Article
Multidisciplinary Sciences
Liying Low, Pablo Fuentes-Utrilla, James Hodson, John D. O'Neil, Amanda E. Rossiter, Ghazala Begum, Kusy Suleiman, Philip Murray, Graham R. Wallace, Nicholas J. Loman, Saaeha Rauz
Summary: This study evaluated the potential of nanopore sequencing for diagnosing bacterial microbial keratitis directly from clinical samples. By optimizing sample collection methods and bioinformatics analysis, accurate bacterial taxa assignments were achieved. The results demonstrate a novel workflow for identifying bacterial microbial keratitis using full-length 16S nanopore sequencing.
Review
Microbiology
Lee J. Kerkhof
Summary: This minireview discusses the improvements in Oxford Nanopore sequencing technology that make the MinION a viable platform for microbial ecology studies. By increasing sequence accuracy, obtaining quantifiable signals, providing a user-friendly data analysis pathway, and requiring modest additional equipment for field sequencing, MinION sequencing has become an attractive option for laboratories with low capital costs and reasonable per sample costs.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Genetics & Heredity
Davide Bolognini, Alberto Magi
Summary: This research evaluates the performance of five long-read SV callers across four long-read aligners using both real and synthetic nanopore datasets. It focuses on the effects of read alignment, sequencing coverage, and variant allele depth on the detection and genotyping of SVs of different types and size ranges. Insights into precision and recall of SV callsets generated by integrating various long-read aligners and SV callers are provided.
FRONTIERS IN GENETICS
(2021)
Article
Infectious Diseases
Katja Kero, Niina Hieta, Teemu Kallonen, Anne Ahtikoski, Hanna K. Laine, Jaana Rautava, Eveliina Munukka
Summary: Next-generation sequencing-based microbiological analysis is a complex method that can profile vaginal microbiome samples, with each step affecting the obtained results. Comparison between Puritan DNA/RNA swab (PS) and Copan FLOQ swab (CS) showed consistent and reliable microbiome profiles. Alpha and beta diversities were evaluated and compared between the two sampling methods, with no significant statistical differences found. Lactobacillus-dominated vaginal microbiome profiles were observed in 43% of women, regardless of the collection method.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2023)
Review
Biochemistry & Molecular Biology
Laura Ciuffreda, Hector Rodriguez-Perez, Carlos Flores
Summary: The introduction of nanopore sequencing technology has significantly improved our ability to study complex microbial samples, allowing real-time sequencing of long reads with low cost and portability. This technology plays a crucial role in resolving complex genomic structures, accessing metagenome assembled genomes, and shows great potential in environmental microbial analysis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Review
Biochemical Research Methods
Dropen Sheka, Nikolay Alabi, Paul M. K. Gordon
Summary: The review discusses the challenges of current bacterial pathogen identification and antimicrobial susceptibility testing methods due to extended turnaround times and high costs, and explores the potential of single molecule sequencing technology to address these issues. Oxford Nanopore Technologies (ONT) products, along with third-party software and databases, are examined for their capabilities in improving speed, accuracy, and cost of diagnostics in clinical settings. Multiple studies support the use of ONT sequencing for real-time diagnostics in common clinical circumstances.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Microbiology
Adriel Latorre-Perez, Helena Gimeno-Valero, Kristie Tanner, Javier Pascual, Cristina Vilanova, Manuel Porcar
Summary: This study evaluated the use of Nanopore sequencing during an expedition to the Tabernas Desert in Spain, finding a strong correlation between Nanopore and culturing data. Portable sequencers have the potential to be key tools for in situ-informed bioprospecting strategies.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Ratanond Koonchanok, Swapna Vidhur Daulatabad, Quoseena Mir, Khairi Reda, Sarath Chandra Janga
Summary: Sequoia is a visual analytics tool that allows interactive exploration of nanopore sequences, enabling detection of post-transcriptional modifications at a single-molecule resolution for building automated classifiers. Insights gleaned through visual analysis should aid in developing rationales, hypotheses, and insights into the dynamic nature of RNA.
