol 2021; 19:e3001006. [PMID: 33760807 PMCID: PMC8021179 DOI: 10.1371/journal.pbio.3001006] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/05/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
Since entering the human population, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2; the causative agent of Coronavirus Disease 2019 [COVID-19]) has spread worldwide, causing >100 million infections and >2 million deaths. While large-scale sequencing efforts have identified numerous genetic variants in SARS-CoV-2 during its circulation, it remains largely unclear whether many of these changes impact adaptation, replication, or transmission of the virus. Here, we characterized 14 different low-passage replication-competent human SARS-CoV-2 isolates representing all major European clades observed during the first pandemic wave in early 2020. By integrating viral sequencing data from patient material, virus stocks, and passaging experiments, together with kinetic virus replication data from nonhuman Vero-CCL81 cells and primary differentiated human bronchial epithelial cells (BEpCs), we observed several SARS-CoV-2 features that associate with distinct phenotypes. Notably, naturally occurring variants in Orf3a (Q57H) and nsp2 (T85I) were associated with poor replication in Vero-CCL81 cells but not in BEpCs, while SARS-CoV-2 isolates expressing the Spike D614G variant generally exhibited enhanced replication abilities in BEpCs. Strikingly, low-passage Vero-derived stock preparation of 3 SARS-CoV-2 isolates selected for substitutions at positions 5/6 of E and were highly attenuated in BEpCs, revealing a key cell-specific function to this region. Rare isolate-specific deletions were also observed in the Spike furin cleavage site during Vero-CCL81 passage, but these were rapidly selected against in BEpCs, underscoring the importance of this site for SARS-CoV-2 replication in primary human cells. Overall, our study uncovers sequence features in SARS-CoV-2 variants that determine cell-specific replication and highlights the need to monitor SARS-CoV-2 stocks carefully when phenotyping newly emerging variants or potential variants of concern.
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Affiliation(s)
- Marie O. Pohl
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Idoia Busnadiego
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Irina Glas
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, ETH and University of Zurich, Zurich, Switzerland
| | - Umut Karakus
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Irene Abela
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Silke Stertz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Benjamin G. Hale
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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22
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Luan Y, Hu H, Liu C, Chen B, Liu X, Xu Y, Luo X, Chen J, Ye B, Huang F, Wang J, Duan C. A proof-of-concept study of an automated solution for clinical metagenomic next-generation sequencing. J Appl Microbiol 2021; 131:1007-1016. [PMID: 33440055 DOI: 10.1111/jam.15003] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
AIMS Metagenomic next-generation sequencing (mNGS) has been utilized for diagnosing infectious diseases. It is a culture-free and hypothesis-free nucleic acid test for diagnosing all pathogens with known genomic sequences, including bacteria, fungi, viruses and parasites. While this technique greatly expands the clinical capacity of pathogen detection, it is a second-line choice due to lengthy procedures and microbial contaminations introduced from wet-lab processes. As a result, we aimed to reduce the hands-on time and exogenous contaminations in mNGS. METHODS AND RESULTS We developed a device (NGSmaster) that automates the wet-lab workflow, including nucleic acid extraction, PCR-free library preparation and purification. It shortens the sample-to-results time to 16 and 18·5 h for DNA and RNA sequencing respectively. We used it to test cultured bacteria for validation of the workflow and bioinformatic pipeline. We also compared PCR-free with PCR-based library prep and discovered no differences in microbial reads. Moreover we analysed results by automation and manual testing and found that automation can significantly reduce microbial contaminations. Finally, we tested artificial and clinical samples and showed mNGS results were concordant with traditional culture. CONCLUSION NGSmaster can fulfil the microbiological diagnostic needs in a variety of sample types. SIGNIFICANCE AND IMPACT OF THE STUDY This study opens up an opportunity of performing in-house mNGS to reduce turnaround time and workload, instead of transferring potentially contagious specimen to a third-party laboratory.
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Affiliation(s)
- Y Luan
- Department of Clinical Laboratory, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - H Hu
- Department of Clinical Laboratory, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - C Liu
- Matridx Biotechnology Co., Ltd, Hangzhou, China
| | - B Chen
- Matridx Biotechnology Co., Ltd, Hangzhou, China
| | - X Liu
- Department of Clinical Laboratory, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Y Xu
- Department of Clinical Laboratory, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - X Luo
- Department of Clinical Laboratory, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - J Chen
- Matridx Biotechnology Co., Ltd, Hangzhou, China
| | - B Ye
- Matridx Biotechnology Co., Ltd, Hangzhou, China
| | - F Huang
- Matridx Biotechnology Co., Ltd, Hangzhou, China
| | - J Wang
- Matridx Biotechnology Co., Ltd, Hangzhou, China
| | - C Duan
- Department of Clinical Laboratory, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
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23
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Li ZY, Dang D, Wu H. Next-generation Sequencing of Cerebrospinal Fluid for the Diagnosis of Unexplained Central Nervous System Infections. Pediatr Neurol 2021; 115:10-20. [PMID: 33310532 DOI: 10.1016/j.pediatrneurol.2020.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Central nervous system infections cause substantial morbidity and mortality in pediatric patients. However, in approximately half of the clinical cases, the etiology is unidentified. As an unbiased molecular diagnostic technology, next-generation sequencing is gradually being applied to investigate central nervous system infections. This review summarizes and critiques the literature on this new technology for etiologic identification of unexplained central nervous system infections in pediatric patients and discusses the future prospects for development of this technology in pediatrics. METHODS A comprehensive PubMed search was conducted of articles published from January 1, 2008, to June 26, 2020 in order to retrieve all available studies on this topic. Other relevant articles were identified from recent reviews and the bibliographies of the retrieved full-text articles. RESULTS Among the 441 studies retrieved, 26 pediatric studies, comprising 15 case reports and 11 case series, used next-generation sequencing as a diagnostic tool. In these 26 studies, next-generation sequencing was performed on cerebrospinal fluid samples from 529 pediatric patients, and potential causal pathogens were identified in 22.1% of the cases. CONCLUSION There is increasing evidence that next-generation sequencing can play a role in identifying the causes of unexplained encephalitis, meningoencephalitis, and meningitis in pediatric patients, although the diagnostic value of next-generation sequencing is difficult to quantify. There is an increasing need for close collaboration between laboratory scientists and clinicians. We believe that further clinical studies should be performed to evaluate the performance of next-generation sequencing for individual targets and in high-risk populations.
