scholarly journals Closed Genome Sequences of Clinical Neisseria gonorrhoeae Strains Obtained from Combined Oxford Nanopore and Illumina Sequencing

2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Richard C. White ◽  
Manolito Torralba ◽  
Kelly Colt ◽  
Frank Harrison ◽  
Karrie Goglin ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Hybrid Approach ◽  
Illumina Miseq ◽  
The United States ◽  
Sequencing Data ◽  
Notifiable Disease ◽  
Genome Sequences ◽  
Content Type ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

Neisseria gonorrhoeae is the etiological agent of gonorrhea, the second most common notifiable disease in the United States. Here, we used a hybrid approach combining Oxford Nanopore Technologies MinION and Illumina MiSeq sequencing data to obtain closed genome sequences of nine clinical N. gonorrhoeae isolates.

scholarly journals Complete Genome Sequence of Staphylococcus arlettae Strain P2, Isolated from a Laboratory Environment

2019 ◽  
Vol 8 (45) ◽  
Author(s):  
Hiroki Yu ◽  
Makoto Taniguchi ◽  
Kazuma Uesaka ◽  
Apirak Wiseschart ◽  
Kusol Pootanakit ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Hybrid Approach ◽  
Illumina Miseq ◽  
Sequencing Data ◽  
Content Type ◽  
Short Read Sequencing ◽  
Oxford Nanopore ◽  
Long Read

Staphylococcus arlettae is one coagulase-negative species in the bacterial genus Staphylococcus. Here, we describe the closed complete genome sequence of S. arlettae strain P2, which was obtained using a hybrid approach combining Oxford Nanopore long-read and Illumina MiSeq short-read sequencing data.

scholarly journals Complete Genome Sequences of Bordetella pertussis Clinical Isolate FR5810 and Reference Strain Tohama from Combined Oxford Nanopore and Illumina Sequencing

2018 ◽  
Vol 7 (19) ◽  
Author(s):  
Valérie Bouchez ◽  
Sarah Louise Baines ◽  
Sophie Guillot ◽  
Sylvain Brisse
Keyword(s):  
Clinical Isolate ◽  
Bordetella Pertussis ◽  
Complete Genome ◽  
Reference Strain ◽  
Sequence Data ◽  
Hybrid Approach ◽  
Genome Sequences ◽  
Content Type ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

Here, we describe the complete genome sequences of two Bordetella pertussis strains, FR5810, a clinical isolate recovered from the respiratory tract of an infant, and Tohama, a key reference strain for the species. Sequences were obtained using a hybrid approach combining Oxford Nanopore Technologies MinION and Illumina NextSeq 500 sequence data.

scholarly journals Complete Genome Sequences for Pseudomonas sp. Strains 29A and 43A

2020 ◽  
Vol 9 (39) ◽  
Author(s):  
David A. Baltrus ◽  
Meara Clark ◽  
Parris T. Humphrey ◽  
Noah K. Whiteman
Keyword(s):  
Complete Genome ◽  
Hybrid Approach ◽  
Flow Cell ◽  
Pseudomonas Sp ◽  
Genome Sequences ◽  
Content Type ◽  
Oxford Nanopore ◽  
Cardamine Cordifolia

ABSTRACT Pseudomonas sp. strains 29A and 43A were originally isolated from the phyllosphere of individual plants of Cardamine cordifolia (Brassicaceae). Here, we report complete genome sequences for these two closely related strains, assembled using a hybrid approach combining Illumina paired-end reads and longer reads sequenced on an Oxford Nanopore MinION flow cell.

scholarly journals Real-Time Sequencing of Mycobacterium tuberculosis: Are We There Yet?

