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Amrita Srivathsan, Bilgenur Baloğlu, Wendy Wang, Wei Xin Tan, Denis Bertrand, Amanda Hui Qi Ng, Esther Jia Hui Boey, Jayce Jia Yu Koh, Niranjan Nagarajan, Rudolf Meier
DNA barcodes are useful for species discovery and species identification, but obtaining barcodes currently requires a well-equipped molecular laboratory, is time-consuming, and/or expensive. We here address these issues by developing a barcoding pipeline for Oxford Nanopore MinION™ and demonstrate that one flowcell can generate barcodes for ~500 specimens despite the high base-call error rates of MinION™ reads. The pipeline overcomes these errors by first summarizing all reads for the same tagged amplicon as a consensus barcode...
April 19, 2018: Molecular Ecology Resources
Lindsey E Minion, Krishnansu S Tewari
Vascular endothelial growth factor (VEGF) has emerged as a therapeutic target in several malignancies, including cervical cancer. Chemotherapy doublets combined with the fully humanized monoclonal antibody, bevacizumab, now constitute first-line therapy for women struggling with recurrent/metastatic cervical carcinoma. Regulatory approval for this indication was based on the phase III randomized trial, GOG 240, which demonstrated a statistically significant and clinically meaningful improvement in overall survival when bevacizumab was added to chemotherapy: 17...
March 2018: Gynecologic Oncology
Rabaab Zahra, Saba Javeed, Bibi Malala, Dmitriy Babenko, Mark A Toleman
Objectives: To discover the Escherichia coli STs and associated resistance mechanisms in the community in Islamabad, Pakistan by analysis of E. coli isolates in sewage. Methods: One hundred and ten E. coli were isolated from sewage across the city of Islamabad without antibiotic bias and confirmed as E. coli by MALDI-TOF MS. Isolates were characterized by fumC/fimH (CH) typing and core-genome MLST. Resistance mechanisms, virulence genes, phylotypes and plasmid incompatibility types were determined in a subset of isolates by in silico analysis...
April 10, 2018: Journal of Antimicrobial Chemotherapy
Chang Liu, Fangzhou Xiao, Jessica Hoisington-Lopez, Kathrin Lang, Philipp Quenzel, Brian Duffy, Robi David Mitra
Oxford Nanopore Technologies' MinION has expanded the current DNA sequencing toolkit by delivering long read lengths and extreme portability. The MinION has the potential to enable expedited point-of-care human leukocyte antigen (HLA) typing, an assay routinely used to assess the immunological compatibility between organ donors and recipients, but the platform's high error rate makes it challenging to type alleles with accuracy. Here, we developed and validated accurate typing of HLA by Oxford nanopore (Athlon), a bioinformatic pipeline that i) maps nanopore reads to a database of known HLA alleles, ii) identifies candidate alleles with the highest read coverage at different resolution levels that are represented as branching nodes and leaves of a tree structure, iii) generates consensus sequences by remapping the reads to the candidate alleles, and iv) calls the final diploid genotype by blasting consensus sequences against the reference database...
April 3, 2018: Journal of Molecular Diagnostics: JMD
Aaron Pomerantz, Nicolás Peñafiel, Alejandro Arteaga, Lucas Bustamante, Frank Pichardo, Luis A Coloma, César L Barrio-Amorós, David Salazar-Valenzuela, Stefan Prost
Background: Advancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here, we tested the feasibility for in situ molecular analyses of endemic fauna using a portable laboratory fitting within a single backpack, in one of the world's most imperiled biodiversity hotspots: the Ecuadorian Chocó rainforest. We utilized portable equipment, including the MinION nanopore sequencer (Oxford Nanopore Technologies) and the miniPCR (miniPCR), to perform DNA extraction, PCR amplification and real-time DNA barcoding of reptile specimens in the field...
April 2, 2018: GigaScience
Joseph A Russell, Brittany Campos, Jennifer Stone, Erik M Blosser, Nathan Burkett-Cadena, Jonathan L Jacobs
The future of infectious disease surveillance and outbreak response is trending towards smaller hand-held solutions for point-of-need pathogen detection. Here, samples of Culex cedecei mosquitoes collected in Southern Florida, USA were tested for Venezuelan Equine Encephalitis Virus (VEEV), a previously-weaponized arthropod-borne RNA-virus capable of causing acute and fatal encephalitis in animal and human hosts. A single 20-mosquito pool tested positive for VEEV by quantitative reverse transcription polymerase chain reaction (RT-qPCR) on the Biomeme two3...
April 3, 2018: Scientific Reports
Liu Lu, Yu Feng, Haiyan Long, Alan McNally, Zhiyong Zong
A carbapenem-resistant Klebsiella pneumoniae was recovered from human blood. Its whole genome sequence was obtained using both Illumina and long-read MinION sequencing. The strain belongs to ST273, which has been found recently and caused an outbreak in Southeast Asia. It has two carbapenemase genes bla NDM-1 (carried by an ST7 IncN self-transmissible plasmid) and bla IMP-4 (located on an self-transmissible IncHI5 plasmid). Non-KPC-producing ST237 may represent a lineage of carbapenem-resistant K. pneumoniae , which warrants further monitoring...