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Affiliation(s)
- Zhen Yu Li
- Department of Pediatrics, The First Hospital of Jilin University, Changchun, Jilin, PR China
| | - Dan Dang
- Department of Pediatrics, The First Hospital of Jilin University, Changchun, Jilin, PR China
| | - Hui Wu
- Department of Pediatrics, The First Hospital of Jilin University, Changchun, Jilin, PR China.
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24
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Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. SMALL METHODS 2021; 5:2000792. [PMID: 33614906 PMCID: PMC7883231 DOI: 10.1002/smtd.202000792] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Indexed: 05/25/2023]
Abstract
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
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Affiliation(s)
- Na Li
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Qing Miao
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Zeshi Song
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Bijie Hu
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
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25
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Weissberg D, Böni J, Rampini SK, Kufner V, Zaheri M, Schreiber PW, Abela IA, Huber M, Sax H, Wolfensberger A. Does respiratory co-infection facilitate dispersal of SARS-CoV-2? investigation of a super-spreading event in an open-space office. Antimicrob Resist Infect Control 2020; 9:191. [PMID: 33267855 PMCID: PMC7708893 DOI: 10.1186/s13756-020-00861-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 11/22/2020] [Indexed: 12/14/2022] Open
Abstract
Background Super-spreaders are individuals infecting disproportionately large numbers of contacts. They probably play a crucial role in the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We describe a super-spreading event within a team working in an open-space office and investigate factors potentially having facilitated SARS-CoV-2 transmission. Methods In this retrospective cohort study, semi-structured telephone interviews with all team members were carried out to identify symptoms, contacts, and adherence to basic hygiene measures. During site visits, we gathered information about workplace and seating arrangements. The secondary attack rate in office and households was calculated. Potential respiratory viral co-infections were assessed by multiplex PCR. SARS-CoV-2 whole-genome sequencing was performed using a tiled-amplicon sequencing approach. Results Of 13 team members, 11 fell ill with Coronavirus disease 2019 (COVID-19). Due to the sequence of events and full genome sequence data, one person was considered the index case for this outbreak, directly infecting 67 to 83% of the teammates. All team members reported repetitive close contacts among themselves during joint computer work, team meetings and a “Happy Birthday” serenade. Two individuals shared nuts and dates. The arrangement of the office and meeting rooms precluded sufficient adherence to physical distancing. The index case and a further individual were diagnosed with an adenovirus serotype 4 co-infection. Conclusion We identified several environmental and behavioral factors that probably have facilitated the transmission of SARS-CoV-2. The relevance of the adenovirus co-infection remains unclear and merits further investigation.
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Affiliation(s)
- Dana Weissberg
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Silvana K Rampini
- Department of Internal Medicine, University Hospital Zurich, University of Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Peter W Schreiber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Irene A Abela
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hugo Sax
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Aline Wolfensberger
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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26
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López-Labrador FX, Brown JR, Fischer N, Harvala H, Van Boheemen S, Cinek O, Sayiner A, Madsen TV, Auvinen E, Kufner V, Huber M, Rodriguez C, Jonges M, Hönemann M, Susi P, Sousa H, Klapper PE, Pérez-Cataluňa A, Hernandez M, Molenkamp R, der Hoek LV, Schuurman R, Couto N, Leuzinger K, Simmonds P, Beer M, Höper D, Kamminga S, Feltkamp MCW, Rodríguez-Díaz J, Keyaerts E, Nielsen XC, Puchhammer-Stöckl E, Kroes ACM, Buesa J, Breuer J, Claas ECJ, de Vries JJC. Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure. J Clin Virol 2020; 134:104691. [PMID: 33278791 DOI: 10.1016/j.jcv.2020.104691] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/16/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023]
Abstract
Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols.
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Affiliation(s)
- F Xavier López-Labrador
- Virology Laboratory, Genomics and Health Area, Centre for Public Health Research (FISABIO-Public Health), Valencia, Spain; CIBERESP, Instituto de Salud Carlos III, Madrid, Spain.
| | - Julianne R Brown
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, United Kingdom.
