scholarly journals Fecal Carriage and Molecular Characterization of Carbapenemase-Producing Enterobacterales in the Pediatric Population in Qatar

2021 ◽  
Author(s):  
Andrés Pérez-López ◽  
Sathyavathi Sundararaju ◽  
Kin Ming Tsui ◽  
Hassan Al-Mana ◽  
Mohammad Rubayet Hasan ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Arabian Peninsula ◽  
Pediatric Population ◽  
Molecular Characteristics ◽  
Whole Genome ◽  
Fecal Carriage ◽  
Demographic Patterns

To the best of our knowledge, this is the first study addressing the molecular characteristics of CPE in a pediatric population in Qatar using whole-genome sequencing. Since several countries in the Arabian Peninsula share relatively similar demographic patterns and international links, it is plausible that the molecular characteristics of CPE in children, at least in the middle and eastern parts of the region, are similar to those observed in our study.

scholarly journals SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Weili Cai ◽  
Schyler Nunziata ◽  
John Rascoe ◽  
Michael J. Stulberg
Keyword(s):  
Whole Genome Sequencing ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Coverage ◽  
Metagenomic Sample ◽  
Liberibacter Asiaticus

AbstractHuanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

scholarly journals Whole-Genome Sequencing: An Effective Strategy for Insertion Information Analysis of Foreign Genes in Transgenic Plants

2020 ◽  
Vol 11 ◽  
Author(s):  
Xu-jing Wang ◽  
Yue Jiao ◽  
Shuo Ma ◽  
Jiang-tao Yang ◽  
Zhi-xing Wang
Keyword(s):  
Whole Genome Sequencing ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Genetically Modified Organisms ◽  
Chromosome 8 ◽  
Foreign Gene ◽  
Whole Genome ◽  
Effective Strategy ◽  
Flanking Sequences

Molecular characterization is a key step in the risk assessment of genetically modified organisms (GMOs) for regulatory approval. Herein, we describe a method for analyzing copy number, insertion loci, and flanking sequences through whole-genome sequencing (WGS) and bioinformatics. Comprehensive molecular characterization of G2-6 transgenic rice was performed using this pipeline. The results showed that one copy of the foreign gene was inserted into rice chromosome 8. There was no vector backbone insertion but an unexpected insertion and DNA rearrangement at the 3′ end of the T-DNA. We also obtained the 5′ and 3′ flanking sequences of the T-DNA. Our results suggested that the use of a combination of WGS and bioinformatics is an effective strategy for the molecular characterization of GMOs.

scholarly journals Comprehensive Characterization of Transgene Integration in a Similar Intragenesis Rice Event Using Paired-end Whole-genome Sequencing Approach

2021 ◽  
Author(s):  
Wenting Xu ◽  
Hanwen Zhang ◽  
Yuchen Zhang ◽  
Rong Li ◽  
Litao Yang
Keyword(s):  
Whole Genome Sequencing ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Rice Chromosome ◽  
Whole Genome ◽  
Transgene Integration ◽  
Gm Rice ◽  
Genome Level ◽  
Comprehensive Characterization

Abstract Efficient, accurate molecular characterization of genetically modified (GM) organisms is challenging, especially for novel transgenic products of cisgenesis/intragenesis transferred with genes/elements of recipient species. Herein, GM rice event G281, involving transfer with native promoters and an RNA interference (RNAi) expression cassette in a process similar to intragenesis, was subjected to molecular characterization using paired-end whole genome sequencing (PE-WGS). The results showed that transgenes integrated at rice chromosome 3 locus 16,439,674 included a 36 bp deletion of rice genomic DNA, and the whole integration contained two copies of the complete transfer DNA (T-DNA) in a head-to-head arrangement. No unintended insertion or backbone sequence of the transformed plasmid were observed at the whole genome level. Molecular characterization of the G281 event will assist risk assessment and application for a commercial license. Additionally, the findings demonstrate the applicability of PE-WGS for molecular characterization of cisgenesis/intragenesis crops.