April 2, 2018: Antimicrobial Agents and Chemotherapy
HyeonSeok Shin, Eunju Lee, Jongoh Shin, So-Ra Ko, Hyung-Seok Oh, Chi-Yong Ahn, Hee-Mock Oh, Byung-Kwan Cho, Suhyung Cho
Interactions between microalgae and bacteria are often obligatory for harmful algal blooms (HABs). Here, we investigated the specific bacterial communities associated with Alexandrium tamarense and Cochlodinium polykrikoides, which cause ecological and economic damage during their blooms. To this end, the bacterial metagenome was selectively isolated from the two dinoflagellates and subsequently used for 16S rRNA analysis via the Nanopore MinION and Illumina sequencing platforms. Although the full-length 16S rRNA reads from the MinION platform showed high correlation in higher taxonomic ranks to the partial-length 16S rRNA reads from the Illumina platform, there was less correlation at the genus and species levels...
March 28, 2018: Scientific Reports
S Fuselli, R P Baptista, A Panziera, A Magi, S Guglielmi, R Tonin, A Benazzo, L G Bauzer, C J Mazzoni, G Bertorelle
The major histocompatibility complex (MHC) acts as an interface between the immune system and infectious diseases. Accurate characterization and genotyping of the extremely variable MHC loci are challenging especially without a reference sequence. We designed a combination of long-range PCR, Illumina short-reads, and Oxford Nanopore MinION long-reads approaches to capture the genetic variation of the MHC II DRB locus in an Italian population of the Alpine chamois (Rupicapra rupicapra). We utilized long-range PCR to generate a 9 Kb fragment of the DRB locus...
March 24, 2018: Heredity
Sharmin Baig, Thor Bech Johannesen, Søren Overballe-Petersen, Jesper Larsen, Anders Rhod Larsen, Marc Stegger
We identified a novel staphylococcal cassette chromosome mec (SCCmec) element in an ST152 methicillin-resistant Staphylococcus aureus (MRSA) isolate by combining Illumina and MinION sequencing. The element contains a new ccrC allotype designated ccrC2. The mec complex resembles mec class A, but with an altered organization of the genes. The element was acknowledged as novel by the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements (IWG-SCC) and designated SCCmec type XIII (9A)...
March 19, 2018: Infection, Genetics and Evolution
Virginie Sauvage, Laure Boizeau, Daniel Candotti, Mathias Vandenbogaert, Annabelle Servant-Delmas, Valérie Caro, Syria Laperche
Until recently, the method of choice to characterize viral diversity consisted in cloning PCR amplicons of full-length viral genomes and Sanger-sequencing of multiple clones. However, this is extremely laborious, time-consuming, and low-throughput. Next generation short-read sequencing appears also limited by its inability to directly sequence full-length viral genomes. The MinION™ device recently developed by Oxford Nanopore Technologies can be a promising alternative by applying long-read single-molecule sequencing directly to the overall amplified products generated in a PCR reaction...
2018: PloS One
Scott A Dee, Fernando V Bauermann, Megan C Niederwerder, Aaron Singrey, Travis Clement, Marcelo de Lima, Craig Long, Gilbert Patterson, Maureen A Sheahan, Ana M M Stoian, Vlad Petrovan, Cassandra K Jones, Jon De Jong, Ju Ji, Gordon D Spronk, Luke Minion, Jane Christopher-Hennings, Jeff J Zimmerman, Raymond R R Rowland, Eric Nelson, Paul Sundberg, Diego G Diel
The goal of this study was to evaluate survival of important viral pathogens of livestock in animal feed ingredients imported daily into the United States under simulated transboundary conditions. Eleven viruses were selected based on global significance and impact to the livestock industry, including Foot and Mouth Disease Virus (FMDV), Classical Swine Fever Virus (CSFV), African Swine Fever Virus (ASFV), Influenza A Virus of Swine (IAV-S), Pseudorabies virus (PRV), Nipah Virus (NiV), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), Swine Vesicular Disease Virus (SVDV), Vesicular Stomatitis Virus (VSV), Porcine Circovirus Type 2 (PCV2) and Vesicular Exanthema of Swine Virus (VESV)...
2018: PloS One
István Prazsák, Dóra Tombácz, Attila Szűcs, Béla Dénes, Michael Snyder, Zsolt Boldogkői
The vaccinia virus is a large, complex virus belonging to the Poxviridae family. Here, we report the complete, annotated genome sequence of the neurovirulent Western Reserve laboratory strain of this virus, which was sequenced on the Pacific Biosciences RS II and Oxford Nanopore MinION platforms.
