scholarly journals Whole-Genome Assembly of Klebsiella pneumoniae Coproducing NDM-1 and OXA-232 Carbapenemases Using Single-Molecule, Real-Time Sequencing

2014 ◽  
Vol 58 (10) ◽  
pp. 5947-5953 ◽  
Author(s):  
Yohei Doi ◽  
Tracy H. Hazen ◽  
Matthew Boitano ◽  
Yu-Chih Tsai ◽  
Tyson A. Clark ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Real Time ◽  
Single Molecule ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Mercury Resistance ◽  
Whole Genome ◽  
Smrt Sequencing ◽  
Single Chromosome ◽  
Content Type

ABSTRACTThe whole-genome sequence of a carbapenem-resistantKlebsiella pneumoniaestrain, PittNDM01, which coproduces NDM-1 and OXA-232 carbapenemases, was determined in this study. The use of single-molecule, real-time (SMRT) sequencing provided a closed genome in a single sequencing run.K. pneumoniaePittNDM01 has a single chromosome of 5,348,284 bp and four plasmids: pPKPN1 (283,371 bp), pPKPN2 (103,694 bp), pPKPN3 (70,814 bp), and pPKPN4 (6,141 bp). The contents of the chromosome were similar to that of theK. pneumoniaereference genome strain MGH 78578, with the exception of a large inversion spanning 23.3% of the chromosome. In contrast, three of the four plasmids are unique. The plasmid pPKPN1, an IncHI1B-like plasmid, carries theblaNDM-1,armA, andqnrB1genes, along with tellurium and mercury resistance operons.blaNDM-1is carried on a unique structure in which Tn125is further bracketed by IS26downstream of a class 1 integron. The IncFIA-like plasmid pPKPN3 also carries an array of resistance elements, includingblaCTX-M-15and a mercury resistance operon. The ColE-type plasmid pPKPN4 carryingblaOXA-232is identical to a plasmid previously reported from France. SMRT sequencing was useful in resolving the complex bacterial genomic structures in thede novoassemblies.

scholarly journals Genomic Analysis of Sarcomyxa edulis Reveals the Basis of Its Medicinal Properties and Evolutionary Relationships

2021 ◽  
Vol 12 ◽  
Author(s):  
Fenghua Tian ◽  
Changtian Li ◽  
Yu Li
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Genomic Analysis ◽  
Single Copy ◽  
Whole Genome Sequence ◽  
Type I ◽  
Whole Genome ◽  
Uridine Diphosphate ◽  
Protein Coding ◽  
Medicinal Value

Yuanmo [Sarcomyxa edulis (Y.C. Dai, Niemelä & G.F. Qin) T. Saito, Tonouchi & T. Harada] is an important edible and medicinal mushroom endemic to Northeastern China. Here we report the de novo sequencing and assembly of the S. edulis genome using single-molecule real-time sequencing technology. The whole genome was approximately 35.65 Mb, with a G + C content of 48.31%. Genome assembly generated 41 contigs with an N50 length of 1,772,559 bp. The genome comprised 9,364 annotated protein-coding genes, many of which encoded enzymes involved in the modification, biosynthesis, and degradation of glycoconjugates and carbohydrates or enzymes predicted to be involved in the biosynthesis of secondary metabolites such as terpene, type I polyketide, siderophore, and fatty acids, which are responsible for the pharmacodynamic activities of S. edulis. We also identified genes encoding 1,3-β-glucan synthase and endo-1,3(4)-β-glucanase, which are involved in polysaccharide and uridine diphosphate glucose biosynthesis. Phylogenetic and comparative analyses of Basidiomycota fungi based on a single-copy orthologous protein indicated that the Sarcomyxa genus is an independent group that evolved from the Pleurotaceae family. The annotated whole-genome sequence of S. edulis can serve as a reference for investigations of bioactive compounds with medicinal value and the development and commercial production of superior S. edulis varieties.