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Heli Harvala
- Microbiology Services, NHS Blood and Transplant, London, United Kingdom.
| | - Sander Van Boheemen
- ErasmusMC, Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
| | - Ondrej Cinek
- Department of Paediatrics and Medical Microbiology, 2nd Faculty of Medicine, Charles University Prague, Czech Republic.
| | - Arzu Sayiner
- Dokuz Eylul University, Faculty of Medicine, Department of Medical Microbiology, Division of Medical Virology. Izmir, Turkey.
| | - Tina Vasehus Madsen
- Department of Clinical Microbiology, University Hospital of Region Zealand, Slagelse, Denmark.
| | - Eeva Auvinen
- Department of Virology, Helsinki University Hospital Laboratory and University of Helsinki, Helsinki, Finland.
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Christophe Rodriguez
- Microbiology Department and NGS Platform, University Hospital Henri Mondor (APHP), Créteil, France.
| | - Marcel Jonges
- Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands; Laboratory of Experimental Virology, Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands.
| | - Mario Hönemann
- Institute of Virology, Leipzig University, Leipzig, Germany.
| | - Petri Susi
- Institute of Biomedicine, University of Turku, Finland.
| | - Hugo Sousa
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal; Virology Service, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal; Molecular Oncology and Viral Pathology Group, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.
| | - Paul E Klapper
- Faculty of Biology, Medicine, and Health, Division of Infection, Immunity, and Respiratory Medicine, University of Manchester, Manchester, United Kingdom.
| | - Alba Pérez-Cataluňa
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Paterna, Valencia, Spain.
| | - Marta Hernandez
- Laboratory of Molecular Biology and Microbiology, Instituto Tecnologico Agrario de Castilla y Leon, Valladolid, Spain.
| | - Richard Molenkamp
- ErasmusMC, Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
| | - Lia van der Hoek
- Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands; Laboratory of Experimental Virology, Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands.
| | - Rob Schuurman
- Department of Virology, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands; Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.
| | - Karoline Leuzinger
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland; Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland.
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany.
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany.
| | - Sergio Kamminga
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Mariet C W Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Jesús Rodríguez-Díaz
- Department of Microbiology and Ecology, Faculty of Medicine, University of Valencia, Valencia, Spain.
| | - Els Keyaerts
- Laboratorium Klinische en Epidemiologische Virologie (Rega Instituut), Leuven, Belgium.
| | - Xiaohui Chen Nielsen
- Department of Clinical Microbiology, University Hospital of Region Zealand, Slagelse, Denmark.
| | | | - Aloys C M Kroes
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Javier Buesa
- Department of Microbiology and Ecology, Faculty of Medicine, University of Valencia, Valencia, Spain.
| | - Judy Breuer
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, United Kingdom.
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Jutte J C de Vries
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
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Santiago-Rodriguez TM, Hollister EB. Potential Applications of Human Viral Metagenomics and Reference Materials: Considerations for Current and Future Viruses. Appl Environ Microbiol 2020; 86:e01794-20. [PMID: 32917759 PMCID: PMC7642086 DOI: 10.1128/aem.01794-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Viruses are ubiquitous particles comprising genetic material that can infect bacteria, archaea, and fungi, as well as human and other animal cells. Given that determining virus composition and function in association with states of human health and disease is of increasing interest, we anticipate that the field of viral metagenomics will continue to expand and be applied in a variety of areas ranging from surveillance to discovery and will rely heavily upon the continued development of reference materials and databases. Information regarding viral composition and function readily translates into biological and clinical applications, including the rapid sequence identification of pathogenic viruses in various sample types. However, viral metagenomic approaches often lack appropriate standards and reference materials to enable cross-study comparisons and assess potential biases which can be introduced at the various stages of collection, storage, processing, and sequence analysis. In addition, implementation of appropriate viral reference materials can aid in the benchmarking of current and development of novel assays for virus identification, discovery, and surveillance. As the field of viral metagenomics expands and standardizes, results will continue to translate into diverse applications.