2017 ◽  
Vol 55 (5) ◽  
pp. 1249-1254 ◽  
Author(s):  
Robyn S. Lee ◽  
Madhukar Pai
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Real Time ◽  
Phylogenetic Trees ◽  
Illumina Miseq ◽  
Turnaround Time ◽  
Epidemiologic Studies ◽  
Content Type ◽  
Leading Role ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

ABSTRACT Whole-genome sequencing has taken a leading role in epidemiologic studies of tuberculosis, but thus far, its real-time clinical utility has been low, in part because of the requirement for culture. In their report in this issue, Votintseva et al. (A. A. Votintseva, P. Bradley, L. Pankhurst, C. del Ojo Elias, M. Loose, K. Nilgiriwala, A. Chatterjee, E. G. Smith, N. Sanderson, T. M. Walker, M. R. Morgan, D. H. Wyllie, A. S. Walker, T. E. A. Peto, D. W. Crook, and Z. Iqbal, J Clin Microbiol 55:1285–1298, 2017, https://doi.org/10.1128/JCM.02483-16 ) present a new method for extracting Mycobacterium tuberculosis DNA directly from smear-positive respiratory samples, making it feasible to generate drug resistance predictions and phylogenetic trees in 44 h with the Illumina MiSeq. They also illustrate the potential for a <24-h turnaround time from DNA extraction to clinically relevant results with Illumina MiniSeq and Oxford Nanopore Technologies MinION. We comment on the promise and limitations of these approaches.

scholarly journals Complete Genome Sequence of the Type Strain Pectobacterium punjabense SS95, Isolated from a Potato Plant with Blackleg Symptoms

2020 ◽  
Vol 9 (32) ◽  
Author(s):  
Sohaib Sarfraz ◽  
Saïd Oulghazi ◽  
Jérémy Cigna ◽  
Shahbaz Talib Sahi ◽  
Kashif Riaz ◽  
...  
Keyword(s):  
Complete Genome ◽  
Type Strain ◽  
Gc Content ◽  
Illumina Miseq ◽  
Blackleg Disease ◽  
Circular Chromosome ◽  
Content Type ◽  
Potato Plants ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

ABSTRACT Pectobacterium punjabense is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of P. punjabense SS95T, which contains a circular chromosome of 4.793 Mb with a GC content of 50.7%.

scholarly journals Complete and Circularized Genome Assemblies of the Kroppenstedtia eburnea Genus Type Strain and the Kroppenstedtia pulmonis Species Type Strain with MiSeq and MinION Sequence Data

2020 ◽  
Vol 9 (44) ◽  
Author(s):  
Christopher A. Gulvik ◽  
Dhwani Batra ◽  
Lori A. Rowe ◽  
Milli Sheth ◽  
Ben W. Humrighouse ◽  
...  
Keyword(s):  
Type Strain ◽  
Sequence Data ◽  
Gene Clusters ◽  
Illumina Miseq ◽  
Putative Gene ◽  
Content Type ◽  
Oxford Nanopore ◽  
Species Type ◽  
Genome Assemblies ◽  
Oxford Nanopore Technologies

ABSTRACT Kroppenstedtia eburnea DSM 45196T and Kroppenstedtia pulmonis W9323T are aerobic, Gram-positive, filamentous, chemoorganotrophic thermoactinomycetes. Here, we report on the complete and circular genome assemblies generated using Illumina MiSeq and Oxford Nanopore Technologies MinION reads. Putative gene clusters predicted to be involved in the production of secondary metabolites were also identified.

scholarly journals Draft Genome Sequences of Three Penicillin-Resistant Neisseria gonorrhoeae Strains Isolated in Cincinnati, Ohio, in 1994

2021 ◽  
Vol 10 (11) ◽  
Author(s):  
Thomas C. Murphy ◽  
Tatum D. Mortimer ◽  
Robert A. Nicholas ◽  
Crista B. Wadsworth
Keyword(s):  
United States ◽  
Neisseria Gonorrhoeae ◽  
Genetic Relationships ◽  
Draft Genome ◽  
The United States ◽  
Resistance Mutations ◽  
Genome Sequences ◽  
Content Type ◽  
Associated Data

ABSTRACT Here, we report the draft genome sequences of three penicillin-resistant Neisseria gonorrhoeae isolates. We include associated data on MICs and genetic relationships to other N. gonorrhoeae strains collected from across the United States. Resistance mutations known to contribute to reduced penicillin susceptibility are annotated in each genome.

