scholarly journals Whole genome amplification and sequencing of low cell numbers directly from a bacteria spiked blood model

2017 ◽  
Author(s):  
Catherine Anscombe ◽  
Raju.V Misra ◽  
Saheer Gharbia
Keyword(s):  
De Novo ◽  
Multiple Displacement Amplification ◽  
Whole Genome Sequence ◽  
Clinical Samples ◽  
Whole Genome ◽  
Bacterial Cells ◽  
E Coli ◽  
Horse Blood ◽  
Sequencing Platforms ◽  
Overnight Culture

AbstractWhilst next generation sequencing is frequently used to whole genome sequence bacteria from cultures, it’s rarely applied directly to clinical samples. Therefore, this study addresses the issue of applying NGS microbial diagnostics directly to blood samples. To demonstrate the potential of direct from blood sequencing a bacteria spiked blood model was developed. Horse blood was spiked with clinical samples of E. coli and S. aureus, and a process developed to isolate bacterial cells whilst removing the majority of host DNA. One sample of each isolate was then amplified using ϕ29 multiple displacement amplification (MDA) and sequenced. The total processing time, from sample to amplified DNA ready for sequencing was 3.5 hours, significantly faster than the 18-hour overnight culture step which is typically required. Both bacteria showed 100% survival through the processing. The direct from sample sequencing resulted in greater than 92% genome coverage of the pathogens whilst limiting the sequencing of host genome (less than 7% of all reads). Analysis of de novo assembled reads allowed accurate genotypic antibiotic resistance prediction. The sample processing is easily applicable to multiple sequencing platforms. Overall this model demonstrates potential to rapidly generate whole genome bacterial data directly from blood.

scholarly journals Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar

2021 ◽  
Author(s):  
Fatma Ben Abid ◽  
Clement K. M. Tsui ◽  
Yohei Doi ◽  
Anand Deshmukh ◽  
Christi L. McElheny ◽  
...  
Keyword(s):  
Common Species ◽  
Clinical Samples ◽  
Whole Genome ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Genes Encoding ◽  
Encoding Genes ◽  
Sequence Types ◽  
Common Sequence

AbstractOne hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). blaNDM-1 (45; 30.2%) and blaOXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).

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 Whole Genome Sequencing Reveals Identification of New Acinetobacter spp. (maqsudiensis) from Local Meat Samples Collected from Dhaka, Bangladesh

2018 ◽  
Author(s):  
Muhammad Maqsud Hossain ◽  
Abdus Sadique ◽  
Aura Rahman ◽  
Abdul Khaleque ◽  
Abdul Mueed Ibne Momen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Acinetobacter Species ◽  
E Coli ◽  
Potential Marker ◽  
Meat Samples ◽  
Generation Technology

In this study we announce the draft genome sequence of a newly identified Acinetobacter species cross-reacting with E. coli serotype 0157:H7. The advent of Next-Generation technology has paved to way to discover new species which could otherwise be misidentified using conventional cultural and serotyping methods. The whole genome sequence of this isolate will help to identify potential marker/s of intervention and further genomic analysis might also shed light onto the virulence properties of this newly identified Acinetobacter species which has been provided the new name of Acinetobacter maqsudiensis.

scholarly journals Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis)

2020 ◽  
Author(s):  
Sabyasachi Mukherjee ◽  
Zexi Cai ◽  
Anupama Mukherjee ◽  
Imsusosang Longkumer ◽  
Moonmoon Mech ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo Assembly ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genomic Architecture

scholarly journals Whole-Genome Sequence of Phage-Resistant Strain Escherichia coli DH5α

2018 ◽  
Vol 6 (10) ◽  
Author(s):  
Jingchao Chen ◽  
Yi Li ◽  
Kun Zhang ◽  
Hailei Wang
Keyword(s):  
Escherichia Coli ◽  
Comparative Analysis ◽  
Genome Sequence ◽  
Resistant Strain ◽  
Resistance Mechanism ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
E Coli ◽  
T4 Bacteriophage