scholarly journals Sequence Type 273 Carbapenem-Resistant Klebsiella pneumoniae Carrying bla NDM-1 and bla IMP-4

2018 ◽  
Vol 62 (6) ◽  
Author(s):  
Lu Liu ◽  
Yu Feng ◽  
Haiyan Long ◽  
Alan McNally ◽  
Zhiyong Zong
Keyword(s):  
Klebsiella Pneumoniae ◽  
Southeast Asia ◽  
Human Blood ◽  
Sequence Type ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Carbapenem Resistant ◽  
Transmissible Plasmid ◽  
Long Read

ABSTRACT A carbapenem-resistant Klebsiella pneumoniae isolate was recovered from human blood. Its whole-genome sequence was obtained using Illumina and long-read MinION sequencing. The strain belongs to sequence type 273 (ST273), which was 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 a self-transmissible IncHI5 plasmid). Non-KPC-producing ST237 may represent a lineage of carbapenem-resistant K. pneumoniae , which warrants further monitoring.

scholarly journals Whole-Genome Sequence of Bacillus megaterium Strain SGAir0080, Isolated from an Indoor Air Sample

2019 ◽  
Vol 8 (50) ◽  
Author(s):  
Namrata Kalsi ◽  
Akira Uchida ◽  
Rikky W. Purbojati ◽  
James N. I. Houghton ◽  
Caroline Chénard ◽  
...  
Keyword(s):  
Single Molecule ◽  
Bacillus Megaterium ◽  
Indoor Air ◽  
Average Length ◽  
Whole Genome Sequence ◽  
Smrt Sequencing ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Air Sample

Bacillus megaterium strain SGAir0080 was isolated from a tropical air sample in Singapore. Its genome was assembled using single-molecule real-time (SMRT) sequencing and MiSeq reads. It has one chromosome of 5.06 Mbp and seven plasmids (average length, 62.8 kbp). It possesses 5,339 protein-coding genes, 130 tRNAs, and 35 rRNAs.

scholarly journals Complete Genome and Methylome Analysis of the Box-Shaped Halophilic Archaeon Haloarcula sinaiiensis ATCC 33800

2021 ◽  
Vol 10 (34) ◽  
Author(s):  
Alexey Fomenkov ◽  
Priya DasSarma ◽  
Sean P. Kennedy ◽  
Richard J. Roberts ◽  
Shiladitya DasSarma
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Complete Genome ◽  
Bioinformatic Analysis ◽  
Halophilic Archaeon ◽  
Smrt Sequencing ◽  
Content Type ◽  
Methylome Analysis

The genome of halophilic archaeon Haloarcula sinaiiensis ATCC 33800 was sequenced and assembled and comprises seven replicons. Four m6A and one m4C modified motifs and their responsible methyltransferase genes have been identified in the genome by single-molecule real-time (SMRT) sequencing and bioinformatic analysis.

scholarly journals Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)

GigaScience ◽  
2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Yu Xing ◽  
Yang Liu ◽  
Qing Zhang ◽  
Xinghua Nie ◽  
Yamin Sun ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Genetic Improvement ◽  
De Novo ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
High Quality ◽  
Chinese Chestnut ◽  
Castanea Mollissima

AbstractBackgroundThe Chinese chestnut (Castanea mollissima) is widely cultivated in China for nut production. This plant also plays an important ecological role in afforestation and ecosystem services. To facilitate and expand the use of C. mollissima for breeding and its genetic improvement, we report here the whole-genome sequence of C. mollissima.FindingsWe produced a high-quality assembly of the C. mollissima genome using Pacific Biosciences single-molecule sequencing. The final draft genome is ∼785.53 Mb long, with a contig N50 size of 944 kb, and we further annotated 36,479 protein-coding genes in the genome. Phylogenetic analysis showed that C. mollissima diverged from Quercus robur, a member of the Fagaceae family, ∼13.62 million years ago.ConclusionsThe high-quality whole-genome assembly of C. mollissima will be a valuable resource for further genetic improvement and breeding for disease resistance and nut quality.