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Perlejewski K, Bukowska-Ośko I, Rydzanicz M, Dzieciątkowski T, Zakrzewska-Pniewska B, Podlecka-Piętowska A, Filipiak A, Barć K, Caraballo Cortés K, Pawełczyk A, Radkowski M, Laskus T. Search for viral agents in cerebrospinal fluid in patients with multiple sclerosis using real-time PCR and metagenomics. PLoS One 2020; 15:e0240601. [PMID: 33112911 PMCID: PMC7592794 DOI: 10.1371/journal.pone.0240601] [Citation(s) in RCA: 4] [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: 03/29/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic, immune-mediated demyelinating disease of the central nervous system of unclear etiology, but there is some evidence that viral infections could be responsible for triggering autoimmune mechanisms against myelin. We searched for viral RNA and DNA in cerebrospinal fluid (CSF) of 34 MS patients and 13 controls using RT-PCR/PCR against common neurotropic viruses. In addition, shotgun DNA- and RNA-based metagenomics were done in 13 MS patients and 4 controls. Specific quantitative real-time RT-PCR/PCR testing revealed the presence of viral nucleic acid in seven (20.59%) MS patients and in one (7.69%) control patient. In MS patients the most frequently detected was human herpesvirus type 6 (HHV-6; 3 cases; 8.82%); followed by Epstein-Barr virus (EBV; 2 cases; 5.88%), varicella zoster virus (VZV; 1 case; 2.94%) and Enterovirus (EV; 1 case; 2.94%). The single identified virus among controls was EBV (7.69%). DNA and RNA metagenomic assays did not identify any known eukaryotic viruses even though three of the analyzed samples were low-level positive by specific quantitative real-time PCR. In conclusion, we detected the presence of Herpesviridae and occasionally Enteroviridae in CSF from patients with MS but their prevalence was not significantly higher than among controls. Metagenomic analysis seems to be less sensitive than real-time RT-PCR/PCR and it did not detect any potential viral pathogens.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
- * E-mail:
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of the Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | | | | | - Agata Filipiak
- University Clinical Center of Medical University of Warsaw, Medical University of Warsaw, Warsaw, Poland
| | - Krzysztof Barć
- University Clinical Center of Medical University of Warsaw, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
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Shen H, Shen D, Song H, Wu X, Xu C, Su G, Liu C, Zhang J. Clinical assessment of the utility of metagenomic next-generation sequencing in pediatric patients of hematology department. Int J Lab Hematol 2020; 43:244-249. [PMID: 33099872 DOI: 10.1111/ijlh.13370] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/27/2020] [Accepted: 09/30/2020] [Indexed: 01/05/2023]
Abstract
INTRODUCTION Metagenomic Next-Generation Sequencing (mNGS) is an emerging technique for microbial identification and diagnosis of infectious diseases. The clinical utility of mNGS, especially its real-world impact on antimicrobial treatment and patient outcome has not been systematically evaluated. METHODS We prospectively assessed the effectiveness of mNGS in 70 febrile inpatients with suspected infections at Hematology department of the Children's Hospital, National Clinical Research Center for Child Health. 69/70 patients were given empirical antibiotics prior to mNGS. A total of 104 samples (62 plasma, 34 throat swabs, 4 bone marrow, 4 bronchoalveolar lavage) were collected on day 1-28 (mean 6.9) following symptom onset and underwent mNGS testing. RESULTS Traditional microbiological tests discovered causal microorganisms in 5/70 (7.14%) patients, which were also detected by mNGS. In addition, mNGS reported possible pathogens when routine tests were negative. Antibiotics were adjusted accordingly in 55/70 (78.6%) patients that led to improvement/relief of symptoms within 3 days. In contrast, mNGS results were considered irrelevant in 15/70 (21.4%) patients by a board of clinicians, based on biochemical, serological, imaging evidence, and experiences. CONCLUSION mNGS expanded the capacity of pathogen detection and made a positive impact on clinical management of suspected infections through (a) differential diagnosis which may rule out infectious diseases and (b) adjustment or de-escalation of empirical antibiotics.
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Affiliation(s)
- Heping Shen
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Diying Shen
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Hua Song
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Xueqin Wu
- Hangzhou Matridx Biotechnology Co., Ltd, Hangzhou, China
| | - Cong Xu
- Hangzhou Matridx Biotechnology Co., Ltd, Hangzhou, China
| | - Guangyu Su
- Hangzhou Matridx Biotechnology Co., Ltd, Hangzhou, China
| | - Chao Liu
- Hangzhou Matridx Biotechnology Co., Ltd, Hangzhou, China
| | - Jingying Zhang
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
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Keller E, Brandi G, Winklhofer S, Imbach LL, Kirschenbaum D, Frontzek K, Steiger P, Dietler S, Haeberlin M, Willms J, Porta F, Waeckerlin A, Huber M, Abela IA, Lutterotti A, Stippich C, Globas C, Varga Z, Jelcic I. Large and Small Cerebral Vessel Involvement in Severe COVID-19: Detailed Clinical Workup of a Case Series. Stroke 2020; 51:3719-3722. [PMID: 33054673 PMCID: PMC7678671 DOI: 10.1161/strokeaha.120.031224] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Supplemental Digital Content is available in the text. Case series indicating cerebrovascular disorders in coronavirus disease 2019 (COVID-19) have been published. Comprehensive workups, including clinical characteristics, laboratory, electroencephalography, neuroimaging, and cerebrospinal fluid findings, are needed to understand the mechanisms.
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Affiliation(s)
- Emanuela Keller
- Neurocritical Care Unit, Department of Neurosurgery and Institute of Intensive Care Medicine (E.K.), University Hospital and University of Zurich, Switzerland
| | - Giovanna Brandi
- Institute of Intensive Care Medicine (G.B., P.S., S.D., J.W.), University Hospital and University of Zurich, Switzerland
| | - Sebastian Winklhofer
- Department of Neuroradiology (S.W., C.S.), University Hospital and University of Zurich, Switzerland
| | - Lukas L Imbach
- Department of Neurology (L.L.I., M. Haeberlin), University Hospital and University of Zurich, Switzerland
| | - Daniel Kirschenbaum
- Department of Neuropathology (D.K., K.F.), University Hospital and University of Zurich, Switzerland
| | - Karl Frontzek
- Department of Neuropathology (D.K., K.F.), University Hospital and University of Zurich, Switzerland
| | - Peter Steiger
- Institute of Intensive Care Medicine (G.B., P.S., S.D., J.W.), University Hospital and University of Zurich, Switzerland
| | - Sabeth Dietler
- Institute of Intensive Care Medicine (G.B., P.S., S.D., J.W.), University Hospital and University of Zurich, Switzerland
| | - Marcellina Haeberlin
- Department of Neurology (L.L.I., M. Haeberlin), University Hospital and University of Zurich, Switzerland
| | - Jan Willms
- Institute of Intensive Care Medicine (G.B., P.S., S.D., J.W.), University Hospital and University of Zurich, Switzerland
| | - Francesca Porta
- Intensive Care Unit, Graubuenden Cantonal Hospital, Chur, Switzerland (F.P., A.W.)
| | - Adrian Waeckerlin
- Intensive Care Unit, Graubuenden Cantonal Hospital, Chur, Switzerland (F.P., A.W.)