scholarly journals Yersinia canariae sp. nov., isolated from a human yersiniosis case

2020 ◽  
Vol 70 (4) ◽  
pp. 2382-2387 ◽  
Author(s):  
Scott V. Nguyen ◽  
David R. Greig ◽  
Daniel Hurley ◽  
Orla Donoghue ◽  
Yu Cao ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Novel Species ◽  
Sequencing Data ◽  
Illumina Hiseq ◽  
Content Type ◽  
Link Type ◽  
The United Kingdom ◽  
Oxford Nanopore ◽  
Long Read ◽  
Oxford Nanopore Technologies

A Gram-negative rod from the Yersinia genus was isolated from a clinical case of yersiniosis in the United Kingdom. Long read sequencing data from an Oxford Nanopore Technologies (ONT) MinION in conjunction with Illumina HiSeq reads were used to generate a finished quality genome of this strain. Overall Genome Related Index (OGRI) of the strain was used to determine that it was a novel species within Yersinia , despite biochemical similarities to Yersinia enterocolitica . The 16S ribosomal RNA gene accessions are MN434982-MN434987 and the accession number for the complete and closed chromosome is CP043727. The type strain is SRR7544370T (=NCTC 14382T/=LMG 31573T).

scholarly journals Complete Genome Sequences of Four Putatively Antibiotic-Producing Bacteria Isolated from Soil in Arkansas, USA

2022 ◽  
Author(s):  
Ruth Plymale ◽  
Griffin Hopkins ◽  
Taylor Johnson ◽  
Taylor Savage ◽  
Danielle Schaal
Keyword(s):  
Complete Genome ◽  
Soil Bacteria ◽  
Hybrid Approach ◽  
Antimicrobial Compounds ◽  
Research Experience ◽  
Genome Sequences ◽  
Valuable Source ◽  
Oxford Nanopore ◽  
Complete Genomes ◽  
Oxford Nanopore Technologies

Soil bacteria can be a valuable source of antimicrobial compounds. Here, we report the complete genomes of four soil bacteria that were isolated by undergraduate microbiology students as part of a course-based research experience. These genomes were assembled using a hybrid approach combining paired-end Illumina reads with Oxford Nanopore Technologies MinION reads.

scholarly journals Nanopore sequencing of Giardia reveals widespread intra-isolate structural variation

2018 ◽  
Author(s):  
Stephen M. J. Pollo ◽  
Sarah J. Reiling ◽  
Janneke Wit ◽  
Matthew L. Workentine ◽  
Rebecca A. Guy ◽  
...  
Keyword(s):  
Hybrid Approach ◽  
Giardia Duodenalis ◽  
Surface Proteins ◽  
Sequencing Data ◽  
Short Reads ◽  
Structural Variant ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Reference Quality ◽  
Oxford Nanopore Technologies

AbstractBackgroundGenomes of the parasite Giardia duodenalis are relatively small for eukaryotic genomes, yet there are only six publicly available. Difficulties in assembling the tetraploid G. duodenalis genome from short read sequencing data likely contribute to this lack of genomic information. We sequenced three isolates of G. duodenalis (AWB, BGS, and beaver) on the Oxford Nanopore Technologies MinION whose long reads have the potential to address genomic areas that are problematic for short reads.ResultsUsing a hybrid approach that combines MinION long reads and Illumina short reads to take advantage of the continuity of the long reads and the accuracy of the short reads we generated reference quality genomes for each isolate. The genomes for two of the isolates were evaluated against the available reference genomes for comparison. The third genome for which there is no previous data was then assembled. The long reads were used to find structural variants in each isolate to examine heterozygosity. Consistent with previous findings based on SNPs, Giardia BGS was found to be considerably more heterozygous than the other isolates that are from Assemblage A. We also find an enrichment of variant-specific surface proteins in some of the structural variant regions.ConclusionsOur results show that the MinION can be used to generate reference quality genomes in Giardia and further be used to identify structural variant regions that are an important source of genetic variation not previously examined in these parasites.

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