Article
Microbiology
Ekaterina Avershina, Stephan A. Frye, Jawad Ali, Arne M. Taxt, Rafi Ahmad
Summary: This study investigates the suitability of the Oxford Nanopore Technology's Flongle sequencing platform for real-time sequencing of bacteria and detection of antibiotic resistance genes directly from blood cultures. The results show that Flongle data allows rapid bacterial identification and detection of resistance genes, although the identification of ARG variants may not always correspond with other sequencing methods.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Luca Marcolungo, Alessandro Passera, Simone Maestri, Elena Segala, Massimiliano Alfano, Francesca Gaffuri, Giovanni Marturano, Paola Casati, Piero Attilio Bianco, Massimo Delledonne
Summary: Rapid and sensitive diagnostic assays for plant pathogens are essential for crop disease management. This study established and evaluated a novel nanopore sequencing-based diagnostic assay, which can detect and characterize quarantine pathogens simultaneously, achieving detection and typing within 13 minutes.
Article
Immunology
Laura T. Phillips, Adam A. Witney, Martina Furegato, Ken G. Laing, Liqing Zhou, S. Tariq Sadiq
Summary: Early versions of nanopore technology show promise as a real-time surveillance tool, capable of accurately identifying closely related Neisseria gonorrhoeae strains and important antimicrobial resistance markers from cultured isolates, with very short sequencing times.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Biotechnology & Applied Microbiology
Alexander Barquero, Simone Marini, Christina Boucher, Jaime Ruiz, Mattia Prosperi
Summary: This study developed a mobile application called KARGAMobile for real-time, portable analysis of antibiotic resistance genes in nanopore sequencing. The app utilizes compressed reference databases and different data structures to save memory usage, and features a user-friendly graphical interface and visual report generation.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Microbiology
Hongying Zhang, Meng Wang, Ximei Han, Ting Wang, Yanjuan Lei, Yu Rao, Peisong Xu, Yunfei Wang, Hongcang Gu
Summary: This study found that targeted nanopore sequencing (TNPseq) can effectively identify pathogens in patients with lower respiratory tract infections (LRTIs), helping physicians to provide timely and precise treatment. Compared to traditional culture methods, TNPseq has higher sensitivity and detection rate, can identify more bacterial infections and mixed infections, and can also detect antimicrobial resistance (AMR) genes, aiding in the appropriate use of antibiotics.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Infectious Diseases
Peihan Li, Kaiying Wang, Shaofu Qiu, Yanfeng Lin, Jing Xie, Jinhui Li, Lizhong Li, Leili Jia, Yongqiang Jiang, Peng Li, Hongbin Song
Summary: This study utilized nanopore and BGI platforms in the identification and genomic analysis of an HAdV outbreak in Hubei province, China in May of 2019, confirming HAdV-55 infection and revealing a close genetic relation to strains isolated in Sichuan province. The combination of different sequencing platforms and the use of mixed samples can effectively improve the accuracy of pathogen detection during infectious disease outbreaks.
INFECTION GENETICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Maria G. Khrenova, Tatiana Panova, Vladimir A. Rodin, Maxim A. Kryakvin, Dmitrii A. Lukyanov, Ilya A. Osterman, Maria Zvereva
Summary: Nanopore sequencing is a new method for determining nucleotide sequences, and in this study, it was used to assemble the genome of an E. coli strain with antibiotic resistance. The Flye program showed the best assembly results compared to other programs. The required coverage depth for successful assembly depends on the read length, with 30x coverage depth sufficient for long reads and 50x needed for shorter reads. Mechanical mixing should be avoided during sample preparation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Hector Rodriguez-Perez, Laura Ciuffreda, Carlos Flores
Summary: NanoRTax is a Nextflow pipeline for nanopore 16S rRNA gene amplicon data that features state-of-the-art taxonomic classification tools and real-time capability. This tool demonstrates the potential for shortening turnaround times in critical care settings and provides a tool for research on early-response strategies for sepsis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Huan Chen, Jun Li, Shanshan Yan, Hui Sun, Chuyi Tan, Meidong Liu, Ke Liu, Huali Zhang, Mingxiang Zou, Xianzhong Xiao
Summary: Shotgun metagenomic sequencing technology demonstrates high accuracy in microbial detection and is especially useful for cases of multiple microbial co-infections and when standard culture methods fail to identify microorganisms.