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Switzerland (M. Huber)
| | - Irene A Abela
- Department of Infectious Diseases and Hospital Epidemiology (I.A.A.), University Hospital and University of Zurich, Switzerland
| | - Andreas Lutterotti
- Neuroimmunology and Multiple Sclerosis Research Section (A.L., I.J.), University Hospital and University of Zurich, Switzerland
| | - Christoph Stippich
- Department of Neuroradiology (S.W., C.S.), University Hospital and University of Zurich, Switzerland
| | - Christoph Globas
- Stroke Unit, Department of Neurology (C.G.), University Hospital and University of Zurich, Switzerland
| | - Zsuzsanna Varga
- Department of Pathology and Molecular Pathology (Z.V.), University Hospital and University of Zurich, Switzerland
| | - Ilijas Jelcic
- Neuroimmunology and Multiple Sclerosis Research Section (A.L., I.J.), University Hospital and University of Zurich, Switzerland
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Perlejewski K, Pawełczyk A, Bukowska-Ośko I, Rydzanicz M, Dzieciątkowski T, Paciorek M, Makowiecki M, Caraballo Cortés K, Grochowska M, Radkowski M, Laskus T. Search for Viral Infections in Cerebrospinal Fluid From Patients With Autoimmune Encephalitis. Open Forum Infect Dis 2020; 7:ofaa468. [PMID: 33209955 PMCID: PMC7643957 DOI: 10.1093/ofid/ofaa468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/30/2020] [Indexed: 12/19/2022] Open
Abstract
Background It has been reported that virus-mediated brain tissue damage can lead to autoimmune encephalitis (AE) characterized by the presence of antibodies against neuronal surface antigens. In the study, we investigate the presence of viruses in cerebrospinal fluid (CSF) from patients with AE using reverse transcription polymerase chain reaction (RT-PCR)/PCR and shotgun metagenomics. Methods CSF samples collected from 200 patients with encephalitis were tested for the presence of antibodies against antiglutamate receptor (NMDAR), contactin-associated protein 2 (CASPR2), glutamate receptors (type AMPA1/2), leucine-rich glioma-inactivated protein 1 (LGI1), dipeptidyl aminopeptidase-like protein 6 (DPPX), and GABA B receptor, and those found positive were further analyzed with real-time RT-PCR/PCR for common viral neuroinfections and shotgun DNA- and RNA-based metagenomics. Results Autoantibodies against neuronal cells were detected in CSF from 8 individuals (4% of all encephalitis patients): 7 (3.5%) had anti-NMDAR and 1 (0.5%) had anti-GABA B. RT-PCR/PCR identified human herpes virus type 1 (HSV-1; 300 copies/mL) and the representative of Enterovirus genus (550 copies/mL) in 1 patient each. Torque teno virus (TTV) was found in another patient using metagenomic analysis, and its presence was confirmed by specific PCR. Conclusions We detected the presence of HSV, TTV, and Enterovirus genus in CSF samples from 3 out of 8 AE patients. These findings support the concept of viral involvement in the pathogenesis of this disease.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | | | | | - Marcin Paciorek
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Michał Makowiecki
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marta Grochowska
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
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Sabatier M, Bal A, Destras G, Regue H, Quéromès G, Cheynet V, Lina B, Bardel C, Brengel-Pesce K, Navratil V, Josset L. Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms 2020; 8:E1539. [PMID: 33036303 PMCID: PMC7601816 DOI: 10.3390/microorganisms8101539] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022] Open
Abstract
Viral metagenomics next-generation sequencing (mNGS) is increasingly being used to characterize the human virome. The impact of viral nucleic extraction on virome profiling has been poorly studied. Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods used for viral mNGS: two automated platforms (eMAG; MagNA Pure 24, MP24) and the manual QIAamp Viral RNA Mini Kit (QIAamp). Clinical respiratory samples (positive for Respiratory Syncytial Virus or Herpes Simplex Virus), one mock sample (including five viruses isolated from respiratory samples), and a no-template control (NTC) were extracted and processed through an mNGS workflow. QIAamp yielded a lower proportion of viral reads for both clinical and mock samples. The sample cross-contamination was higher when using MP24, with up to 36.09% of the viral reads mapping to mock viruses in the NTC (vs. 1.53% and 1.45% for eMAG and QIAamp, respectively). The highest number of viral reads mapping to bacteriophages in the NTC was found with QIAamp, suggesting reagent contamination. Our results highlight the importance of the extraction method choice for accurate virome characterization.
