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

2019 ◽  
Author(s):  
Scott V. Nguyen ◽  
David R. Greig ◽  
Daniel Hurley ◽  
Yu Cao ◽  
Evonne McCabe ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Novel Species ◽  
Accession Number ◽  
Sequencing Data ◽  
Illumina Hiseq ◽  
Link Type ◽  
The United Kingdom ◽  
Oxford Nanopore ◽  
16S Ribosomal Rna Gene ◽  
Long Read

ABSTRACTA 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 Technology (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 CFS3336T (=NCTC 14382T/ =LMG Accession under process).

scholarly journals Draft Genome Sequence of Pandrug-Resistant Pseudomonas aeruginosa SPA03, Isolated from a Patient with Benign Prostatic Hyperplasia

2021 ◽  
Vol 10 (22) ◽  
Author(s):  
Chanakya Pachi Pulusu ◽  
Balaram Khamari ◽  
Manmath Lama ◽  
Arun Sai Kumar Peketi ◽  
Prakash Kumar ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Benign Prostatic Hyperplasia ◽  
Sequence Data ◽  
Draft Genome ◽  
Prostatic Hyperplasia ◽  
Illumina Hiseq ◽  
Content Type ◽  
Oxford Nanopore ◽  
Long Read ◽  
Oxford Nanopore Technologies

The draft genome of pandrug-resistant Pseudomonas aeruginosa strain SPA03, which belongs to global high-risk sequence type 357 (ST357) and was isolated from a patient with benign prostatic hyperplasia, is presented in this report. The genome assembly was generated by combining short-read Illumina HiSeq-X Ten and long-read Oxford Nanopore Technologies MinION sequence data using the Unicycler assembler.

scholarly journals NanoPack: visualizing and processing long read sequencing data

2017 ◽  
Author(s):  
Wouter De Coster ◽  
Svenn D’Hert ◽  
Darrin T. Schultz ◽  
Marc Cruts ◽  
Christine Van Broeckhoven
Keyword(s):  
Web Service ◽  
Graphical User Interface ◽  
Source Code ◽  
Supplementary Information ◽  
Command Line ◽  
Sequencing Data ◽  
Link Type ◽  
Oxford Nanopore ◽  
Long Read ◽  
Oxford Nanopore Technologies

AbstractSummary: Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.Availability and Implementation: The NanoPack tools are written in Python3 and released under the GNU GPL3.0 Licence. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools.Contact:[email protected] information: Supplementary tables and figures are available at Bioinformatics online.

scholarly journals Complete Genome Sequence of Rubrobacter xylanophilus Strain AA3-22, Isolated from Arima Onsen in Japan

2019 ◽  
Vol 8 (34) ◽  
Author(s):  
Natsuki Tomariguchi ◽  
Kentaro Miyazaki
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Hot Spring ◽  
Sequencing Data ◽  
Short Read ◽  
Content Type ◽  
Short Read Sequencing ◽  
Oxford Nanopore ◽  
Long Read

Rubrobacter xylanophilus strain AA3-22, belonging to the phylum Actinobacteria, was isolated from nonvolcanic Arima Onsen (hot spring) in Japan. Here, we report the complete genome sequence of this organism, which was obtained by combining Oxford Nanopore long-read and Illumina short-read sequencing data.

scholarly journals Updated Genome Sequence for the Probiotic Bacterium Bifidobacterium animalis subsp. lactis BB-12

2021 ◽  
Vol 10 (27) ◽  
Author(s):  
Kristian Jensen ◽  
Kosai Al-Nakeeb ◽  
Anna Koza ◽  
Ahmad A. Zeidan
Keyword(s):  
Genome Sequence ◽  
Probiotic Bacterium ◽  
Content Type ◽  
Short Read Sequencing ◽  
Bifidobacterium Animalis ◽  
Oxford Nanopore ◽  
Hybrid Genome ◽  
Long Read ◽  
Sequencing Platforms ◽  
Oxford Nanopore Technologies

The genome of Bifidobacterium animalis subsp. lactis BB-12 was sequenced using Oxford Nanopore Technologies long-read and Illumina short-read sequencing platforms. A hybrid genome assembly approach was used to construct an updated complete genome sequence for BB-12 containing 1,944,152 bp, with a G+C content of 60.5% and 1,615 genes.

scholarly journals Complete Genome Sequence of Vibrio rotiferianus Strain AM7

2020 ◽  
Vol 9 (21) ◽  
Author(s):  
Kentaro Miyazaki ◽  
Apirak Wiseschart ◽  
Kusol Pootanakit ◽  
Kei Kitahara
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
The Novel ◽  
Sequencing Data ◽  
Short Read ◽  
Content Type ◽  
Short Read Sequencing ◽  
Oxford Nanopore ◽  
Long Read

ABSTRACT We isolated the novel strain Vibrio rotiferianus AM7 from the shell of an abalone. In this article, we report the complete genome sequence of this organism, which was obtained by combining Oxford Nanopore long-read and Illumina short-read sequencing data.