ABSTRACT The genomes of many strains of Escherichia coli have been sequenced, as this organism is a classic model bacterium. Here, we report the genome sequence of Escherichia coli DH5α, which is resistant to a T4 bacteriophage (CCTCC AB 2015375), while its other homologous E. coli strains, such as E. coli BL21, DH10B, and MG1655, are not resistant to phage invasions. Thus, understanding of the genome of the DH5α strain, along with comparative analysis of its genome sequence along with other sequences of E. coli strains, may help to reveal the bacteriophage resistance mechanism of E. coli .

scholarly journals Whole-Genome Sequence of Pantoea americana Strain VS1, an Extended-Spectrum β-Lactamase-Producing Epibiont Isolated from Magnolia grandiflora

2017 ◽  
Vol 5 (46) ◽  
Author(s):  
Pushpa Lata ◽  
Subramaniam S. Govindarajan ◽  
Feng Qi ◽  
Jian-Liang Li ◽  
Santosh K. Maurya ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Coding Sequences ◽  
Central Florida ◽  
Magnolia Grandiflora ◽  
Extended Spectrum

ABSTRACT Pantoea americana strain VS1, an extended-spectrum β-lactamase-producing epibiont, was isolated from Magnolia grandiflora in central Florida, USA. Here, we report the de novo whole-genome sequence of this strain, which consists of a total of 191 contigs spanning 5,412,831 bp, with a GC content of 57.3% and comprising 4,836 predicted coding sequences.

scholarly journals Whole-Genome Sequencing of Six Borrelia miyamotoi Clinical Strains Isolated in Russia

2018 ◽  
Vol 6 (1) ◽  
Author(s):  
Konstantin V. Kuleshov ◽  
Joris Koetsveld ◽  
Irina A. Goptar ◽  
Mikhail L. Markelov ◽  
Nadezhda M. Kolyasnikova ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequencing ◽  
Russian Federation ◽  
Complete Sequence ◽  
Whole Genome Sequence ◽  
Borrelia Miyamotoi ◽  
Whole Genome ◽  
The Russian Federation ◽  
Sequencing Platforms ◽  
Generation Sequencing

ABSTRACT Here, we report the whole-genome sequence of six clinical Borrelia miyamotoi isolates from the Russian Federation. Using two independent next-generation sequencing platforms, we determined the complete sequence of the chromosome and several plasmids. All strains have an Asian genotype with 99.8% chromosome nucleotide similarity with B. miyamotoi strain FR64b.

scholarly journals The complete genome sequence of Stevia rebaudiana, the Sweetleaf

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 751
Author(s):  
Kathleen O'Neill ◽  
Stacy Pirro
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Related Species ◽  
Complete Genome ◽  
De Novo ◽  
Stevia Rebaudiana ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Link Type ◽  
Sequence Read Archive

The Sweetleaf (Stevia rebaudiana: Asteraceae) is widely grown for use as a sweetener.  We present the whole genome sequence and annotation of this species.  A total of 146,838,888 paired-end reads consisting of 22.2G bases were obtained by sequencing one leaf from a commercially grown seedling.  The reads were assembled by a de-novo method followed by alignment to related species.   Annotation was performed via GenMark-ES. The raw and assembled data is publicly available via GenBank: Sequence Read Archive (SRR6792730) and Assembly (GCA_009936405).

scholarly journals Whole-Genome Sequencing of a Year-Round Fruiting Jackfruit Variety Reveals Very High Single Nucleotide Polymorphisms in Inter-Genic Regions

2021 ◽  
Author(s):  
Tofazzal Islam ◽  
Nadia Afroz ◽  
ChuShin Koh ◽  
M. Nazmul Haque ◽  
Md. Jillur Rahman ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genome Sequence ◽  
De Novo ◽  
Agricultural Research ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Tropical Fruit