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Affiliation(s)
- Marina Sabatier
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Grégory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
| | - Grégory Quéromès
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
| | - Valérie Cheynet
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Claire Bardel
- Université Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, F-69100 Villeurbanne, France;
| | - Karen Brengel-Pesce
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Université Claude Bernard Lyon 1, F-69000 Lyon, France;
- European Virus Bioinformatics Center, Leutragraben 1, D-07743 Jena, Germany
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
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Ong CWM, Migliori GB, Raviglione M, MacGregor-Skinner G, Sotgiu G, Alffenaar JW, Tiberi S, Adlhoch C, Alonzi T, Archuleta S, Brusin S, Cambau E, Capobianchi MR, Castilletti C, Centis R, Cirillo DM, D'Ambrosio L, Delogu G, Esposito SMR, Figueroa J, Friedland JS, Ho BCH, Ippolito G, Jankovic M, Kim HY, Rosales Klintz S, Ködmön C, Lalle E, Leo YS, Leung CC, Märtson AG, Melazzini MG, Najafi Fard S, Penttinen P, Petrone L, Petruccioli E, Pontali E, Saderi L, Santin M, Spanevello A, van Crevel R, van der Werf MJ, Visca D, Viveiros M, Zellweger JP, Zumla A, Goletti D. Epidemic and pandemic viral infections: impact on tuberculosis and the lung: A consensus by the World Association for Infectious Diseases and Immunological Disorders (WAidid), Global Tuberculosis Network (GTN), and members of the European Society of Clinical Microbiology and Infectious Diseases Study Group for Mycobacterial Infections (ESGMYC). Eur Respir J 2020; 56:2001727. [PMID: 32586885 PMCID: PMC7527651 DOI: 10.1183/13993003.01727-2020] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 06/12/2020] [Indexed: 01/08/2023]
Abstract
Major epidemics, including some that qualify as pandemics, such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), HIV, influenza A (H1N1)pdm/09 and most recently COVID-19, affect the lung. Tuberculosis (TB) remains the top infectious disease killer, but apart from syndemic TB/HIV little is known regarding the interaction of viral epidemics and pandemics with TB. The aim of this consensus-based document is to describe the effects of viral infections resulting in epidemics and pandemics that affect the lung (MERS, SARS, HIV, influenza A (H1N1)pdm/09 and COVID-19) and their interactions with TB. A search of the scientific literature was performed. A writing committee of international experts including the European Centre for Disease Prevention and Control Public Health Emergency (ECDC PHE) team, the World Association for Infectious Diseases and Immunological Disorders (WAidid), the Global Tuberculosis Network (GTN), and members of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Mycobacterial Infections (ESGMYC) was established. Consensus was achieved after multiple rounds of revisions between the writing committee and a larger expert group. A Delphi process involving the core group of authors (excluding the ECDC PHE team) identified the areas requiring review/consensus, followed by a second round to refine the definitive consensus elements. The epidemiology and immunology of these viral infections and their interactions with TB are discussed with implications for diagnosis, treatment and prevention of airborne infections (infection control, viral containment and workplace safety). This consensus document represents a rapid and comprehensive summary on what is known on the topic.
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Affiliation(s)
- Catherine Wei Min Ong
- Dept of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore
- These authors contributed equally
- Members of ESGMYC
| | - Giovanni Battista Migliori
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri IRCCS, Tradate, Italy
- These authors contributed equally
| | - Mario Raviglione
- Centre for Multidisciplinary Research in Health Science, University of Milan, Milan, Italy
- Global Studies Institute, University of Geneva, Geneva, Switzerland
| | | | - Giovanni Sotgiu
- Clinical Epidemiology and Medical Statistics Unit, Dept of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Jan-Willem Alffenaar
- Sydney Pharmacy School, University of Sydney, Sydney, Australia
- Westmead Hospital, Sydney, Australia
- Marie Bashir Institute of Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
- Members of ESGMYC
| | - Simon Tiberi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Division of Infection, Royal London Hospital, Barts Health NHS Trust, London, UK
- Members of ESGMYC
| | - Cornelia Adlhoch
- Public Health Emergency Team, European Centre for Disease Prevention and Control, Stockholm, Sweden
- European Centre for Disease Prevention and Control Public Health Emergency team co-authors
| | - Tonino Alonzi
- Translational Research Unit, Epidemiology and Preclinical Research Dept, "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS, Rome, Italy
| | - Sophia Archuleta
- Dept of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Sergio Brusin
- Public Health Emergency Team, European Centre for Disease Prevention and Control, Stockholm, Sweden
- European Centre for Disease Prevention and Control Public Health Emergency team co-authors
| | - Emmanuelle Cambau
- AP-HP-Lariboisiere, Bacteriologie, Laboratory Associated to the National Reference Centre for Mycobacteria, IAME UMR1137, INSERM, University of Paris, Paris, France
- Members of ESGMYC
| | - Maria Rosaria Capobianchi
- Laboratory of Virology, Epidemiology and Preclinical Research Dept, "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS, Rome, Italy
| | - Concetta Castilletti
- Laboratory of Virology, Epidemiology and Preclinical Research Dept, "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS, Rome, Italy
| | - Rosella Centis
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri IRCCS, Tradate, Italy
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Members of ESGMYC
| | | | - Giovanni Delogu
- Università Cattolica Sacro Cuore, Roma, Italy
- Mater Olbia Hospital, Olbia, Italy
- Members of ESGMYC
