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Fuentenebro Navas D, Steens JA, de Lannoy C, Noordijk B, Pfeffer M, de Ridder D, H.J. Staals R, Schmid S. Nanopores Reveal the Stoichiometry of Single Oligoadenylates Produced by Type III CRISPR-Cas. ACS NANO 2024; 18:16505-16515. [PMID: 38875527 PMCID: PMC11223493 DOI: 10.1021/acsnano.3c11769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
Cyclic oligoadenylates (cOAs) are small second messenger molecules produced by the type III CRISPR-Cas system as part of the prokaryotic immune response. The role of cOAs is to allosterically activate downstream effector proteins that induce dormancy or cell death, and thus abort viral spread through the population. Interestingly, different type III systems have been reported to utilize different cOA stoichiometries (with 3 to 6 adenylate monophosphates). However, so far, their characterization has only been possible in bulk and with sophisticated equipment, while a portable assay with single-molecule resolution has been lacking. Here, we demonstrate the label-free detection of single cOA molecules using a simple protein nanopore assay. It sensitively identifies the stoichiometry of individual cOA molecules and their mixtures from synthetic and enzymatic origin. To achieve this, we trained a convolutional neural network (CNN) and validated it with a series of experiments on mono- and polydisperse cOA samples. Ultimately, we determined the stoichiometric composition of cOAs produced enzymatically by the CRISPR type III-A and III-B variants of Thermus thermophilus and confirmed the results by liquid chromatography-mass spectroscopy (LC-MS). Interestingly, both variants produce cOAs of nearly identical composition (within experimental uncertainties), and we discuss the biological implications of this finding. The presented nanopore-CNN workflow with single cOA resolution can be adapted to many other signaling molecules (including eukaryotic ones), and it may be integrated into portable handheld devices with potential point-of-care applications.
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Affiliation(s)
- David Fuentenebro Navas
- Laboratory
of Biophysics, Wageningen University and
Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Jurre A. Steens
- Laboratory
of Microbiology, Wageningen University and
Research, Stippeneng
4, 6708WE Wageningen, The Netherlands
| | - Carlos de Lannoy
- Bioinformatics
Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
- Department
of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Ben Noordijk
- Bioinformatics
Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Michael Pfeffer
- Department
of Chemistry, University of Basel, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Dick de Ridder
- Bioinformatics
Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Raymond H.J. Staals
- Laboratory
of Microbiology, Wageningen University and
Research, Stippeneng
4, 6708WE Wageningen, The Netherlands
| | - Sonja Schmid
- Laboratory
of Biophysics, Wageningen University and
Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
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2
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Baron R, Haick H. Mobile Diagnostic Clinics. ACS Sens 2024; 9:2777-2792. [PMID: 38775426 PMCID: PMC11217950 DOI: 10.1021/acssensors.4c00636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 06/29/2024]
Abstract
This article reviews the revolutionary impact of emerging technologies and artificial intelligence (AI) in reshaping modern healthcare systems, with a particular focus on the implementation of mobile diagnostic clinics. It presents an insightful analysis of the current healthcare challenges, including the shortage of healthcare workers, financial constraints, and the limitations of traditional clinics in continual patient monitoring. The concept of "Mobile Diagnostic Clinics" is introduced as a transformative approach where healthcare delivery is made accessible through the incorporation of advanced technologies. This approach is a response to the impending shortfall of medical professionals and the financial and operational burdens conventional clinics face. The proposed mobile diagnostic clinics utilize digital health tools and AI to provide a wide range of services, from everyday screenings to diagnosis and continual monitoring, facilitating remote and personalized care. The article delves into the potential of nanotechnology in diagnostics, AI's role in enhancing predictive analytics, diagnostic accuracy, and the customization of care. Furthermore, the article discusses the importance of continual, noninvasive monitoring technologies for early disease detection and the role of clinical decision support systems (CDSSs) in personalizing treatment guidance. It also addresses the challenges and ethical concerns of implementing these advanced technologies, including data privacy, integration with existing healthcare infrastructure, and the need for transparent and bias-free AI systems.
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Affiliation(s)
- Roni Baron
- Department
of Biomedical Engineering, Technion—Israel
Institute of Technology, Haifa 3200003, Israel
| | - Hossam Haick
- Department
of Chemical Engineering and the Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 3200003, Israel
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3
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Willis CRG, Calvaruso M, Angeloni D, Baatout S, Benchoua A, Bereiter-Hahn J, Bottai D, Buchheim JI, Carnero-Diaz E, Castiglioni S, Cavalieri D, Ceccarelli G, Chouker A, Cialdai F, Ciofani G, Coppola G, Cusella G, Degl'Innocenti A, Desaphy JF, Frippiat JP, Gelinsky M, Genchi G, Grano M, Grimm D, Guignandon A, Herranz R, Hellweg C, Iorio CS, Karapantsios T, van Loon J, Lulli M, Maier J, Malda J, Mamaca E, Morbidelli L, Osterman A, Ovsianikov A, Pampaloni F, Pavezlorie E, Pereda-Campos V, Przybyla C, Rettberg P, Rizzo AM, Robson-Brown K, Rossi L, Russo G, Salvetti A, Risaliti C, Santucci D, Sperl M, Tabury K, Tavella S, Thielemann C, Willaert R, Monici M, Szewczyk NJ. How to obtain an integrated picture of the molecular networks involved in adaptation to microgravity in different biological systems? NPJ Microgravity 2024; 10:50. [PMID: 38693246 PMCID: PMC11063135 DOI: 10.1038/s41526-024-00395-3] [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: 12/19/2022] [Accepted: 04/08/2024] [Indexed: 05/03/2024] Open
Abstract
Periodically, the European Space Agency (ESA) updates scientific roadmaps in consultation with the scientific community. The ESA SciSpacE Science Community White Paper (SSCWP) 9, "Biology in Space and Analogue Environments", focusses in 5 main topic areas, aiming to address key community-identified knowledge gaps in Space Biology. Here we present one of the identified topic areas, which is also an unanswered question of life science research in Space: "How to Obtain an Integrated Picture of the Molecular Networks Involved in Adaptation to Microgravity in Different Biological Systems?" The manuscript reports the main gaps of knowledge which have been identified by the community in the above topic area as well as the approach the community indicates to address the gaps not yet bridged. Moreover, the relevance that these research activities might have for the space exploration programs and also for application in industrial and technological fields on Earth is briefly discussed.