Review
Agriculture, Dairy & Animal Science
Margaret D. Weinroth, Aeriel D. Belk, Chris Dean, Noelle Noyes, Dana K. Dittoe, Michael J. Rothrock, Steven C. Ricke, Phillip R. Myer, Madison T. Henniger, Gustavo A. Ramirez, Brian B. Oakley, Katie Lynn Summers, Asha M. Miles, Taylor B. Ault-Seay, Zhongtang Yu, Jessica L. Metcalf, James E. Wells
Summary: Microbiome studies in animal science using 16S rRNA gene sequencing are becoming more common. This review serves as a guide for animal scientists less familiar with this method, discussing common issues and considerations in planning such studies.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Microbiology
Bryan T. T. Gemler, Chiranjit Mukherjee, Carrie Howland, Patrick A. A. Fullerton, Rachel R. R. Spurbeck, Lindsay A. Catlin, Anthony Smith, Angela T. T. Minard-Smith, Craig Bartling
Summary: Applied metagenomics, a hypothesis-free approach for identifying pathogens, has been limited in its application in clinical diagnostics due to workflow-specific requirements and computational constraints. To address these challenges, UltraSEQ, a transformative metagenomic bioinformatic tool, was developed and successfully demonstrated accurate detection and characterization of microbial samples, including disease-causing infections.
MICROBIOLOGY SPECTRUM
(2023)
Article
Medicine, Research & Experimental
Linfan Su, Yixian Qiao, Jinmei Luo, Rong Huang, Zhiwei Li, Hongbing Zhang, Hongmei Zhao, Jing Wang, Yi Xiao
Summary: This study analyzed the changes in the sputum microbiome of AECOPD patients and found correlations with clinical indices. The results suggest that microbial dysbiosis may contribute to disease progression and provide potential microbial biomarkers for the diagnosis of AECOPD.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Mattia Furlan, Anna Delgado-Tejedor, Logan Mulroney, Mattia Pelizzola, Eva Maria Novoa, Tommaso Leonardi
Summary: The covalent modification of RNA molecules plays fundamental roles in cellular processes, and nanopore direct RNA sequencing technology offers a way to detect modifications at a single-molecule resolution. However, analyzing the data for RNA modification detection remains a complex task with many challenges. Various approaches have been proposed to address this issue, resulting in a diverse range of tools available.
Article
Immunology
Miquel Rozas, Francois Brillet, Chris Callewaert, Bernhard Paetzold
Summary: This study used MinION(TM) nanopore sequencing technology to classify and analyze skin bacteria, finding that the existing protocols have biases in estimating the relative abundance of certain skin microbiome genera. By changing the amplification protocols, the accuracy of taxonomic classification for these three main skin bacterial genera can be improved. The study shows that MinION(TM) nanopore technology has great potential in studying skin microbiomes.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Bijayalaxmi Sahoo, Praveen Kumar Guttula, Mukesh Kumar Gupta
Summary: This study evaluated different sperm purification and RNA extraction methods for long-read RNA sequencing of poly(A) transcriptome in goat spermatozoa. Results showed that sperm purification by 1 h swim-up in sp-TL medium and using a monophasic solution of GITC with phenol and DTT resulted in the highest yield of large sized RNAs suitable for long-read RNAseq of poly(A) transcripts.