| | - Susanna M R Esposito
- Pediatric Clinic, Pietro Barilla Children's Hospital, University of Parma, Parma, Italy
| | | | - Jon S Friedland
- St George's, University of London, London, UK
- Members of ESGMYC
| | - Benjamin Choon Heng Ho
- Tuberculosis Control Unit, Dept of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Giuseppe Ippolito
- Scientific Direction, "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS, Rome, Italy
| | - Mateja Jankovic
- School of Medicine, University of Zagreb and Clinic for Respiratory Diseases, University Hospital Center Zagreb, Zagreb, Croatia
- Members of ESGMYC
| | - Hannah Yejin Kim
- Sydney Pharmacy School, University of Sydney, Sydney, Australia
- Westmead Hospital, Sydney, Australia
- Marie Bashir Institute of Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
| | - Senia Rosales Klintz
- Public Health Emergency Team, European Centre for Disease Prevention and Control, Stockholm, Sweden
- European Centre for Disease Prevention and Control Public Health Emergency team co-authors
| | - Csaba Ködmön
- Public Health Emergency Team, European Centre for Disease Prevention and Control, Stockholm, Sweden
- European Centre for Disease Prevention and Control Public Health Emergency team co-authors
| | - Eleonora Lalle
- Laboratory of Virology, Epidemiology and Preclinical Research Dept, "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS, Rome, Italy
| | - Yee Sin Leo
- National Centre for Infectious Diseases, Singapore
| | - Chi-Chiu Leung
- Hong Kong Tuberculosis, Chest and Heart Diseases Association, Wanchai, Hong Kong, China
| | - Anne-Grete Märtson
- Dept of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Saeid Najafi Fard
- Translational Research Unit, Epidemiology and Preclinical Research Dept, "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS, Rome, Italy
| | - Pasi Penttinen
- Public Health Emergency Team, European Centre for Disease Prevention and Control, Stockholm, Sweden
- European Centre for Disease Prevention and Control Public Health Emergency team co-authors
| | - Linda Petrone
- Translational Research Unit, Epidemiology and Preclinical Research Dept, "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS, Rome, Italy
| | - Elisa Petruccioli
- Translational Research Unit, Epidemiology and Preclinical Research Dept, "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS, Rome, Italy
| | | | - Laura Saderi
- Clinical Epidemiology and Medical Statistics Unit, Dept of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Miguel Santin
- Dept of Infectious Diseases, Bellvitge University Hospital-Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
- Dept of Clinical Science, University of Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
- Members of ESGMYC
| | - Antonio Spanevello
- Division of Pulmonary Rehabilitation, Istituti Clinici Scientifici Maugeri, IRCCS, Tradate, Italy
- Dept of Medicine and Surgery, Respiratory Diseases, University of Insubria, Varese-Como, Italy
| | - Reinout van Crevel
- Radboudumc Center for Infectious Diseases, Radboud Institute for Health Sciences, Radboudumc, Nijmegen, The Netherlands
- Centre for Tropical Medicine and Global Health, Nuffield Dept of Medicine, University of Oxford, Oxford, UK
- Members of ESGMYC
| | - Marieke J van der Werf
- Public Health Emergency Team, European Centre for Disease Prevention and Control, Stockholm, Sweden
- European Centre for Disease Prevention and Control Public Health Emergency team co-authors
| | - Dina Visca
- Division of Pulmonary Rehabilitation, Istituti Clinici Scientifici Maugeri, IRCCS, Tradate, Italy
- Dept of Medicine and Surgery, Respiratory Diseases, University of Insubria, Varese-Como, Italy
| | - Miguel Viveiros
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, NOVA University of Lisbon, Lisbon, Portugal
- Members of ESGMYC
| | | | - Alimuddin Zumla
- Dept of Infection, Division of Infection and Immunity, University College London and NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, London, UK
| | - Delia Goletti
- Translational Research Unit, Epidemiology and Preclinical Research Dept, "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS, Rome, Italy
- Saint Camillus International University of Health and Medical Sciences, Rome, Italy
- Members of ESGMYC
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34
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Perlejewski K, Bukowska-Ośko I, Rydzanicz M, Pawełczyk A, Caraballo Cortѐs K, Osuch S, Paciorek M, Dzieciątkowski T, Radkowski M, Laskus T. Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations. Sci Rep 2020; 10:16173. [PMID: 32999423 PMCID: PMC7528011 DOI: 10.1038/s41598-020-73156-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/07/2020] [Indexed: 12/12/2022] Open
Abstract
Identification of pathogens causing viral encephalitis remains challenging, and in over 50% of cases the etiologic factor remains undetermined. Next-generation sequencing (NGS) based metagenomics has been successfully used to detect novel and rare infections, but its value for routine diagnosis of encephalitis remains unclear. The aim of the present study was to determine the sensitivity of shotgun metagenomic sequencing protocols, which include preamplification, and testing it against cerebrospinal fluid (CSF) samples from encephalitis patients. For sensitivity testing HIV and HBV positive sera were serially diluted in CSF from an uninfected patient. NGS repeatedly detected HIV and HBV sequences present at concentrations from 105 to 102 and from 105 to 10 viral copies/reaction, respectively. However, when the same protocols were applied to RT-PCR/PCR positive CSF samples from 6 patients with enteroviral encephalitis (median viral load 47 copies/ml) and 15 patients with HSV, CMV or VZV encephalitis (median viral load 148 copies/ml), only 7 (28.6%) were identified as positive. In conclusions, while NGS has the advantage of being able to identify a wide range of potential pathogens it seems to be less sensitive compared to the standard amplification-based assays in the diagnosis of encephalitis, where low viral loads are common.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland.