scholarly journals Lineage-Specific Methyltransferases Define the Methylome of the Globally Disseminated Escherichia coli ST131 Clone

mBio ◽  
2015 ◽  
Vol 6 (6) ◽  
Author(s):  
Brian M. Forde ◽  
Minh-Duy Phan ◽  
Jayde A. Gawthorne ◽  
Melinda M. Ashcroft ◽  
Mitchell Stanton-Cook ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Methylation ◽  
Real Time ◽  
Single Molecule ◽  
Mobile Genetic Elements ◽  
Sequence Type ◽  
Type I ◽  
Smrt Sequencing ◽  
Content Type ◽  
E Coli

ABSTRACTEscherichia colisequence type 131 (ST131) is a clone of uropathogenicE. colithat has emerged rapidly and disseminated globally in both clinical and community settings. Members of the ST131 lineage from across the globe have been comprehensively characterized in terms of antibiotic resistance, virulence potential, and pathogenicity, but to date nothing is known about the methylome of these important human pathogens. Here we used single-molecule real-time (SMRT) PacBio sequencing to determine the methylome ofE. coliEC958, the most-well-characterized completely sequenced ST131 strain. Our analysis of 52,081 methylated adenines in the genome of EC958 discovered threem6A methylation motifs that have not been described previously. Subsequent SMRT sequencing of isogenic knockout mutants identified the two type I methyltransferases (MTases) and one type IIG MTase responsible form6A methylation of novel recognition sites. Although both type I sites were rare, the type IIG sites accounted for more than 12% of all methylated adenines in EC958. Analysis of the distribution of MTase genes across 95 ST131 genomes revealed their prevalence is highly conserved within the ST131 lineage, with most variation due to the presence or absence of mobile genetic elements on which individual MTase genes are located.IMPORTANCEDNA modification plays a crucial role in bacterial regulation. Despite several examples demonstrating the role of methyltransferase (MTase) enzymes in bacterial virulence, investigation of this phenomenon on a whole-genome scale has remained elusive until now. Here we used single-molecule real-time (SMRT) sequencing to determine the first complete methylome of a strain from the multidrug-resistantE. colisequence type 131 (ST131) lineage. By interrogating the methylome computationally and with further SMRT sequencing of isogenic mutants representing previously uncharacterized MTase genes, we defined the target sequences of three novel ST131-specific MTases and determined the genomic distribution of all MTase target sequences. Using a large collection of 95 previously sequenced ST131 genomes, we identified mobile genetic elements as a major factor driving diversity in DNA methylation patterns. Overall, our analysis highlights the potential for DNA methylation to dramatically influence gene regulation at the transcriptional level within a well-definedE. coliclone.

scholarly journals Draft Whole-Genome Sequence of a Klebsiella pneumoniae Strain Isolated from a Marmoset in Thailand

2021 ◽  
Vol 10 (31) ◽  
Author(s):  
Komkiew Pinpimai ◽  
Wijit Bunlunara ◽  
Katriya Chankow ◽  
Rachod Tantilertcharoen ◽  
Pongthai Boonkam ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Negative Bacterium ◽  
Gram Negative ◽  
Content Type

Klebsiella pneumoniae is a Gram-negative bacterium that can cause infection in various kinds of animals and humans. Here, we report the genome sequence of K. pneumoniae isolated from a captive marmoset in Thailand.

scholarly journals Spread of Carbapenem-Resistant Klebsiella pneumoniae in an Intensive Care Unit: A Whole-Genome Sequence-Based Prospective Observational Study

2021 ◽  
Author(s):  
Li Wei ◽  
Linfei Wu ◽  
Hongxia Wen ◽  
Yu Feng ◽  
Shichao Zhu ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Intensive Care ◽  
Klebsiella Pneumoniae ◽  
Prospective Observational Study ◽  
Opportunistic Pathogen ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Carbapenem Resistant ◽  
Human Infections