ANALYTICAL BIOCHEMISTRY
(2021)
Article
Microbiology
Annie Wing-Tung Lee, Chloe Toi-Mei Chan, Lily Lok-Yee Wong, Cheuk-Yi Yip, Wing-Tung Lui, Kai-Chun Cheng, Jake Siu-Lun Leung, Lam-Kwong Lee, Ivan Tak-Fai Wong, N. G. Timothy Ting-Leung, Hiu-Yin Lao, Gilman Kit-Hang Siu
Summary: Microbes in the built environment have been identified as a potential source of infectious diseases. The use of long-read taxonomic tools for microbial evaluations using nanopore sequencing has shown promising results. This study analyzed the performance of different taxonomic classifiers for microbial community analysis and provided recommendations for species-level classification and culturable species identification using 16S-nanopore dataset.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Clinical Neurology
Brian M. Cerny, Tasha Rhoads, Sophie I. Leib, Kyle J. Jennette, Karen S. Basurto, Nicole M. Durkin, Gabriel P. Ovsiew, Zachary J. Resch, Jason R. Soble
Summary: This study found that combining both accuracy and response latency scores on the VSVT increases predictive utility for identifying performance invalidity. All VSVT measures were useful in classifying validity groups, with both independent and combined usage showing significant effects.
APPLIED NEUROPSYCHOLOGY-ADULT
(2022)
Article
Microbiology
Fanny Wegner, Tim Roloff, Michael Huber, Samuel Cordey, Alban Ramette, Yannick Gerth, Claire Bertelli, Madlen Stange, Helena M. B. Seth-Smith, Alfredo Mari, Karoline Leuzinger, Lorenzo Cerutti, Keith Harshman, Ioannis Xenarios, Philippe Le Mercier, Pascal Bittel, Stefan Neuenschwander, Onya Opota, Jonas Fuchs, Marcus Panning, Charlotte Michel, Marie Hallin, Thomas Demuyser, Ricardo De Mendonca, Paul Savelkoul, Jozef Dingemans, Brian van der Veer, Stefan A. Boers, Eric C. J. Claas, Jordy P. M. Coolen, Willem J. G. Melchers, Marianne Gunell, Teemu Kallonen, Tytti Vuorinen, Antti J. Hakanen, Eva Bernhoff, Marit Andrea Klokkhammer Hetland, Hadar Golan Berman, Sheera Adar, Jacob Moran-Gilad, Dana G. Wolf, Stephen L. Leib, Oliver Nolte, Laurent Kaiser, Stefan Schmutz, Verena Kufner, Maryam Zaheri, Alexandra Trkola, Hege Vangstein Aamot, Hans H. Hirsch, Gilbert Greub, Adrian Egli
Summary: This pilot external quality assessment aimed to improve pathogen surveillance sequencing by establishing a framework between laboratories. Participating laboratories used different methods and analysis pipelines, but most were able to generate complete genomes. There was consensus on the majority of reporting criteria, although discrepancies were found in lineage and cluster assignments. The pilot program was considered successful, highlighting the high quality of participating laboratories and providing valuable feedback.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Valentina Dona, Alban Ramette, Vincent Perreten
Summary: This study sequenced the genomes of Actinobacillus pleuropneumoniae strains of different serotypes and found that the genomes were similar, with differences mainly in genes encoding serotype-specific antigens. The study also identified the presence of transposable elements and CRISPR-Cas systems, suggesting a possible exchange of virulence-related factors through horizontal gene transfer. This research is important for diagnostic tests, vaccine development, epidemiological studies, and monitoring antibiotic resistance and virulence gene evolution in A. pleuropneumoniae.
MICROBIAL GENOMICS
(2022)
Article
Clinical Neurology
Kirsten Guse, Nina Hagemann, Lisa Thiele, Jana Remlinger, Anke Salmen, Robert Hoepner, Irene Keller, Patricia Meyer, Denis Grandgirard, Stephen L. Leib, Erik Vassella, Giuseppe Locatelli, Dirk M. Hermann, Andrew Chan
Summary: This study investigates the mutual and combined interactions between autoimmune neuroinflammation and cerebral ischemia. It found that mice with severe autoimmune disease showed a reduction in infarct size after ischemia, indicating a protective influence of CNS autoantigen-specific autoimmunity on primary tissue damage. These findings suggest the involvement of myeloid cell-driven anti-inflammatory mechanisms in mitigating ischemic injury in the acute phase of autoimmune disease.
NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION
(2022)
Article
Immunology
Helly Hammer, Robert Hoepner, Christoph Friedli, Stephen L. Leib, Franziska Suter-Riniker, Lara Diem, Nicole Kamber, Andrew Chan, Anke Salmen, Christian P. Kamm
Summary: This study compared the antibody response in multiple sclerosis patients after vaccination with two mRNA vaccines. The results showed that the protective antibody titers were low and decreased over time.
Article
Microbiology
C. Graedel, N. R. Ireddy, M. C. Koch, C. Baumann, M. A. Terrazos Miani, M. T. Barbani, J. Steinlin-Schopfer, F. Suter-Riniker, S. L. Leib, A. Ramette
Summary: This study reports on the genomic sequences of human enteroviruses (EVs) identified in respiratory samples in Bern, Switzerland, in 2018 and 2019. In addition to providing sequences for coxsackievirus A2, echovirus 11, and echovirus 30, the study determined the sequences of rare EV-D68 and EV-C105 genotypes circulating in Switzerland.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Infectious Diseases
Jacob Kofler, Alban Ramette, Patricia Iseli, Lea Stauber, Jens Fichtner, Sara Droz, Annina Zihler Berner, Anna Bettina Meier, Michelle Begert, Sabine Negri, Anne Jachmann, Peter Michael Keller, Cornelia Staehelin, Barbara Gruetzmacher
Summary: Two diphtheria outbreaks occurred in a Swiss asylum center from July to October 2022, one of which is still ongoing. The outbreaks mainly affected minors, with six symptomatic respiratory diphtheria cases that required antitoxin treatment. Phylogenomic analysis revealed evidence of both imported and locally transmitted toxigenic strains in respiratory and skin lesion samples. Due to the significant number of cases (n=20) and the wide genetic diversity observed in a single center, increased awareness and changes in public health measures are necessary to prevent and control diphtheria outbreaks.
Article
Infectious Diseases
Suraj Balakrishna, Tom Loosli, Maryam Zaheri, Paul Frischknecht, Michael Huber, Katharina Kusejko, Sabine Yerly, Karoline Leuzinger, Matthieu Perreau, Alban Ramette, Chris Wymant, Christophe Fraser, Paul Kellam, Astrid Gall, Hans H. Hirsch, Marcel Stoeckle, Andri Rauch, Matthias Cavassini, Enos Bernasconi, Julia Notter, Alexandra Calmy, Huldrych F. Gunthard, Karin J. Metzner, Roger D. Kouyos
Summary: This study compared the reliability of Sanger sequencing and Next-generation sequencing (NGS) in detecting HIV drug resistance mutations (DRMs). The results showed good agreement between the two methods when detecting mutations at a threshold of 5% or higher. However, at lower thresholds, NGS detected a substantial number of low-frequency mutations, which were likely to be sequencing errors.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Immunology
Marco Labarile, Tom Loosli, Marius Zeeb, Katharina Kusejko, Michael Huber, Hans H. Hirsch, Matthieu Perreau, Alban Ramette, Sabine Yerly, Matthias Cavassini, Manuel Battegay, Andri Rauch, Alexandra Calmy, Julia Notter, Enos Bernasconi, Christoph Fux, Huldrych F. Gunthard, Chloe Pasin, Roger D. Kouyos
Summary: This study investigated and predicted the dynamics of HIV transmission in Switzerland using a network-based clustering method and statistical learning approaches. The study found that network characteristics can capture major heterogeneities in transmission and that cluster structure has the potential for real-time prediction of ongoing transmission.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Virology
Claude Saegerman, Marie-France Humblet, Marc Leandri, Gaelle Gonzalez, Paul Heyman, Hein Sprong, Monique L'Hostis, Sara Moutailler, Sarah I. Bonnet, Nadia Haddad, Nathalie Boulanger, Stephen Leib, Thierry Hoch, Etienne Thiry, Laure Bournez, Jana Kerlik, Aurelie Velay, Solveig Jore, Elsa Jourdain, Emmanuelle Gilot-Fromont, Katharina Brugger, Julia Geller, Marie Studahl, Natasa Knap, Tatjana Avsic-Zupanc, Daniel P. Ruzek, Tizza Zomer, Rene Bodker, Thomas F. H. Berger, Sandra Martin-Latil, Nick De Regge, Alice A. Raffetin, Sandrine Lacour, Matthias Klein, Tinne Lernout, Elsa Quillery, Zdenek Hubalek, Francisco Ruiz-Fons, Agustin Estrada-Pena, Philippe Fravalo, Pauline Kooh, Florence Etore, Celine M. Gossner, Bethan Purse
Summary: Tick-borne encephalitis (TBE) is an endemic viral disease in Eurasia, primarily transmitted to humans through ticks and occasionally through unpasteurized milk products. The European Centre for Disease Prevention and Control has reported an increase in TBE incidence over the years, as well as its emergence in new areas. Through expert knowledge elicitation, we identified nine key drivers for TBE emergence and increased incidence, including changes in human behavior, eating habits, landscape, humidity, difficulty in controlling reservoirs and vectors, temperature, wildlife compartments, increase in autochthonous wild mammals, and distribution of tick species vectors.