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of the Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortѐs
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Sylwia Osuch
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marcin Paciorek
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | | | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
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35
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Carbo EC, Buddingh EP, Karelioti E, Sidorov IA, Feltkamp MC, Borne PAVD, Verschuuren JJ, Kroes AC, Claas EC, de Vries JJ. Improved diagnosis of viral encephalitis in adult and pediatric hematological patients using viral metagenomics. J Clin Virol 2020; 130:104566. [DOI: 10.1016/j.jcv.2020.104566] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/23/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023]
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36
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Au CC, Hon KL, Leung AKC, Torres AR. Childhood Infectious Encephalitis: An Overview of Clinical Features, Investigations, Treatment, and Recent Patents. RECENT PATENTS ON INFLAMMATION & ALLERGY DRUG DISCOVERY 2020; 14:156-165. [PMID: 33238854 DOI: 10.2174/1872213x14999201124195724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Infectious encephalitis is a serious and challenging condition to manage. This overview summarizes the current literature regarding the etiology, clinical manifestations, diagnosis, management, and recent patents of acute childhood infectious encephalitis. METHODS We used PubMed Clinical Queries as a search engine and used keywords of "encephalitis" AND "childhood" Patents were searched using the key term "encephalitis" in google.patents.- com and patentsonline.com. RESULTS Viral encephalitis is the most common cause of acute infectious encephalitis in children. In young children, the clinical manifestations can be non-specific. Provision of empiric antimicrobial therapy until a specific infectious organism has been identified, which in most cases includes acyclovir, is the cornerstone of therapy. Advanced investigation tools, including nucleic acid-based test panel and metagenomic next-generation sequencing, improve the diagnostic yield of identifying an infectious organism. Supportive therapy includes adequate airway and oxygenation, fluid and electrolyte balance, cerebral perfusion pressure support, and seizure control. Recent patents are related to the diagnosis, treatment, and prevention of acute infectious encephalitis. CONCLUSION Viral encephalitis is the most common cause of acute infectious encephalitis in children and is associated with significant morbidity. Recent advances in understanding the genetic basis and immunological correlation of infectious encephalitis may improve treatment. Third-tier diagnostic tests may be incorporated into clinical practice. Treatment is targeted at the infectious process but remains mostly supportive. However, specific antimicrobial agents and vaccines development is ongoing.
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Affiliation(s)
- Cheuk C Au
- Department of Paediatrics and Adolescent Medicine, The Hong Kong Children's Hospital, Kowloon Bay, Kowloon, Hong Kong
| | - Kam L Hon
- Department of Paediatrics and Adolescent Medicine, The Hong Kong Children's Hospital, Kowloon Bay, Kowloon, Hong Kong
| | - Alexander K C Leung
- Department of Pediatrics, The University of Calgary and The Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Alcy R Torres
- Department of Pediatrics, Division of Pediatric Neurology, Pediatric Traumatic Brain Injury Program, Associate Professor of Pediatrics and Neurology, Boston University, School of Medicine, Boston, MA, United States
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37
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Lieberman JA, Naureckas Li C, Lamb GS, Kane DA, Stewart MK, Mamedov RA, Cookson BT, Salipante SJ. Case Report: Comparison of Plasma Metagenomics to Bacterial PCR in a Case of Prosthetic Valve Endocarditis. Front Pediatr 2020; 8:575674. [PMID: 33489996 PMCID: PMC7819283 DOI: 10.3389/fped.2020.575674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Molecular assays for infectious diseases have emerged as important clinical decision-making tools. Unbiased, metagenomic next-generation sequencing is a novel approach holding promise to detect pathogens missed by conventional modalities and to deconvolute admixed nucleic acid sequences from polymicrobial infections in order to identify constituent pathogens. Recent studies have raised concerns about the clinical impact of metagenomics assays and whether their expense is justified. Here, we report a case of polyclonal Streptococcus cristatus endocarditis in a 14-year-old woman with a history of Tetralogy of Fallot. Three sets of admission blood cultures and a commercial plasma metagenomics assay were negative for pathogens, despite persistent vegetations observed on the valve during a later procedure. Multiple strains of Streptococcus cristatus were identified from the explanted valve by amplicon-based 16S rRNA sequencing, confirming the patient had received appropriate antibiotic therapy. This case highlights limitations in the use and interpretation of clinical metagenomics for infectious disease diagnosis and indicates that the clinical yield of these tools may depend upon infection type and anatomic location.
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Affiliation(s)
- Joshua A Lieberman
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, United States
| | - Caitlin Naureckas Li
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States
| | - Gabriella S Lamb
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States
| | - David A Kane
- Department of Cardiology, Boston Children's Hospital, Boston, MA, United States
| | - Mary K Stewart
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, United States
| | - Ruslan A Mamedov
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, United States
| | - Brad T Cookson
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, United States.,Department of Microbiology, University of Washington, Seattle, WA, United States
| | - Stephen J Salipante
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, United States
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