Article
Biochemical Research Methods
Aimeric Bruno, Jean-Marc Aury, Stefan Engelen
Summary: BoardION is an interactive web application designed for analyzing the efficiency of ONT sequencing runs, allowing users to optimize data quality and compare multiple flowcells. It enables users to remotely monitor experiments and assess library preparation protocols or sample quality in real time.
BMC BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Emira Cherif, Fatou Seck Thiam, Mohammad Salma, Georgina Rivera-Ingraham, Fabienne Justy, Theo Deremarque, Damien Breugnot, Jean-Claude Doudou, Rodolphe Elie Gozlan, Marine Combe
Summary: This article introduces an amplicon-based nanopore sequencing pipeline for analyzing the genetic diversity of SARS-CoV-2 and other pathogens. The pipeline integrates multiple bioinformatics tools, allowing users with minimal bioinformatics skills to perform downstream analysis steps with a simple command line and configuration file.
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
Engineering, Environmental
Yujie Wang, Jun Ma, Liu Yang, Yuqi Li, Ming Chen
Summary: This study developed a novel approach using a bio-hybrid carbon material activated by peroxymonosulfate to effectively eliminate E. coli bacteria and its antibiotic resistance genes in water. Furthermore, through nanopore sequencing and Illumina sequencing analysis, the composition and base preference of gene-degrading intermediates were revealed, providing important insights into the gene degradation process.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Biochemical Research Methods
Lu Chen, Xue Gao, Wenzhi Xue, Shishan Yuan, Mingqiu Liu, Zhi Sun
Summary: We established a nanopore-sequencing-based mNGS protocol for rapid detection of viral pathogens in swine. The protocol demonstrated high sensitivity and accuracy in identifying and characterizing different types of viral pathogens in clinical samples.
JOURNAL OF VIROLOGICAL METHODS
(2022)
Article
Multidisciplinary Sciences
Balazs Kakuk, Dora Tombacz, Zsolt Balazs, Norbert Moldovan, Zsolt Csabai, Gabor Torma, Klara Megyeri, Michael Snyder, Zsolt Boldogkoi
Summary: Long-read sequencing (LRS) is a powerful new approach that offers significant advantages over traditional short-read sequencing. In this study, two third-generation LRS platforms were used to analyze the human cytomegalovirus transcriptome, revealing numerous novel transcript variants and a highly complex meshwork of transcriptional read-throughs and overlaps.
SCIENTIFIC REPORTS
(2021)
Article
Oncology
Devika Ganesamoorthy, Alan James Robertson, Wenhan Chen, Michael B. Hall, Minh Duc Cao, Kaltin Ferguson, Sunil R. Lakhani, Katia Nones, Peter T. Simpson, Lachlan J. M. Coin
Summary: This study conducted deep sequencing analysis of plasma samples, revealing a higher fraction of unique somatic mutations in plasma samples that were not detected in matched tumour samples. Sequencing of di-nucleosome bound cfDNA fragments may increase recovery of tumour mutations from plasma.
Article
Biochemistry & Molecular Biology
Jennifer R. Baker, Peter J. Cossar, Mark A. T. Blaskovich, Alysha G. Elliott, Johannes Zuegg, Matthew A. Cooper, Peter J. Lewis, Adam McCluskey
Summary: Five focused compound libraries were synthesized and screened for antibiotic and anti-fungal activity. Modifications of the terminal aromatic moiety were explored, resulting in the discovery of compounds with improved activity.