Article
Multidisciplinary Sciences
Alexander Ernst, Indre Piragyte, Ayisha Marwa Mp, Ngoc Dung Le, Denis Grandgirard, Stephen L. Leib, Andrew Oates, Nadia Mercader
Summary: Drug repurposing is an important strategy in COVID-19 treatment, but the potential effects on embryogenesis are not well-studied. Using the zebrafish embryo model, researchers tested the effects of 162 marketed drugs on cardiovascular development and found adverse effects of certain drugs used for COVID-19 treatment. Zebrafish can be used to study the immune-modulating properties of COVID-19 compounds and the potential secondary defects on embryogenesis need to be considered.
SCIENTIFIC REPORTS
(2023)
Article
Water Resources
Hang Guan, Veronica Caggia, Andrea Gomez-Chamorro, Daniela Fischer, Miquel Coll-Crespi, Xiaowen Liu, Teresa Chavez-Capilla, Klaus Schlaeppi, Alban Ramette, Adrien Mestrot, Moritz Bigalke
Summary: This study examined the effects of soil microbial disturbance and maize plants on arsenic concentration and speciation in soil water. It was found that microbial disturbance increased the release of arsenic into soil water, especially for organic arsenic species. The abiotic sterilization of soil also increased arsenic release, but this effect was mitigated by the presence of maize in the pots.
EXPOSURE AND HEALTH
(2023)
Article
Microbiology
T. C. Scheier, J. Franz, M. Boumasmoud, F. Andreoni, B. Chakrakodi, B. Duvnjak, A. Egli, W. Zingg, A. Ramette, A. Wolfensberger, R. D. Kouyos, S. D. Brugger
Summary: This study evaluated the application of FT-IR spectroscopy in VREfm outbreak investigations. The results showed that FT-IR spectroscopy had reproducible basic performance, and its readouts showed high agreement with WGS analysis in clinical outbreak investigations. FT-IR spectroscopy had a higher discriminatory power than MLST in outbreak investigations. Therefore, FT-IR spectroscopy is a promising technique that can assist in outbreak investigations with an affordable cost and a turnaround time of less than one day.
MICROBIOLOGY SPECTRUM
(2023)
Article
Neuroimaging
Josua Zimmermann, Nicole Friedli, Francesco Bavato, Philipp Staempfli, Rebecca Coray, Markus R. Baumgartner, Denis Grandgirard, Stephen L. Leib, Antje Opitz, Erich Seifritz, Ann-Kathrin Stock, Christian Beste, David M. Cole, Boris B. Quednow
Summary: This study used diffusion tensor imaging and neurofilament light chain analysis to investigate white matter alterations in chronic MDMA users. The results showed increased fractional anisotropy in several white matter tracts, but no significant differences in neurofilament light chain levels. Therefore, this human study did not observe the axonal degradation demonstrated in animal models of MDMA use.
NEUROIMAGE-CLINICAL
(2022)