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Affiliation(s)
- Craig R G Willis
- School of Chemistry and Biosciences, Faculty of Life Sciences, University of Bradford, Bradford, United Kingdom
| | - Marco Calvaruso
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Cefalù, Italy
| | - Debora Angeloni
- Institute of Biorobotics, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Sarah Baatout
- Laboratory of Radiobiology, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | | | - Juergen Bereiter-Hahn
- Institute for Cell and Neurobiol. Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Daniele Bottai
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - Judith-Irina Buchheim
- Laboratory "Translational Research, Stress & Immunity", LMU University Hospital Munich, Munich, Germany
| | - Eugénie Carnero-Diaz
- Institute Systematic, Evolution, Biodiversity, Sorbonne University, NMNH, CNRS, EPHE, UA, Paris, France
| | - Sara Castiglioni
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | | | - Gabriele Ceccarelli
- Department of Public Health, Experimental Medicine and Forensic, University of Pavia, Pavia, Italy
| | - Alexander Chouker
- Laboratory "Translational Research, Stress & Immunity", LMU University Hospital Munich, Munich, Germany
| | - Francesca Cialdai
- ASAcampus Joint Laboratory, ASA Res. Div., DSBSC-University of Florence, Florence, Italy
| | - Gianni Ciofani
- Smart Bio-Interfaces, Istituto Italiano di Tecnologia, 56025, Pontedera, PI, Italy
| | - Giuseppe Coppola
- Institue of Applied Science and Intelligent Sistems - CNR, Naples, Italy
| | - Gabriella Cusella
- Department of Public Health, Experimental Medicine and Forensic, University of Pavia, Pavia, Italy
| | - Andrea Degl'Innocenti
- Smart Bio-Interfaces, Istituto Italiano di Tecnologia, 56025, Pontedera, PI, Italy
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Jean-Francois Desaphy
- Department of Precision and Regenerative Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Jean-Pol Frippiat
- Stress, Immunity, Pathogens Laboratory, SIMPA, Université de Lorraine, Nancy, France
| | - Michael Gelinsky
- Centre for Translational Bone, Joint & Soft Tissue Research, TU Dresden, Dresden, Germany
| | - Giada Genchi
- Smart Bio-Interfaces, Istituto Italiano di Tecnologia, 56025, Pontedera, PI, Italy
| | - Maria Grano
- Department of Precision and Regenerative Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Daniela Grimm
- Department of Microgravity and Translational Regenerative Medicine, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Alain Guignandon
- SAINBIOSE, INSERM U1059, Université Jean Monnet, F-42000, Saint-Etienne, France
| | - Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Christine Hellweg
- Radiation Biology Dept., Inst. of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | | | | | - Jack van Loon
- Amsterdam University Medical Center, ACTA/VU, Amsterdam, Netherlands
| | - Matteo Lulli
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Jeanette Maier
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Jos Malda
- Department of Orthopaedics, Univ. Med. Center Utrecht & Dept. Clinical Sciences, Utrecht Univ, Utrecht, The Netherlands
| | - Emina Mamaca
- European and International Affairs Dept, Ifremer centre Bretagne, Plouzané, France
| | | | - Andreas Osterman
- Max von Pettenkofer Institute, Virology, LMU Munich & DZIF, Partner Site Munich, Munich, Germany
| | - Aleksandr Ovsianikov
- 3D Printing and Biofabrication, Inst. Materials Science and Technology, TU Wien, Vienna, Austria
| | - Francesco Pampaloni
- Buchmann Inst. for Molecular Life Sciences, Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Elizabeth Pavezlorie
- Ludwig Boltzmann Inst. for Traumatology, Res. Center in Cooperation with AUVA, Vienna, Austria
| | - Veronica Pereda-Campos
- GSBMS/URU EVOLSAN - Medecine Evolutive, Université Paul Sabatier Toulouse III, Toulouse, France
| | - Cyrille Przybyla
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Palavas les Flots, France
| | - Petra Rettberg
- DLR, Institute of Aerospace Medicine, Research Group Astrobiology, Köln, Germany
| | - Angela Maria Rizzo
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Kate Robson-Brown
- Department of Engineering Mathematics, and Dept of Anthropology and Archaeology, University of Bristol, Bristol, UK
| | - Leonardo Rossi
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Giorgio Russo
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Cefalù, Italy
| | - Alessandra Salvetti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Chiara Risaliti
- ASAcampus Joint Laboratory, ASA Res. Div., DSBSC-University of Florence, Florence, Italy
| | - Daniela Santucci
- Center for Behavioural Sciences and Mental Health, Ist. Superiore Sanità, Rome, Italy
| | | | - Kevin Tabury
- Laboratory of Radiobiology, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Sara Tavella
- IRCCS Ospedale Policlinico San Martino and University of Genoa, DIMES, Genoa, Italy
| | | | - Ronnie Willaert
- Research Group NAMI and NANO, Vrije Universiteit Brussels, Brussels, Belgium
| | - Monica Monici
- ASAcampus Joint Laboratory, ASA Res. Div., DSBSC-University of Florence, Florence, Italy
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4
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Holzschuh A, Lerch A, Fakih BS, Aliy SM, Ali MH, Ali MA, Bruzzese DJ, Yukich J, Hetzel MW, Koepfli C. Using a mobile nanopore sequencing lab for end-to-end genomic surveillance of Plasmodium falciparum: A feasibility study. PLOS GLOBAL PUBLIC HEALTH 2024; 4:e0002743. [PMID: 38300956 PMCID: PMC10833559 DOI: 10.1371/journal.pgph.0002743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024]
Abstract
Genomic epidemiology holds promise for malaria control and elimination efforts, for example by informing on Plasmodium falciparum genetic diversity and prevalence of mutations conferring anti-malarial drug resistance. Limited sequencing infrastructure in many malaria-endemic areas prevents the rapid generation of genomic data. To address these issues, we developed and validated assays for P. falciparum nanopore sequencing in endemic sites using a mobile laboratory, targeting key antimalarial drug resistance markers and microhaplotypes. Using two multiplexed PCR reactions, we amplified six highly polymorphic microhaplotypes and ten drug resistance markers. We developed a bioinformatics workflow that allows genotyping of polyclonal malaria infections, including minority clones. We validated the panels on mock dried blood spot (DBS) and rapid diagnostic test (RDT) samples and archived DBS, demonstrating even, high read coverage across amplicons (range: 580x to 3,212x median coverage), high haplotype calling accuracy, and the ability to explore within-sample diversity of polyclonal infections. We field-tested the feasibility of rapid genotyping in Zanzibar in close collaboration with the local malaria elimination program using DBS and routinely collected RDTs as sample inputs. Our assay identified haplotypes known to confer resistance to known antimalarials in the dhfr, dhps and mdr1 genes, but no evidence of artemisinin partial resistance. Most infections (60%) were polyclonal, with high microhaplotype diversity (median HE = 0.94). In conclusion, our assays generated actionable data within a few days, and we identified current challenges for implementing nanopore sequencing in endemic countries to accelerate malaria control and elimination.
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Affiliation(s)
- Aurel Holzschuh
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
| | - Anita Lerch
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Bakar S. Fakih
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania
| | - Safia Mohammed Aliy
- Zanzibar Malaria Elimination Programme, Ministry of Health, Zanzibar, United Republic of Tanzania
| | - Mohamed Haji Ali
- Zanzibar Malaria Elimination Programme, Ministry of Health, Zanzibar, United Republic of Tanzania
| | - Mohamed Ali Ali
- Zanzibar Malaria Elimination Programme, Ministry of Health, Zanzibar, United Republic of Tanzania
| | - Daniel J. Bruzzese
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Joshua Yukich
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, United States of America
| | - Manuel W. Hetzel
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
| | - Cristian Koepfli
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
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5
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Andreescu M. Epigenetic Alterations That Are the Backbone of Immune Evasion in T-cell Malignancies. Cureus 2024; 16:e51662. [PMID: 38179322 PMCID: PMC10766007 DOI: 10.7759/cureus.51662] [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] [Accepted: 01/04/2024] [Indexed: 01/06/2024] Open
Abstract
Epigenetic alterations are heritable and enduring modifications in gene expression that play a pivotal role in immune evasion. These include alterations to noncoding RNA, DNA methylation, and histone modifications. DNA methylation plays a crucial role in normal cell growth and development but alterations in methylation patterns such as hypermethylation or hypomethylation can enable tumor and viral cells to evade host immune responses. Histone modifications can also inhibit immune responses by promoting the expression of genes involved in suppressing normal immune function. In the case of T-cell lymphoma, adult T-cell lymphomas (ATL) also undergo immune evasion through the exceptional function of its accessory and regulatory genes. Epigenetic therapies are emerging as a promising adjunct to traditional immunotherapy and chemotherapy regimens. Clinical trials are currently investigating the use of epigenetic therapies in combination with immunotherapies and chemotherapies for more effective treatment of ATL and other cancers. This review highlights epigenetic alterations that are widely found in T-cell malignancies.