March 15, 2018: Genome Announcements
Cosimo Cumbo, Luciana Impera, Crescenzio Francesco Minervini, Paola Orsini, Luisa Anelli, Antonella Zagaria, Nicoletta Coccaro, Giuseppina Tota, Angela Minervini, Paola Casieri, Claudia Brunetti, Antonella Russo Rossi, Elisa Parciante, Giorgina Specchia, Francesco Albano
For monitoring minimal residual disease (MRD) in chronic myeloid leukemia (CML) the most recommended method is quantitative RT-PCR (RT-qPCR) for measuring BCR-ABL1 transcripts. Several studies reported that a DNA-based assay enhances the sensitivity of detection of the BCR-ABL1 genomic rearrangement, even if its characterization results difficult. We developed a DNA-based method for detecting and quantifying residual BCR-ABL1 positive leukemic stem cells in CML patients. We propose two alternative approaches: the first one is a fluorescence in situ hybridization (FISH)-based step followed by Sanger sequencing; the second one employs MinION, a single molecule sequencer based on nanopore technology...
February 16, 2018: Oncotarget
Shan Wei, Zachary R Weiss, Zev Williams
Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples' genomic DNA in under three hours, including library preparation and sequencing...
March 14, 2018: G3: Genes—Genomes—Genetics
Jane Kaye, Sharon F Terry, Eric Juengst, Sarah Coy, Jennifer R Harris, Don Chalmers, Edward S Dove, Isabelle Budin-Ljøsne, Clement Adebamowo, Emilomo Ogbe, Louise Bezuidenhout, Michael Morrison, Joel T Minion, Madeleine J Murtagh, Jusaku Minari, Harriet Teare, Rosario Isasi, Kazuto Kato, Emmanuelle Rial-Sebbag, Patricia Marshall, Barbara Koenig, Anne Cambon-Thomsen
BACKGROUND: Governments, funding bodies, institutions, and publishers have developed a number of strategies to encourage researchers to facilitate access to datasets. The rationale behind this approach is that this will bring a number of benefits and enable advances in healthcare and medicine by allowing the maximum returns from the investment in research, as well as reducing waste and promoting transparency. As this approach gains momentum, these data-sharing practices have implications for many kinds of research as they become standard practice across the world...
March 7, 2018: Human Genomics
Luke W Anson, Kevin Chau, Nicholas Sanderson, Sarah Hoosdally, Phelim Bradley, Zamin Iqbal, Hang Phan, Dona Foster, Sarah Oakley, Marcus Morgan, Tim E A Peto, Modernizing Medical Microbiology Informatics Group Mmmig, Derrick W Crook, Louise J Pankhurst
PURPOSE: Speed of bloodstream infection diagnosis is vital to reduce morbidity and mortality. Whole genome sequencing (WGS) performed directly from liquid blood culture could provide single-assay species and antibiotic susceptibility prediction; however, high inhibitor and human cell/DNA concentrations limit pathogen recovery. We develop a method for the preparation of bacterial DNA for WGS-based diagnostics direct from liquid blood culture. METHODOLOGY: We evaluate three commercial DNA extraction kits: BiOstic Bacteraemia, Amplex Hyplex and MolYsis Plus...
March 2018: Journal of Medical Microbiology
Zinnat Shahina, Amira M El-Ganiny, Jessica Minion, Malcolm Whiteway, Taranum Sultana, Tanya E S Dahms
Background: Cinnamon ( Cinnamomum zeylanicum) bark extract exhibits potent inhibitory activity against Candida albicans but the antifungal mechanisms of this essential oil remain largely unexplored. Results: We analyzed the impact of cinnamon bark oil on C. albicans RSY150, and clinical strains isolated from patients with candidemia and candidiasis. The viability of RSY150 was significantly compromised in a dose dependent manner when exposed to cinnamon bark oil, with extensive cell surface remodelling at sub inhibitory levels (62...
2018: Fungal Biology and Biotechnology
Raga Krishnakumar, Anupama Sinha, Sara W Bird, Harikrishnan Jayamohan, Harrison S Edwards, Joseph S Schoeniger, Kamlesh D Patel, Steven S Branda, Michael S Bartsch
Emerging sequencing technologies are allowing us to characterize environmental, clinical and laboratory samples with increasing speed and detail, including real-time analysis and interpretation of data. One example of this is being able to rapidly and accurately detect a wide range of pathogenic organisms, both in the clinic and the field. Genomes can have radically different GC content however, such that accurate sequence analysis can be challenging depending upon the technology used. Here, we have characterized the performance of the Oxford MinION nanopore sequencer for detection and evaluation of organisms with a range of genomic nucleotide bias...
February 16, 2018: Scientific Reports
Miten Jain, Sergey Koren, Karen H Miga, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes, Sunir Malla, Hannah Marriott, Tom Nieto, Justin O'Grady, Hugh E Olsen, Brent S Pedersen, Arang Rhie, Hollian Richardson, Aaron R Quinlan, Terrance P Snutch, Louise Tee, Benedict Paten, Adam M Phillippy, Jared T Simpson, Nicholas J Loman, Matthew Loose
We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ∼30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ∼3 Mb). We developed a protocol to generate ultra-long reads (N50 > 100 kb, read lengths up to 882 kb)...
January 29, 2018: Nature Biotechnology
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