Article
Biochemistry & Molecular Biology
Ramar Perumal Samy, Stephen P. P. Mackessy, Alagarmalai Jeyasankar, Mano Ranjana Ponraj, Octavio Luiz Franco, Matthew A. A. Cooper, Matheswaran Kandasamy, Tapan Kumar Mohanta, Jebasingh Bhagavathsingh, Sakthivel Vaiyapuri
Summary: PaTx-II, an active component from the venom of the Mulga Snake, showed potent antimicrobial activity and promoted wound healing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Engineering, Environmental
Shuxin Zhang, Jiahua Shi, Elipsha Sharma, Xuan Li, Shuhong Gao, Xu Zhou, Jake O'Brien, Lachlan Coin, Yanchen Liu, Muttucumaru Sivakumar, Faisal Hai, Guangming Jiang
Summary: This study investigated the recovery of Campylobacter spp. from wastewater and their decay under different simulated sewer reactor conditions. The results showed that the recovery of Campylobacter spp. varied with their concentrations in wastewater and the detection limit of quantification methods. The concentration reduction of Campylobacter spp. in sewers followed a two-phase reduction model, with the faster reduction in the first phase mainly due to partitioning onto sewer biofilms. The total decay of Campylobacter spp. varied in different types of sewer reactors.
Article
Multidisciplinary Sciences
Mark R. R. Davies, Nadia Keller, Stephan Brouwer, Magnus G. G. Jespersen, Amanda J. J. Cork, Andrew J. Hayes, Miranda E. E. Pitt, David M. P. De Oliveira, Nichaela Harbison-Price, Olivia M. M. Bertolla, Daniel G. G. Mediati, Bodie F. F. Curren, George Taiaroa, Jake A. A. Lacey, Helen V. V. Smith, Ning-Xia Fang, Lachlan J. M. Coin, Kerrie Stevens, Steven Y. C. Tong, Martina Sanderson-Smith, Jai J. J. Tree, Adam D. D. Irwin, Keith Grimwood, Benjamin P. P. Howden, Amy V. V. Jennison, Mark J. J. Walker
Summary: A new variant of Streptococcus pyogenes serotype M1 (M1(UK)) has been reported in the UK, which exhibits enhanced expression of the superantigen SpeA. A single SNP in the 5' leader sequence of ssrA is responsible for the upregulation of SpeA expression. This variant has also been observed in Australia and is associated with epidemic scarlet fever in Asia.
NATURE COMMUNICATIONS
(2023)
Review
Chemistry, Multidisciplinary
Angelo Frei, Anthony D. D. Verderosa, Alysha G. G. Elliott, Johannes Zuegg, Mark A. T. Blaskovich
Summary: Metal ions have antimicrobial activity and are considered as potential new antibiotics. Metal complexes can also be used for antimicrobial photodynamic therapy and radionuclide diagnosis of bacterial infections.
NATURE REVIEWS CHEMISTRY
(2023)
Article
Microbiology
Andrew Chen, Jiaman Sun, Guillaume Martin, Lesley-Ann Gray, Eva Hribova, Pavla Christelova, Nabila Yahiaoui, Steve Rounsley, Rebecca Lyons, Jacqueline Batley, Ning Chen, Sharon Hamill, Subash K. Rai, Lachlan Coin, Brigitte Uwimana, Angelique D'Hont, Jaroslav Dolezel, David Edwards, Rony Swennen, Elizabeth A. B. Aitken
Summary: In this study, the resistance to Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4) in Musa acuminata ssp. malaccensis was characterized. QTL-seq analysis of an F2 population segregating for resistance revealed a major QTL on the long arm of chromosome 3. This research provides a foundation for marker assisted selection in breeding programs and identification of resistance genes.
Article
Biology
Bing Zhang, Wanida Phetsang, M. Rhia L. Stone, Sanjaya Kc, Mark S. S. Butler, Matthew A. A. Cooper, Alysha G. G. Elliott, Urszula Lapinska, Margaritis Voliotis, Krasimira Tsaneva-Atanasova, Stefano Pagliara, Mark A. T. Blaskovich
Summary: Antimicrobial resistance is a critical concern for human health, and this study presents the development of vancomycin fluorescent probes that can be used for detecting and visualizing Gram-positive bacteria as well as for measuring outer membrane permeabilization in Gram-negative bacteria. The probes were synthesized by modifying vancomycin with an azide substituent, enabling it to undergo copper-catalyzed azide-alkyne cycloaddition reactions. The probes exhibited similar antibacterial profiles to the parent vancomycin antibiotic and were versatile tools for various detection and imaging techniques.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Annick van Niekerk, M. Cassiem Joseph, Angela Kavanagh, Hue Dinh, Andrew J. Swarts, Selwyn F. Mapolie, Johannes Zuegg, Amy K. Cain, Alysha G. Elliott, Mark A. T. Blaskovich, Angelo Frei
Summary: Infections associated with antibiotic resistance (AMR) are projected to become the leading cause of death in the coming decades due to over-prescription of antibiotics and a lack of new drug development. A community-driven initiative, Community for Open Antimicrobial Drug Discovery (CO-ADD), has identified metal-based drugs as a potential and untapped source for combating AMR. Testing of 18 palladium (Pd) and ruthenium (Ru) complexes has revealed that Pd complexes, particularly Pd1, exhibit potent antifungal activity against Candida glabrata. Furthermore, in-vivo studies in Galleria mellonella larvae have demonstrated the non-toxic nature of these compounds.