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Lehman A, Ellis J, Nalintya E, Bahr NC, Loyse A, Rajasingham R. Advanced HIV disease: A review of diagnostic and prophylactic strategies. HIV Med 2023; 24:859-876. [PMID: 37041113 PMCID: PMC10642371 DOI: 10.1111/hiv.13487] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/13/2023] [Indexed: 04/13/2023]
Abstract
BACKGROUND Despite expanded access to antiretroviral therapy (ART) and the rollout of the World Health Organization's (WHO) 'test-and-treat' strategy, the proportion of people with HIV (PWH) presenting with advanced HIV disease (AHD) remains unchanged at approximately 30%. Fifty percent of persons with AHD report prior engagement to care. ART failure and insufficient retention in HIV care are major causes of AHD. People living with AHD are at high risk for opportunistic infections and death. In 2017, the WHO published guidelines for the management of AHD that included a comprehensive package of care for screening and prophylaxis of major opportunistic infections (OIs). In the interim, ART regimens have evolved: integrase inhibitors are first-line therapy globally, and the diagnostic landscape is evolving. The objective of this review is to highlight novel point-of-care (POC) diagnostics and treatment strategies that can facilitate OI screening and prophylaxis for persons with AHD. METHODS We reviewed the WHO guidelines for recommendations for persons with AHD. We summarized the scientific literature on current and emerging diagnostics, along with emerging treatment strategies for persons with AHD. We also highlight the key research and implementation gaps together with potential solutions. RESULTS While POC CD4 testing is being rolled out in order to identify persons with AHD, this alone is insufficient; implementation of the Visitect CD4 platform has been challenging given operational and test interpretation issues. Numerous non-sputum POC TB diagnostics are being evaluated, many with limited sensitivity. Though imperfect, these tests are designed to provide rapid results (within hours) and are relatively affordable for resource-poor settings. While novel POC diagnostics are being developed for cryptococcal infection, histoplasmosis and talaromycosis, implementation science studies are urgently needed to understand the clinical benefit of these tests in the routine care. CONCLUSIONS Despite progress with HIV treatment and prevention, a persistent 20%-30% of PWH present to care with AHD. Unfortunately, these persons with AHD continue to carry the burden of HIV-related morbidity and mortality. Investment in the development of additional POC or near-bedside CD4 platforms is urgently needed. Implementation of POC diagnostics theoretically could improve HIV retention in care and thereby reduce mortality by overcoming delays in laboratory testing and providing patients and healthcare workers with timely same-day results. However, in real-world scenarios, people with AHD have multiple comorbidities and imperfect follow-up. Pragmatic clinical trials are needed to understand whether these POC diagnostics can facilitate timely diagnosis and treatment, thereby improving clinical outcomes such as HIV retention in care.
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Affiliation(s)
- Alice Lehman
- Division of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jayne Ellis
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Nathan C. Bahr
- Division of Infectious Diseases, University of Kansas, Kansas City, Kansas, USA
| | - Angela Loyse
- Division of Infection and Immunity Research Institute, St George’s University of London, London, UK
| | - Radha Rajasingham
- Division of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, Minnesota, USA
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Montoro-Dasi L, Lorenzo-Rebenaque L, Marco-Fuertes A, Vega S, Marin C. Holistic Strategies to Control Salmonella Infantis: An Emerging Challenge in the European Broiler Sector. Microorganisms 2023; 11:1765. [PMID: 37512937 PMCID: PMC10386103 DOI: 10.3390/microorganisms11071765] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Salmonella spp. has been globally recognized as one of the leading causes of acute human bacterial gastroenteritis resulting from the consumption of animal-derived products. Salmonella Enteritidis, S. Typhimurium, and its monophasic variant are the main serovars responsible for human disease. However, a serovar known as S. Infantis has emerged as the fourth most prevalent serovar associated with human disease. A total of 95% of isolated S. Infantis serovars originate from broilers and their derived products. This serovar is strongly associated with an elevated antimicrobial (AMR) and multidrug resistance, a resistance to disinfectants, an increased tolerance to environmental mercury, a heightened virulence, and an enhanced ability to form biofilms and attach to host cells. Furthermore, this serovar harbors genes that confer resistance to colistin, a last-resort antibiotic in human medicine, and it has the potential to acquire additional transferable AMR against other critically important antimicrobials, posing a new and significant challenge to global public health. This review provides an overview of the current status of the S. Infantis serovar in the poultry sector, focusing on its key virulence factors, including its virulence genes, antimicrobial resistance, and biofilm formation. Additionally, novel holistic strategies for controlling S. Infantis along the entire food chain are presented in this review.
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Affiliation(s)
- Laura Montoro-Dasi
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Santiago Ramón y Cajal 20, 45115 Alfara del Patriarca, Valencia, Spain
| | - Laura Lorenzo-Rebenaque
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Santiago Ramón y Cajal 20, 45115 Alfara del Patriarca, Valencia, Spain
| | - Ana Marco-Fuertes
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Santiago Ramón y Cajal 20, 45115 Alfara del Patriarca, Valencia, Spain
| | - Santiago Vega
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Santiago Ramón y Cajal 20, 45115 Alfara del Patriarca, Valencia, Spain
| | - Clara Marin
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Santiago Ramón y Cajal 20, 45115 Alfara del Patriarca, Valencia, Spain
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8
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Edridge A, Namazzi R, Tebulo A, Mfizi A, Deijs M, Koekkoek S, de Wever B, van der Ende A, Umiwana J, de Jong MD, Jans J, Verhoeven-Duif N, Titulaer M, van Karnebeek C, Seydel K, Taylor T, Asiimwe-Kateera B, van der Hoek L, Kabayiza JC, Mallewa M, Idro R, Boele van Hensbroek M, van Woensel JBM. Viral, Bacterial, Metabolic, and Autoimmune Causes of Severe Acute Encephalopathy in Sub-Saharan Africa: A Multicenter Cohort Study. J Pediatr 2023; 258:113360. [PMID: 36828342 DOI: 10.1016/j.jpeds.2023.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/11/2023] [Accepted: 02/19/2023] [Indexed: 02/24/2023]
Abstract
OBJECTIVES To assess whether viral, bacterial, metabolic, and autoimmune diseases are missed by conventional diagnostics among children with severe acute encephalopathy in sub-Saharan Africa. STUDY DESIGN One hundred thirty-four children (6 months to 18 years) presenting with nontraumatic coma or convulsive status epilepticus to 1 of 4 medical referral centers in Uganda, Malawi, and Rwanda were enrolled between 2015 and 2016. Locally available diagnostic tests could be supplemented in 117 patients by viral, bacterial, and 16s quantitative polymerase chain reaction testing, metagenomics, untargeted metabolomics, and autoimmune immunohistochemistry screening. RESULTS Fourteen (12%) cases of viral encephalopathies, 8 (7%) cases of bacterial central nervous system (CNS) infections, and 4 (4%) cases of inherited metabolic disorders (IMDs) were newly identified by additional diagnostic testing as the most likely cause of encephalopathy. No confirmed cases of autoimmune encephalitis were found. Patients for whom additional diagnostic testing aided causal evaluation (aOR 3.59, 90% CI 1.57-8.36), patients with a viral CNS infection (aOR 7.91, 90% CI 2.49-30.07), and patients with an IMD (aOR 9.10, 90% CI 1.37-110.45) were at increased risk for poor outcome of disease. CONCLUSIONS Viral and bacterial CNS infections and IMDs are prevalent causes of severe acute encephalopathy in children in Uganda, Malawi, and Rwanda that are missed by conventional diagnostics and are associated with poor outcome of disease. Improved diagnostic capacity may increase diagnostic yield and might improve outcome of disease.