Klebsiella pneumoniae can be an opportunistic pathogen with the oral cavity and gut the main origin. However, carbapenem-resistant Klebsiella pneumoniae (CRKP) can be found in patient surroundings and is a serious threat for human infections.

scholarly journals Whole-Genome Sequence of Hafnia alvei HUMV-5920, a Human Isolate

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
María Lázaro-Díez ◽  
Santiago Redondo-Salvo ◽  
Aroa Arboleya-Agudo ◽  
Javier Gonzalo Ocejo-Vinyals ◽  
Itziar Chapartegui-González ◽  
...  
Keyword(s):  
Adult Patient ◽  
Single Molecule ◽  
Genome Assembly ◽  
Complete Genome ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Smrt Sequencing ◽  
Protein Coding ◽  
Hafnia Alvei ◽  
Protein Coding Genes

A clinical isolate of Hafnia alvei (strain HUMV-5920) was obtained from a urine sample from an adult patient. We report here its complete genome assembly using PacBio single-molecule real-time (SMRT) sequencing, which resulted in a chromosome with 4.5 Mb and a circular contig of 87 kb. About 4,146 protein-coding genes are predicted from this assembly.

scholarly journals Applying Rapid Whole-Genome Sequencing To Predict Phenotypic Antimicrobial Susceptibility Testing Results among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates

2018 ◽  
Vol 63 (1) ◽  
Author(s):  
Pranita D. Tamma ◽  
Yunfan Fan ◽  
Yehudit Bergman ◽  
Geo Pertea ◽  
Abida Q. Kazmi ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Real Time ◽  
Genome Sequencing ◽  
Susceptibility Testing ◽  
Whole Genome ◽  
Nanopore Sequencing ◽  
Short Read ◽  
Content Type ◽  
The Real ◽  
Carbapenem Resistant

ABSTRACT Standard antimicrobial susceptibility testing (AST) approaches lead to delays in the selection of optimal antimicrobial therapy. Here, we sought to determine the accuracy of antimicrobial resistance (AMR) determinants identified by Nanopore whole-genome sequencing in predicting AST results. Using a cohort of 40 clinical isolates (21 carbapenemase-producing carbapenem-resistant Klebsiella pneumoniae, 10 non-carbapenemase-producing carbapenem-resistant K. pneumoniae, and 9 carbapenem-susceptible K. pneumoniae isolates), three separate sequencing and analysis pipelines were performed, as follows: (i) a real-time Nanopore analysis approach identifying acquired AMR genes, (ii) an assembly-based Nanopore approach identifying acquired AMR genes and chromosomal mutations, and (iii) an approach using short-read correction of Nanopore assemblies. The short-read correction of Nanopore assemblies served as the reference standard to determine the accuracy of Nanopore sequencing results. With the real-time analysis approach, full annotation of acquired AMR genes occurred within 8 h from subcultured isolates. Assemblies sufficient for full resistance gene and single-nucleotide polymorphism annotation were available within 14 h from subcultured isolates. The overall agreement of genotypic results and anticipated AST results for the 40 K. pneumoniae isolates was 77% (range, 30% to 100%) and 92% (range, 80% to 100%) for the real-time approach and the assembly approach, respectively. Evaluating the patients contributing the 40 isolates, the real-time approach and assembly approach could shorten the median time to effective antibiotic therapy by 20 h and 26 h, respectively, compared to standard AST. Nanopore sequencing offers a rapid approach to both accurately identify resistance mechanisms and to predict AST results for K. pneumoniae isolates. Bioinformatics improvements enabling real-time alignment, coupled with rapid extraction and library preparation, will further enhance the accuracy and workflow of the Nanopore real-time approach.

Sign in / Sign up

Export Citation Format

Share Document