Abstract Background Jackfruit (Artocarpus heterophyllus Lam.) is a tropical and sub-tropical fruit tree distributed in Asia, Africa, and South America. It is the national fruit of Bangladesh and produces fruit in the summer season only. However, a year-round jackfruit variety, BARI Kanthal-3 developed by Bangladesh Agricultural Research Institute (BARI) provides fruits from September to June. This study aimed to evaluate the agronomic performance of BARI Kanthal-3 and to generate a draft whole genome sequence to obtain molecular insights of this important unique variety. Results Number of fruits, average each fruit weight, fruit yield per plant, edible portion in fruit and ß carotene content of BARI Kanthal-3 (n = 5) were 422/plant/year, 5.60 kg, 236.32 kg/year, 53.5% and 3614 mg/100g, respectively. During de novo assembly, 817.7 Mb of the BARI Kanthal-3 genome was scaffolded. However, in the reference-guided genome assembly, almost 843 Mb of the BARI Kanthal-3 genome was scaffolded. Through BUSCO assessment, 97.2% of the core genes were represented in the assembly with 1.3% and 1.5% either fragmented or missing, respectively. By comparing the single copy orthologues (SCOs) in three closely and one distantly related species of BARI Kanthal-3, 706 SCOs were found to be shared across the genomes of the five species. The phylogenetic analysis of the shared SCOs showed that A. heterophyllus is the closest species to BARI Kantal-3. The estimated genome size of BARI Kanthal-3 was 1.04 giga base pairs (Gbp) with a heterozygosity rate of 1.62%. The estimated GC content was 34.10%. Variant analysis revealed that BARI Kanthal-3 includes 5.7 M (35%) and 10.4 M (65%) simple and heterozygous single nucleotide polymorphisms (SNPs), and about 90% of all these polymorphisms are located in inter-genic regions. Conclusion The whole-genome sequence of A. heterophyllus cv. BARI Kanthal-3 reveals extremely high single nucleotide polymorphisms in inter-genic regions. The findings of this study will help better understanding the evolution, domestication, phylogenetic relationships, year-round fruiting and the markers development for molecular breeding of this highly nutritious fruit crop.

Whole-genome sequence-guided PCR for the rapid identification of thePseudomonas aeruginosa ST175 high-risk clone directly from clinical samples

2020 ◽  
Author(s):  
Gabriel Cabot ◽  
Paula Lara-Esbrí ◽  
Xavier Mulet ◽  
Antonio Oliver
Keyword(s):  
High Risk ◽  
Sensitivity And Specificity ◽  
Genome Sequence ◽  
Treatment Strategies ◽  
High Sensitivity ◽  
Whole Genome Sequence ◽  
Clinical Samples ◽  
Whole Genome ◽  
Pcr Assay ◽  
Pcr Targeting

Abstract Objectives Pseudomonas aeruginosa frequently show MDR/XDR profiles, which are associated with worldwide-disseminated high-risk clones (HRCs). We developed a PCR assay for the detection in clinical samples of ST175, an HRC that is widespread in European countries. Methods The whole-genome sequence was obtained for one ST175 isolate using a PacBio RSII sequencer. Reads from multiple isolates belonging to ST175 and the PAO1 reference strain were mapped against the ST175 genome to identify potentially specific regions. Once curated, using the BLAST database to search for the presence of those regions in any other organism, we designed a specific PCR for the detection of ST175. Results Assembly of the ST175 PacBio-sequenced genome resulted in three contigs with a total length of 7 087 985 bases, encoding 6566 coding sequences. Specific regions for ST175 genomes were detected and a PCR targeting a 318 bp fragment located within a 3177 bp ORF coding for a putative reverse transcriptase was designed. The PCR test was first evaluatedin silico against 229 XDRP. aeruginosa genomes (73 ST175) from two multicentre studies, yielding 100% sensitivity and specificity. Then, the PCR was evaluatedin vitro in 25 isolates (12 ST175) and in 120 clinical samples (30 urine samples, 30 blood cultures, 30 sputum samples and 30 rectal swabs) of which 10% contained ST175, yielding again 100% sensitivity and specificity. Conclusions The PCR assay developed, showing high sensitivity and specificity for the detection of the ST175 HRC directly from clinical samples, could become a useful tool for guiding infection control and treatment strategies in areas with a high prevalence of this clone.

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