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Affiliation(s)
- Arthur Edridge
- Amsterdam Centre for Global Child Health, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
| | - Ruth Namazzi
- Department of Paediatrics, Makerere University, Kampala, Uganda
| | - Andrew Tebulo
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Anan Mfizi
- Department of Paediatrics, University Teaching Hospital of Kigali, Kigali, Rwanda
| | - Martin Deijs
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Sylvie Koekkoek
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Bob de Wever
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Arie van der Ende
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeanine Umiwana
- Department of Paediatrics, University Teaching Hospital of Kigali, Kigali, Rwanda
| | - Menno D de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Judith Jans
- Laboratory of Metabolic Diseases, UMC Utrecht, Utrecht, The Netherlands
| | | | | | - Clara van Karnebeek
- Departments of Pediatrics and Human Genetics, Emma Center for Personalized Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Karl Seydel
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi; Department of Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, MI
| | - Terrie Taylor
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi; Department of Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, MI
| | | | - Lia van der Hoek
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jean-Claude Kabayiza
- Department of Paediatrics, University Teaching Hospital of Kigali, Kigali, Rwanda
| | - Macpherson Mallewa
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Richard Idro
- Department of Paediatrics, Makerere University, Kampala, Uganda
| | - Michael Boele van Hensbroek
- Amsterdam Centre for Global Child Health, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Job B M van Woensel
- Amsterdam Centre for Global Child Health, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Paediatric Intensive Care Unit, Emma Children's Hospital, Amsterdam UMC, Amsterdam, The Netherlands
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9
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Andersen P, Barksdale S, Barclay RA, Smith N, Fernandes J, Besse K, Goldfarb D, Barbero R, Dunlap R, Jones-Roe T, Kelly R, Miao S, Ruhunusiri C, Munns A, Mosavi S, Sanson L, Munns D, Sahoo S, Swahn O, Hull K, White D, Kolb K, Noroozi F, Seelam J, Patnaik A, Lepene B. Magnetic hydrogel particles improve nanopore sequencing of SARS-CoV-2 and other respiratory viruses. Sci Rep 2023; 13:2163. [PMID: 36750714 PMCID: PMC9903261 DOI: 10.1038/s41598-023-29206-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Presented here is a magnetic hydrogel particle enabled workflow for capturing and concentrating SARS-CoV-2 from diagnostic remnant swab samples that significantly improves sequencing results using the Oxford Nanopore Technologies MinION sequencing platform. Our approach utilizes a novel affinity-based magnetic hydrogel particle, circumventing low input sample volumes and allowing for both rapid manual and automated high throughput workflows that are compatible with Nanopore sequencing. This approach enhances standard RNA extraction protocols, providing up to 40 × improvements in viral mapped reads, and improves sequencing coverage by 20-80% from lower titer diagnostic remnant samples. Furthermore, we demonstrate that this approach works for contrived influenza virus and respiratory syncytial virus samples, suggesting that it can be used to identify and improve sequencing results of multiple viruses in VTM samples. These methods can be performed manually or on a KingFisher automation platform.
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Affiliation(s)
- P Andersen
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA.
| | - S Barksdale
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - R A Barclay
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - N Smith
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - J Fernandes
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - K Besse
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - D Goldfarb
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - R Barbero
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - R Dunlap
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - T Jones-Roe
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - R Kelly
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - S Miao
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - C Ruhunusiri
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - A Munns
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - S Mosavi
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - L Sanson
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - D Munns
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - S Sahoo
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - O Swahn
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - K Hull
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - D White
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - K Kolb
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - F Noroozi
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - J Seelam
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - A Patnaik
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA
| | - B Lepene
- Ceres Nanosciences, Inc., Manassas, VA, 20110, USA.
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10
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Ahmadi A, Khezri A, Nørstebø H, Ahmad R. A culture-, amplification-independent, and rapid method for identification of pathogens and antibiotic resistance profile in bovine mastitis milk. Front Microbiol 2023; 13:1104701. [PMID: 36687564 PMCID: PMC9852903 DOI: 10.3389/fmicb.2022.1104701] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Introduction Rapid and accurate diagnosis of causative pathogens in mastitis would minimize the imprudent use of antibiotics and, therefore, reduce the spread of antimicrobial resistance. Whole genome sequencing offers a unique opportunity to study the microbial community and antimicrobial resistance (AMR) in mastitis. However, the complexity of milk samples and the presence of a high amount of host DNA in milk from infected udders often make this very challenging. Methods Here, we tested 24 bovine milk samples (18 mastitis and six non-mastitis) using four different commercial kits (Qiagens' DNeasy® PowerFood® Microbial, Norgens' Milk Bacterial DNA Isolation, and Molzyms' MolYsis™ Plus and Complete5) in combination with filtration, low-speed centrifugation, nuclease, and 10% bile extract of male bovine (Ox bile). Isolated DNA was quantified, checked for the presence/absence of host and pathogen using PCR and sequenced using MinION nanopore sequencing. Bioinformatics analysis was performed for taxonomic classification and antimicrobial resistance gene detection. Results The results showed that kits designed explicitly for bacterial DNA isolation from food and dairy matrices could not deplete/minimize host DNA. Following using MolYsis™ Complete 5 + 10% Ox bile + micrococcal nuclease combination, on average, 17% and 66.5% of reads were classified as bovine and Staphylococcus aureus reads, respectively. This combination also effectively enriched other mastitis pathogens, including Escherichia coli and Streptococcus dysgalactiae. Furthermore, using this approach, we identified important AMR genes such as Tet (A), Tet (38), fosB-Saur, and blaZ. We showed that even 40 min of the MinION run was enough for bacterial identification and detecting the first AMR gene. Conclusion We implemented an effective method (sensitivity of 100% and specificity of 92.3%) for host DNA removal and bacterial DNA enrichment (both gram-negative and positive) directly from bovine mastitis milk. To the best of our knowledge, this is the first culture- and amplification-independent study using nanopore-based metagenomic sequencing for real-time detection of the pathogen (within 5 hours) and the AMR profile (within 5-9 hours), in mastitis milk samples. These results provide a promising and potential future on-farm adaptable approach for better clinical management of mastitis.
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Affiliation(s)
- Asal Ahmadi
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | | | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway,Institute of Clinical Medicine, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway,*Correspondence: Rafi Ahmad,
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11
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Rapid Oxford Nanopore Technologies MinION Sequencing Workflow for Campylobacter jejuni Identification in Broilers on Site—A Proof-of-Concept Study. Animals (Basel) 2022; 12:ani12162065. [PMID: 36009653 PMCID: PMC9405271 DOI: 10.3390/ani12162065] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/04/2022] [Accepted: 08/10/2022] [Indexed: 12/03/2022] Open
Abstract
Campylobacter is recognised as one of the most important foodborne bacteria, with a worldwide health and socioeconomic impact. This bacterium is one of the most important zoonotic players in poultry, where efficient and fast detection methods are required. Current official culture methods for Campylobacter enumeration in poultry usually include >44 h of culture and >72 h for identification, thus requiring at least five working shifts (ISO/TS 10272-2:2017). Here, we have assembled a portable sequencing kit composed of the Bento Lab and the MinION and developed a workflow for on-site farm use that is able to detect and report the presence of Campylobacter from caecal samples in less than five hours from sampling time, as well as the relationship of Campylobacter with other caecal microbes. Beyond that, our workflow may offer a cost-effective and practical method of microbiologically monitoring poultry at the farm. These results would demonstrate the possibility of carrying out rapid on-site screening to monitor the health status of the poultry farm/flock during the production chain.