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 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 Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK

2021 ◽  
Vol 7 (8) ◽  
Author(s):  
Rebecca K. Locke ◽  
David R. Greig ◽  
Claire Jenkins ◽  
Tim J. Dallman ◽  
Lauren A. Cowley
Keyword(s):  
Type Species ◽  
Multidrug Resistant ◽  
Resistance Locus ◽  
Content Type ◽  
Link Type ◽  
Shigella Species ◽  
Oxford Nanopore ◽  
Sex With Men ◽  
The Uk ◽  
Oxford Nanopore Technologies

Shigellosis in men who have sex with men (MSM) is caused by multidrug resistant Shigellae, exhibiting resistance to antimicrobials including azithromycin, ciprofloxacin and more recently the third-generation cephalosporins. We sequenced four bla CTX-M-27-positive MSM Shigella isolates (2018–20) using Oxford Nanopore Technologies; three S. sonnei (identified as two MSM clade 2, one MSM clade 5) and one S. flexneri 3a, to explore AMR context. All S. sonnei isolates harboured Tn7/Int2 chromosomal integrons, whereas S. flexneri 3a contained the Shigella Resistance Locus. All strains harboured IncFII pKSR100-like plasmids (67-83kbp); where present bla CTX-M-27 was located on these plasmids flanked by IS26 and IS903B, however bla CTX-M-27 was lost in S. flexneri 3a during storage between Illumina and Nanopore sequencing. IncFII AMR regions were mosaic and likely reorganised by IS26; three of the four plasmids contained azithromycin-resistance genes erm(B) and mph(A) and one harboured the pKSR100 integron. Additionally, all S. sonnei isolates possessed a large IncB/O/K/Z plasmid, two of which carried aph(3’)-Ib/aph(6)-Id/sul2 and tet(A). Monitoring the transmission of mobile genetic elements with co-located AMR determinants is necessary to inform empirical treatment guidance and clinical management of MSM-associated shigellosis.

scholarly journals Pseudomonas kirkiae sp. nov., a novel species isolated from oak in the United Kingdom, and phylogenetic considerations of the genera Pseudomonas, Azotobacter and Azomonas

2020 ◽  
Vol 70 (4) ◽  
pp. 2426-2434 ◽  
Author(s):  
Victoria Bueno-Gonzalez ◽  
Carrie Brady ◽  
Sandra Denman ◽  
Joël Allainguillaume ◽  
Dawn Arnold
Keyword(s):  
United Kingdom ◽  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The United Kingdom ◽  
Species Comparisons

As the current episode of Acute Oak Decline (AOD) continues to affect native British oak in the United Kingdom, ongoing isolations from symptomatic and healthy oak have yielded a large Pseudomonas species population. These strains could be divided into taxa representing three potential novel species. Recently, two of these taxa were described as novel Pseudomonas species in the Pseudomonas fluorescens lineage. Here, we demonstrate using a polyphasic approach that the third taxon represents another novel Pseudomonas species. The 16S rRNA gene sequencing assigned the strains to the Pseudomonas aeruginosa lineage, while multilocus sequence analysis (based on partial gyrB, rpoB and rpoD sequences) placed the 13 strains in a single cluster on the border of the Pseudomonas stutzeri group. Whole genome intra-species comparisons (based on average nucleotide identity and in silico DNA–DNA hybridization) confirmed that the strains belong to a single taxon, while the inter-species comparisons with closest phylogenetic relatives yielded similarity values below the accepted species threshold. Therefore, we propose these strains as a novel species, namely Pseudomonas kirkiae sp. nov., with the type strain FRB 229T (P4CT=LMG 31089T=NCPPB 4674T). The phylogenetic analyses performed in this study highlighted the difficulties in assigning novel species to the genus Pseudomonas due to its polyphyletic nature and close relationship to the genus Azotobacter . We further propose that a thorough taxonomic re-evaluation of the genus Pseudomonas is essential and should be performed in the near future.

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