Article
Biology
Fuyi Li, Xudong Guo, Yue Bi, Runchang Jia, Miranda E. Pitt, Shirui Pan, Shuqin Li, Robin B. Gasser, Lachlan JM. Coin, Jiangning Song
Summary: A deep learning-based approach called Digerati was developed for the rapid and accurate identification of PE and PPE family proteins. Digerati achieved a significantly better performance (-18-20%) than alignment-based methods. It is expected to facilitate high-throughput identification and analysis of PE/PPE family members.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Genetics & Heredity
Michael B. Hall, Leandro Lima, Lachlan J. M. Coin, Zamin Iqbal
Summary: Tuberculosis, a global pandemic disease, is facing an increasing challenge of antimicrobial resistance. The World Health Organization (WHO) aims to achieve universal access to drug susceptibility testing (DST), and whole-genome sequencing followed by genotype-based prediction of DST is a promising approach. In this study, we developed DrPRG (Drug resistance Prediction with Reference Graphs) by constructing a reference graph for Mycobacterium tuberculosis drug resistance using a global dataset of isolates. We compared DrPRG with existing graph-based and haplotype-based tools and found that DrPRG performs better in terms of sensitivity, specificity, computational memory usage, and runtime.
MICROBIAL GENOMICS
(2023)
Article
Medicine, Research & Experimental
Dominic Habgood-Coote, Clare Wilson, Chisato Shimizu, Anouk M. Barendregt, Ria Philipsen, Rachel Galassini, Irene Rivero Calle, Lesley Workman, Philipp K. A. Agyeman, Gerben Ferwerda, Suzanne T. Anderson, J. Merlijn van den Berg, Marieke Emonts, Enitan D. Carrol, Colin G. Fink, Ronald de Groot, Martin L. Hibberd, John Kanegaye, Mark P. Nicol, Stephane Paulus, Andrew J. Pollard, Antonio Salas, Fatou Secka, Luregn J. Schlapbach, Adriana H. Tremoulet, Michael Walther, Werner Zenz, Michiel van der Flier, Heather J. Zar, Taco Kuijpers, Jane C. Burns, Federico Martinon-Torres, Victoria J. Wright, Lachlan J. M. Coin, Aubrey J. Cunnington, Jethro A. Herberg, Michael Levin, Myrsini Kaforou
Summary: A panel of genes in blood can be used to discriminate various infectious and inflammatory diseases, allowing for reliable prediction of categories such as bacterial infection, viral infection, malaria, tuberculosis, or inflammatory disease.
Article
Biochemistry & Molecular Biology
Fuyi Li, Xudong Guo, Dongxu Xiang, Miranda E. Pitt, Arnold Bainomugisa, Lachlan J. M. Coin
Summary: In this study, a machine learning-based bioinformatics approach called PEPPER was developed to rapidly and accurately identify PE_PGRS proteins. Experimental results showed that PEPPER outperformed existing methods in terms of prediction accuracy and speed.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Gareth E. Boer, Shane M. Hickey, Alysha G. Elliott, Frederick M. Pfeffer
Summary: Convergent, late-stage introduction of acylguanidine moieties is a useful strategy for rapid development of novel compounds. In this study, a method for synthesizing a range of acylguanidine compounds was reported, and it was successfully applied to generate a new antimicrobial agent.
NEW JOURNAL OF CHEMISTRY
(2022)