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12
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Abstract
MOTIVATION Nanopore sequencers allow targeted sequencing of interesting nucleotide sequences by rejecting other sequences from individual pores. This feature facilitates the enrichment of low-abundant sequences by depleting overrepresented ones in-silico. Existing tools for adaptive sampling either apply signal alignment, which cannot handle human-sized reference sequences, or apply read mapping in sequence space relying on fast graphical processing units (GPU) base callers for real-time read rejection. Using nanopore long-read mapping tools is also not optimal when mapping shorter reads as usually analyzed in adaptive sampling applications. RESULTS Here, we present a new approach for nanopore adaptive sampling that combines fast CPU and GPU base calling with read classification based on Interleaved Bloom Filters. ReadBouncer improves the potential enrichment of low abundance sequences by its high read classification sensitivity and specificity, outperforming existing tools in the field. It robustly removes even reads belonging to large reference sequences while running on commodity hardware without GPUs, making adaptive sampling accessible for in-field researchers. Readbouncer also provides a user-friendly interface and installer files for end-users without a bioinformatics background. AVAILABILITY AND IMPLEMENTATION The C++ source code is available at https://gitlab.com/dacs-hpi/readbouncer. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Ahmad Lutfi
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, 14482 Potsdam, Germany
- Department of Mathematics and Computer Science, Free University of Berlin, 14195 Berlin, Germany
| | - Kilian Rutzen
- Genome Sequencing Unit (MF2), Robert Koch Institute, 13353 Berlin, Germany
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13
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Nagel JH, Wingfield MJ, Slippers B. Next-generation sequencing provides important insights into the biology and evolution of the Botryosphaeriaceae. FUNGAL BIOL REV 2021. [DOI: 10.1016/j.fbr.2021.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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14
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Bonnet I, Enouf V, Morel F, Ok V, Jaffré J, Jarlier V, Aubry A, Robert J, Sougakoff W. A Comprehensive Evaluation of GeneLEAD VIII DNA Platform Combined to Deeplex Myc-TB ® Assay to Detect in 8 Days Drug Resistance to 13 Antituberculous Drugs and Transmission of Mycobacterium tuberculosis Complex Directly From Clinical Samples. Front Cell Infect Microbiol 2021; 11:707244. [PMID: 34778100 PMCID: PMC8586210 DOI: 10.3389/fcimb.2021.707244] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/04/2021] [Indexed: 11/21/2022] Open
Abstract
The GeneLEAD VIII (Diagenode, Belgium) is a new, fully automated, sample-to-result precision instrument for the extraction of DNA and PCR detection of Mycobacterium tuberculosis complex (MTBC) directly from clinical samples. The Deeplex Myc-TB® assay (Genoscreen, France) is a diagnostic kit based on the deep sequencing of a 24-plexed amplicon mix allowing simultaneously the detection of resistance to 13 antituberculous (antiTB) drugs and the determination of spoligotype. We evaluated the performance of a strategy combining the both mentioned tools to detect directly from clinical samples, in 8 days, MTBC and its resistance to 13 antiTB drugs, and identify potential transmission of strains from patient-to-patient. Using this approach, we screened 112 clinical samples (65 smear-negative) and 94 MTBC cultured strains. The sensitivity and the specificity of the GeneLEAD/Deeplex Myc-TB approach for MTBC detection were 79.3% and 100%, respectively. One hundred forty successful Deeplex Myc-TB results were obtained for 46 clinical samples and 94 strains, a total of 85.4% of which had a Deeplex Myc-TB susceptibility and resistance prediction consistent with phenotypic drug susceptibility testing (DST). Importantly, the Deeplex Myc-TB assay was able to detect 100% of the multidrug-resistant (MDR) MTBC tested. The lowest concordance rates were for pyrazinamide, ethambutol, streptomycin, and ethionamide (84.5%, 81.5%, 73%, and 55%, respectively) for which the determination of susceptibility or resistance is generally difficult with current tools. One of the main difficulties of Deeplex Myc-TB is to interpret the non-synonymous uncharacterized variants that can represent up to 30% of the detected single nucleotide variants. We observed a good level of concordance between Deeplex Myc-TB-spoligotyping and MIRU-VNTR despite a lower discriminatory power for spoligotyping. The median time to obtain complete results from clinical samples was 8 days (IQR 7–13) provided a high-throughput NGS sequencing platform was available. Our results highlight that the GeneLEAD/Deeplex Myc-TB approach could be a breakthrough in rapid diagnosis of MDR TB in routine practice.
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Affiliation(s)
- Isabelle Bonnet
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Vincent Enouf
- Plateforme de Microbiologie Mutualisée (P2M), Pasteur International Bioresources network (PIBnet), Institut Pasteur, Paris, France
| | - Florence Morel
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Vichita Ok
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Jérémy Jaffré
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Vincent Jarlier
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France
| | - Alexandra Aubry
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Jérôme Robert
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Wladimir Sougakoff
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
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15
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Point-of-care molecular diagnosis of Mycoplasma pneumoniae including macrolide sensitivity using quenching probe polymerase chain reaction. PLoS One 2021; 16:e0258694. [PMID: 34648603 PMCID: PMC8516298 DOI: 10.1371/journal.pone.0258694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/02/2021] [Indexed: 12/22/2022] Open
Abstract
Objectives Macrolides are generally considered to be the drugs of choice for treatment of patients with Mycoplasma pneumoniae infection. However, macrolide-resistant M. pneumoniae has been emerging since about 2000. The Smart Gene® system (MIZUHO MEDY Co., Ltd., Tosu, Japan) is a novel fully automated system for detection of pathogens using the method of quantitative polymerase chain reaction (qPCR) with QProbe (QProbe PCR). The entire procedure is completed within 50 min and the size of the instrument is small (15 x 34 x 30 cm). The purpose of this study was to evaluate the usefulness of the Smart Gene® system for detection of M. pneumoniae and detection of a point mutation at domain V of the 23S rRNA gene of M. pneumoniae. Materials Pharyngeal swab samples were collected from 154 patients who were suspected of having respiratory tract infections associated with M. pneumoniae. Results Compared with the results of qPCR, the sensitivity and specificity of the Smart Gene® system were 98.7% (78/79) and 100.0% (75/75), respectively. A point mutation at domain V of the 23S rRNA gene was detected from 7 (9.0%) of 78 M. pneumoniae-positive samples by the Smart Gene® system and these results were confirmed by direct sequencing. The minimum inhibitory concentrations of clarithromycin among the 5 isolates of M. pneumoniae with a point mutation at domain V of the 23S rRNA gene were >64 μg/ml and those among the 33 isolates without a mutation in the 23S rRNA gene were <0.0625 μg/ml. Conclusion The Smart Gene® system is a rapid and accurate assay for detection of the existence of M. pneumoniae and a point mutation at domain V of the 23S rRNA gene of M. pneumoniae at the same time. The Smart Gene® system is suitable for point-of-care testing in both hospital and outpatient settings.
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16
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Martin C, Stebbins B, Ajmani A, Comendul A, Hamner S, Hasan NA, Colwell R, Ford T. Nanopore-based metagenomics analysis reveals prevalence of mobile antibiotic and heavy metal resistome in wastewater. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1572-1585. [PMID: 33459951 DOI: 10.1007/s10646-020-02342-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
In-depth studies of the microbiome and mobile resistome profile of different environments is central to understanding the role of the environment in antimicrobial resistance (AMR), which is one of the urgent threats to global public health. In this study, we demonstrated the use of a rapid (and easily portable) sequencing approach coupled with user-friendly bioinformatics tools, the MinION (Oxford Nanopore Technologies), on the evaluation of the microbial as well as mobile metal and antibiotic resistome profile of semi-rural wastewater. A total of 20 unique phyla, 43 classes, 227 genera, and 469 species were identified in samples collected from the Amherst Wastewater Treatment Plant, both from primary and secondary treated wastewater. Alpha diversity indices indicated that primary samples were significantly richer and more microbially diverse than secondary samples. A total of 1041 ARGs, 68 MRGs, and 17 MGEs were detected in this study. There were more classes of AMR genes in primary than secondary wastewater, but in both cases multidrug, beta-lactam and peptide AMR predominated. Of note, OXA β-lactamases, some of which are also carbapenemases, were enriched in secondary samples. Metal resistance genes against arsenic, copper, zinc and molybdenum were the dominant MRGs in the majority of the samples. A larger proportion of resistome genes were located in chromosome-derived sequences except for mobilome genes, which were predominantly located in plasmid-derived sequences. Genetic elements related to transposase were the most common MGEs in all samples. Mobile or MGE/plasmid-associated resistome genes that confer resistance to last resort antimicrobials such as carbapenems and colistin were detected in most samples. Worryingly, several of these potentially transferable genes were found to be carried by clinically-relevant hosts including pathogenic bacterial species in the orders Aeromonadales, Clostridiales, Enterobacterales and Pseudomonadales. This study demonstrated that the MinION can be used as a metagenomics approach to evaluate the microbiome, resistome, and mobilome profile of primary and secondary wastewater.
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Affiliation(s)
| | | | - Asha Ajmani
- University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | | | | | - Nur A Hasan
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Rita Colwell
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Timothy Ford
- University of Massachusetts Lowell, Lowell, MA, 01854, USA.
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17
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Reteng P, Nguyen Thuy L, Tran Thi Minh T, Mares-Guia MAMDM, Torres MC, de Filippis AMB, Orba Y, Kobayashi S, Hayashida K, Sawa H, Hall WW, Nguyen Thi LA, Yamagishi J. A targeted approach with nanopore sequencing for the universal detection and identification of flaviviruses. Sci Rep 2021; 11:19031. [PMID: 34561471 PMCID: PMC8463598 DOI: 10.1038/s41598-021-98013-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 08/27/2021] [Indexed: 11/09/2022] Open
Abstract
Nucleic acid test (NAT), most typically quantitative PCR, is one of the standard methods for species specific flavivirus diagnosis. Semi-comprehensive NATs such as pan-flavivirus PCR which covers genus Flavivirus are also available; however, further specification by sequencing is required for species level differentiation. In this study, a semi-comprehensive detection system that allows species differentiation of flaviviruses was developed by integration of the pan-flavivirus PCR and Nanopore sequencing. In addition, a multiplexing method was established by adding index sequences through the PCR with a streamlined bioinformatics pipeline. This enables defining cut-off values for observed read counts. In the laboratory setting, this approach allowed the detection of up to nine different flaviviruses. Using clinical samples collected in Vietnam and Brazil, seven different flaviviruses were also detected. When compared to a commercial NAT, the sensitivity and specificity of our system were 66.7% and 95.4%, respectively. Conversely, when compared to our system, the sensitivity and specificity of the commercial NAT were 57.1% and 96.9%, respectively. In addition, Nanopore sequencing detected more positive samples (n = 8) compared to the commercial NAT (n = 6). Collectively, our study has established a semi-comprehensive sequencing-based diagnostic system for the detection of flaviviruses at extremely affordable costs, considerable sensitivity, and only requires simple experimental methods.
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Affiliation(s)
- Patrick Reteng
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Linh Nguyen Thuy
- Center for Bio-Medical Research, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Tam Tran Thi Minh
- Center for Bio-Medical Research, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | | | | | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shintaro Kobayashi
- Laboratory of Public Health, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Kyoko Hayashida
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Global Virus Network, Baltimore, USA
| | - William W Hall
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Global Virus Network, Baltimore, USA
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland
| | - Lan Anh Nguyen Thi
- Center for Bio-Medical Research, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Junya Yamagishi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
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18
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Gimenez AM, Marques RF, Regiart M, Bargieri DY. Diagnostic Methods for Non-Falciparum Malaria. Front Cell Infect Microbiol 2021; 11:681063. [PMID: 34222049 PMCID: PMC8248680 DOI: 10.3389/fcimb.2021.681063] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Malaria is a serious public health problem that affects mostly the poorest countries in the world, killing more than 400,000 people per year, mainly children under 5 years old. Among the control and prevention strategies, the differential diagnosis of the Plasmodium-infecting species is an important factor for selecting a treatment and, consequently, for preventing the spread of the disease. One of the main difficulties for the detection of a specific Plasmodium sp is that most of the existing methods for malaria diagnosis focus on detecting P. falciparum. Thus, in many cases, the diagnostic methods neglect the other non-falciparum species and underestimate their prevalence and severity. Traditional methods for diagnosing malaria may present low specificity or sensitivity to non-falciparum spp. Therefore, there is high demand for new alternative methods able to differentiate Plasmodium species in a faster, cheaper and easier manner to execute. This review details the classical procedures and new perspectives of diagnostic methods for malaria non-falciparum differential detection and the possibilities of their application in different circumstances.
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Affiliation(s)
- Alba Marina Gimenez
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rodolfo F. Marques
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Matías Regiart
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Daniel Youssef Bargieri
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Simo Tchetgna H, Descorps-Declère S, Selekon B, Kwasiborski A, Vandenbogaert M, Manuguerra JC, Gessain A, Caro V, Nakouné E, Berthet N. Molecular characterization of a new highly divergent Mobala related arenavirus isolated from Praomys sp. rodents. Sci Rep 2021; 11:10188. [PMID: 33986310 PMCID: PMC8119949 DOI: 10.1038/s41598-021-88046-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/06/2021] [Indexed: 12/02/2022] Open
Abstract
Arenaviruses represent a family of viruses that are naturally present in rodents belonging to subfamily Murinae, Neotominae or Sigmodontinae. Except for Lassa virus, little information is available on other Old-World arenaviruses. Here, we describe strain AnRB3214, a virus isolated from a presumed Praomys sp. rodent in the Central African Republic in 1981 and assigned to Ippy virus based on antigenic similarity. The strain was simultaneously sequenced on Illumina NovaSeq 6000 and MinION Mk1B devices and analysed with various bioinformatics tools. We show that the best genome coverage and depth were obtained with the Kaiju and Minimap2 classification and identification tools, on either the MinION or the Illumina reads. The genetic analysis of AnRB3214 fragments showed 68% to 79% similarity with the Mobala and Gairo mammarenaviruses at the nucleic acid level. Strain AnRB3214 had a truncated nucleoprotein smaller than that of other Old World arenaviruses. Molecular clock analysis suggests that this strain diverged from Mobala virus at least 400 years ago. Finally, this study illustrates the importance of genomics in the identification of archived viruses and expands on the diversity of African arenaviruses, because strain AnRB3214 is either a variant or a close relative of Mobala virus, and not Ippy virus.
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Affiliation(s)
- Huguette Simo Tchetgna
- Centre for Research in Infectious Diseases, Yaoundé, Cameroon.,The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai - Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens, Shanghai, 200031, China
| | - Stephane Descorps-Declère
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | | | - Aurelia Kwasiborski
- Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Unité Environnement et Risques Infectieux, Paris, France
| | - Mathias Vandenbogaert
- Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Unité Environnement et Risques Infectieux, Paris, France
| | - Jean-Claude Manuguerra
- Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Unité Environnement et Risques Infectieux, Paris, France
| | - Antoine Gessain
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, Institut Pasteur, Paris, France.,Centre National de Recherche Scientifique (CNRS) UMR3569, Paris, France
| | - Valérie Caro
- Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Unité Environnement et Risques Infectieux, Paris, France
| | | | - Nicolas Berthet
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai - Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens, Shanghai, 200031, China. .,Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Unité Environnement et Risques Infectieux, Paris, France.
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20
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Jun KI, Oh BL, Kim N, Shin JY, Moon J. Microbial diagnosis of endophthalmitis using nanopore amplicon sequencing. Int J Med Microbiol 2021; 311:151505. [PMID: 33930723 DOI: 10.1016/j.ijmm.2021.151505] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/11/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES We investigated whether nanopore amplicon sequencing of aqueous humor was capable of rapid pathogen identification in infectious endophthalmitis. METHODS 5 cases of culture-positive bacterial endophthalmitis and 3 cases of fungal endophthalmitis (1 culture-positive and 2 presumed) were included. DNA was extracted from the aqueous humor and vitreous specimen, and PCR of bacterial rDNA (16S) and fungal rDNA (ITS1 and D1/2/3) was performed. Then, nanopore amplicon sequencing was performed for 2 h. The results of amplicon sequencing were compared to those of conventional culture studies. RESULTS In all cases, pathogens were identified by amplicon sequencing of aqueous humor specimens. In 3 cases of bacterial endophthalmitis, the identified microbes were confirmed by culture studies of both aqueous humor and vitreous specimens. In 2 cases of bacterial and 1 case of fungal endophthalmitis, the identified pathogens were confirmed only by culture studies of vitreous specimens. In all cases, amplicon sequencing identified pathogen in a shorter turnaround time than culture studies. In 2 cases with negative culture results, amplicon sequencing of aqueous humor identified fungal pathogens. CONCLUSIONS Our data demonstrates the potential of amplicon nanopore sequencing using aqueous humor to enable rapid, sensitive and less invasive microbial diagnosis of endophthalmitis.
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Affiliation(s)
- Kang Il Jun
- Division of Infectious Disease, Department of Internal Medicine, Ewha Womans University Seoul Hospital, Seoul, South Korea
| | - Baek-Lok Oh
- Department of Ophthalmology, Seoul National University Hospital, Seoul, South Korea
| | - Narae Kim
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea
| | - Joo Young Shin
- Department of Ophthalmology, Seoul National University College of Medicine, SMG-SNU Boramae Medical Center, Seoul, South Korea.
| | - Jangsup Moon
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea; Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea.
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21
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Modernizing the Toolkit for Arthropod Bloodmeal Identification. INSECTS 2021; 12:insects12010037. [PMID: 33418885 PMCID: PMC7825046 DOI: 10.3390/insects12010037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 11/24/2022]
Abstract
Simple Summary The ability to identify the source of vertebrate blood in mosquitoes, ticks, and other blood-feeding arthropod vectors greatly enhances our knowledge of how vector-borne pathogens are spread. The source of the bloodmeal is identified by analyzing the remnants of blood remaining in the arthropod at the time of capture, though this is often fraught with challenges. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification with a focus on progress made in the field over the past decade. We highlight genome regions that can be used to identify the vertebrate source of arthropod bloodmeals as well as technological advances made in other fields that have introduced innovative new ways to identify vertebrate meal source based on unique properties of the DNA sequence, protein signatures, or residual molecules present in the blood. Additionally, engineering progress in miniaturization has led to a number of field-deployable technologies that bring the laboratory directly to the arthropods at the site of collection. Although many of these advancements have helped to address the technical challenges of the past, the challenge of successfully analyzing degraded DNA in bloodmeals remains to be solved. Abstract Understanding vertebrate–vector interactions is vitally important for understanding the transmission dynamics of arthropod-vectored pathogens and depends on the ability to accurately identify the vertebrate source of blood-engorged arthropods in field collections using molecular methods. A decade ago, molecular techniques being applied to arthropod blood meal identification were thoroughly reviewed, but there have been significant advancements in the techniques and technologies available since that time. This review highlights the available diagnostic markers in mitochondrial and nuclear DNA and discusses their benefits and shortcomings for use in molecular identification assays. Advances in real-time PCR, high resolution melting analysis, digital PCR, next generation sequencing, microsphere assays, mass spectrometry, and stable isotope analysis each offer novel approaches and advantages to bloodmeal analysis that have gained traction in the field. New, field-forward technologies and platforms have also come into use that offer promising solutions for point-of-care and remote field deployment for rapid bloodmeal source identification. Some of the lessons learned over the last decade, particularly in the fields of DNA barcoding and sequence analysis, are discussed. Though many advancements have been made, technical challenges remain concerning the prevention of sample degradation both by the arthropod before the sample has been obtained and during storage. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification and reviews how advances in molecular technology over the past decade have been applied in this unique biomedical context.
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Abstract
Long DNA and RNA reads from nanopore and PacBio technologies have many applications, but the raw reads have a substantial error rate. More accurate sequences can be obtained by merging multiple reads from overlapping parts of the same sequence. lamassemble aligns up to ∼1000 reads to each other, and makes a consensus sequence, which is often much more accurate than the raw reads. It is useful for studying a region of interest such as an expanded tandem repeat or other disease-causing mutation.
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Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples. J Clin Microbiol 2020; 58:JCM.00632-20. [PMID: 32727827 PMCID: PMC7512157 DOI: 10.1128/jcm.00632-20] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/21/2020] [Indexed: 12/21/2022] Open
Abstract
Targeted next-generation sequencing (tNGS) has emerged as a comprehensive alternative to existing methods for drug susceptibility testing (DST) of Mycobacterium tuberculosis from patient sputum samples for clinical diagnosis of drug-resistant tuberculosis (DR-TB). However, the complexity of sequencing platforms has limited their uptake in low-resource settings. The goal of this study was to evaluate the use of the tNGS-based DST solution Genoscreen Deeplex Myc-TB, for use on the compact, low-cost Oxford Nanopore Technologies MinION sequencer. One hundred four DNA samples extracted from smear-positive sputum sediments, previously sequenced using the Deeplex assay on an Illumina MiniSeq, were resequenced on MinION after applying a custom library preparation. MinION read quality, mapping statistics, and variant calling were computed using an in-house pipeline and compared to the reference MiniSeq data. The average percentage of MinION reads mapped to an H37RV reference genome was 90.8%, versus 99.5% on MiniSeq. The mean depths of coverage were 4,151× and 4,177× on MinION and MiniSeq, respectively, with heterogeneous distribution across targeted genes. Composite reference coverage breadth was >99% for both platforms. We observed full concordance between technologies in reporting the clinically relevant drug-resistant markers, including full gene deletions. In conclusion, we demonstrated that the workflow and sequencing data obtained from Deeplex on MinION are comparable to those for the MiniSeq, despite the higher raw error rates on MinION, with the added advantage of MinION's portability, versatility, and low capital costs. Targeted NGS on MinION is a promising DST solution for rapidly providing clinically relevant data to manage complex DR-TB cases.
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Determining the Suitability of MinION's Direct RNA and DNA Amplicon Sequencing for Viral Subtype Identification. Viruses 2020; 12:v12080801. [PMID: 32722480 PMCID: PMC7472323 DOI: 10.3390/v12080801] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/21/2022] Open
Abstract
The MinION sequencer is increasingly being used for the detection and outbreak surveillance of pathogens due to its rapid throughput. For RNA viruses, MinION's new direct RNA sequencing is the next significant development. Direct RNA sequencing studies are currently limited and comparisons of its diagnostic performance relative to different DNA sequencing approaches are lacking as a result. We sought to address this gap and sequenced six subtypes from the mycovirus CHV-1 using MinION's direct RNA sequencing and DNA sequencing based on a targeted viral amplicon. Reads from both techniques could correctly identify viral presence and species using BLAST, though direct RNA reads were more frequently misassigned to closely related CHV species. De novo consensus sequences were error prone but suitable for viral species identification. However, subtype identification was less accurate from both reads and consensus sequences. This is due to the high sequencing error rate and the limited sequence divergence between some CHV-1 subtypes. Importantly, neither RNA nor amplicon sequencing reads could be used to obtain reliable intra-host variants. Overall, both sequencing techniques were suitable for virus detection, though limitations are present due to the error rate of MinION reads.
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Marsela M, Hayashida K, Nakao R, Chatanga E, Gaithuma AK, Naoko K, Musaya J, Sugimoto C, Yamagishi J. Molecular identification of trypanosomes in cattle in Malawi using PCR methods and nanopore sequencing: epidemiological implications for the control of human and animal trypanosomiases. Parasite 2020; 27:46. [PMID: 32686644 PMCID: PMC7370688 DOI: 10.1051/parasite/2020043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 06/25/2020] [Indexed: 11/24/2022] Open
Abstract
This study aimed to identify trypanosomes infecting cattle in Malawi in order to understand the importance of cattle in the transmission dynamics of Human African Trypanosomiasis (HAT) and Animal African Trypanosomosis (AAT). A total of 446 DNA samples from cattle blood from three regions of Malawi were screened for African trypanosomes by ITS1 PCR. The obtained amplicons were sequenced using a portable next-generation sequencer, MinION, for validation. Comparison of the results from ITS1 PCR and MinION sequencing showed that combining the two methods provided more accurate species identification than ITS1 PCR alone. Further PCR screening targeting the serum resistance-associated (SRA) gene was conducted to detect Trypanosoma brucei rhodesiense. Trypanosoma congolense was the most prevalent Trypanosoma sp., which was found in Nkhotakota (10.8%; 20 of 185), followed by Kasungu (2.5%; 5 of 199). Of note, the prevalence of T. b. rhodesiense detected by SRA PCR was high in Kasungu and Nkhotakota showing 9.5% (19 of 199) and 2.7% (5 of 185), respectively. We report the presence of animal African trypanosomes and T. b. rhodesiense from cattle at the human-livestock-wildlife interface for the first time in Malawi. Our results confirmed that animal trypanosomes are important causes of anemia in cattle and that cattle are potential reservoirs for human African trypanosomiasis in Malawi.
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Affiliation(s)
- Megasari Marsela
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Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University Kita-20, Nishi-10, Kita-ku Sapporo 001-0020 Hokkaido Japan
| | - Kyoko Hayashida
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Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University Kita-20, Nishi-10, Kita-ku Sapporo 001-0020 Hokkaido Japan
| | - Ryo Nakao
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Laboratory of Parasitology, Veterinary Medicine Faculty, Hokkaido University Kita-18, Nishi-9, Kita-ku Sapporo 060-0818 Hokkaido Japan
| | - Elisha Chatanga
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Laboratory of Parasitology, Veterinary Medicine Faculty, Hokkaido University Kita-18, Nishi-9, Kita-ku Sapporo 060-0818 Hokkaido Japan
| | - Alex Kiarie Gaithuma
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Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University Kita-20, Nishi-10, Kita-ku Sapporo 001-0020 Hokkaido Japan
| | - Kawai Naoko
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Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University Kita-20, Nishi-10, Kita-ku Sapporo 001-0020 Hokkaido Japan
| | - Janelisa Musaya
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Department of Pathology, College of Medicine, University of Malawi P/Bag 360 Chichiri 30096 Blantyre 3 Malawi
| | - Chihiro Sugimoto
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Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University Kita-20, Nishi-10, Kita-ku Sapporo 001-0020 Hokkaido Japan
| | - Junya Yamagishi
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Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University Kita-20, Nishi-10, Kita-ku Sapporo 001-0020 Hokkaido Japan
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International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University Kita-20, Nishi-10, Kita-ku Sapporo 001-0020 Hokkaido Japan
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Mboowa G. Current and emerging diagnostic tests available for the novel COVID-19 global pandemic. AAS Open Res 2020; 3:8. [PMID: 32537561 PMCID: PMC7255909 DOI: 10.12688/aasopenres.13059.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2020] [Indexed: 02/01/2023] Open
Abstract
On March 11, 2020 the World Health Organization (WHO) upgraded the status of the coronavirus disease 2019 (COVID-19) outbreak from epidemic to a global pandemic. This infection is caused by a novel coronavirus, SARS-CoV-2. Several rapid diagnostic tests have been developed at an astonishing pace; however, COVID-19 requires more highly specific rapid point-of-care diagnostic tests. This review describes the currently available testing approaches, as well as the available test assays including the Xpert® Xpress SARS-CoV-2 test (takes
~45 min) and Abbott ID COVID-19 test (5 min) as easy to use point-of-care tests for diagnosis of novel COVID-19 that have so far received the US Food and Drug Administration emergency use authorizations clearance. This review is correct as of the date published and will be updated as more diagnostic tests come to light.
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Affiliation(s)
- Gerald Mboowa
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Disease Institute, Makerere University, Kampala, Uganda.,Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
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27
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Hong NTT, Anh NT, Mai NTH, Nghia HDT, Nhu LNT, Thanh TT, Phu NH, Deng X, van Doorn HR, Chau NVV, Delwart E, Thwaites G, Tan LV. Performance of Metagenomic Next-Generation Sequencing for the Diagnosis of Viral Meningoencephalitis in a Resource-Limited Setting. Open Forum Infect Dis 2020; 7:ofaa046. [PMID: 32158774 PMCID: PMC7051036 DOI: 10.1093/ofid/ofaa046] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/06/2020] [Indexed: 12/12/2022] Open
Abstract
Background Meningoencephalitis is a devastating disease worldwide. Current diagnosis fails to establish the cause in ≥50% of patients. Metagenomic next-generation sequencing (mNGS) has emerged as pan-pathogen assays for infectious diseases diagnosis, but few studies have been conducted in resource-limited settings. Methods We assessed the performance of mNGS in the cerebrospinal fluid (CSF) of 66 consecutively treated adults with meningoencephalitis in a tertiary referral hospital for infectious diseases in Vietnam, a resource-limited setting. All mNGS results were confirmed by viral-specific polymerase chain reaction (PCR). As a complementary analysis, 6 viral PCR-positive samples were analyzed using MinION-based metagenomics. Results Routine diagnosis could identify a virus in 15 (22.7%) patients, including herpes simplex virus (HSV; n = 7) and varicella zoster virus (VZV; n = 1) by PCR, and mumps virus (n = 4), dengue virus (DENV; n = 2), and Japanese encephalitis virus (JEV; n = 1) by serological diagnosis. mNGS detected HSV, VZV, and mumps virus in 5/7, 1/1, and 1/4 of the CSF positive by routine assays, respectively, but it detected DENV and JEV in none of the positive CSF. Additionally, mNGS detected enteroviruses in 7 patients of unknown cause. Metagenomic MinION-Nanopore sequencing could detect a virus in 5/6 PCR-positive CSF samples, including HSV in 1 CSF sample that was negative by mNGS, suggesting that the sensitivity of MinION is comparable with that of mNGS/PCR. Conclusions In a single assay, metagenomics could accurately detect a wide spectrum of neurotropic viruses in the CSF of meningoencephalitis patients. Further studies are needed to determine the value that real-time sequencing may contribute to the diagnosis and management of meningoencephalitis patients, especially in resource-limited settings where pathogen-specific assays are limited in number.
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Affiliation(s)
| | - Nguyen To Anh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Ho Dang Trung Nghia
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | | | - Tran Tan Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Hoan Phu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Department of Medicine, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, California, USA.,Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Eric Delwart
- Vitalant Research Institute, San Francisco, California, USA.,Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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