scholarly journals Identification and Molecular Characterization of Recombinant Potato Virus Y (PVY) in Potato from South Korea, PVYNTN Strain

Plant Disease ◽  
2019 ◽  
Vol 103 (1) ◽  
pp. 137-142 ◽  
Author(s):  
Mohamad Chikh-Ali ◽  
Mariana Rodriguez-Rodriguez ◽  
Kelsie J. Green ◽  
Dong-Jun Kim ◽  
Sang-Min Chung ◽  
...  
Keyword(s):  
South Korea ◽  
Whole Genome Sequencing ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Potato Production ◽  
Whole Genome ◽  
Rt Pcr

Potato is an important source of food in South Korea, and viruses represent a significant threat to sustainable and profitable potato production. However, information about viruses affecting the potato crop in South Korea is limited. In 2017, potato plants of five cultivars exhibiting foliar mosaic, crinkling, and mottle were collected in two seed potato production areas, in Gangwon-do and Jeollabuk-do Provinces, and subjected to virus testing and characterization. Potato virus Y (PVY) was found associated with mosaic symptoms, and samples were characterized using reverse transcription polymerase chain reaction (RT-PCR) and whole genome sequencing. All analyzed PVY-positive samples were found to represent the same recombinant PVY strain: PVYNTN. Three PVY isolates were subjected to whole genome sequencing using overlapping RT-PCR fragments and Sanger methodology, and all three were confirmed to represent strain PVYNTNa after a recombination analysis of the complete genomes. In phylogenetic analysis, the three South Korean isolates were placed most closely to several PVYNTNa isolates reported from Japan and Vietnam, suggesting a common source of infection. This is the first report and complete molecular characterization of a PVYNTN strain present in the country, and because this strain induces tuber necrotic ringspot disease in susceptible cultivars of potato, appropriate management tools need to be implemented to mitigate potential tuber quality losses.

scholarly journals Molecular characterization of PRKN structural variations identified through whole-genome sequencing

2018 ◽  
Vol 6 (6) ◽  
pp. 1243-1248 ◽  
Author(s):  
Paloma Bravo ◽  
Hossein Darvish ◽  
Abbas Tafakhori ◽  
Luis J. Azcona ◽  
Amir Hossein Johari ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Structural Variations

scholarly journals Rapid identification, capsular typing and molecular characterization of Streptococcus pneumoniae by using whole genome nanopore sequencing

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
S. Garcia-Garcia ◽  
A. Perez-Arguello ◽  
D. Henares ◽  
N. Timoneda ◽  
C. Muñoz-Almagro
Keyword(s):  
Streptococcus Pneumoniae ◽  
Whole Genome Sequencing ◽  
Real Time ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Rapid Identification ◽  
Whole Genome ◽  
Genomic Epidemiology ◽  
Capsular Typing

Abstract Background Whole genome sequencing has emerged as a useful tool for identification and molecular characterization of pathogens. MinION (Oxford Nanopore) is a real-time third generation sequencer whose portability, affordability and speed in data production make of it an attractive device for whole genome sequencing. The objective of this study is to evaluate MinION sequencer for pathogen identification and molecular characterization of Streptococcus pneumoniae isolated at a children’s Hospital. Whole genome sequencing of 32 Streptococcus pneumoniae invasive isolates, previously characterized by standard methods (Quellung reaction, Multiplex PCR and Sanger-MLST), were performed. DNA was extracted using ZymoBIOMICS DNA Microprep kit. Quantification and purity of DNA was assessed by Qubit and Nanodrop, respectively. Library preparation was performed using the Rapid Barcoding Kit. Real-time workflow EPI2ME platform “What’s it in my pot” was used for species identification. Fast5 sequences were converted into FASTQ by Albacore software. Reads were assembled using CANU software. PathogenWatch, genomic epidemiology and pubmlst online tools were used for capsular typing and/or whole genome-MLST profile. Results Rapid identification of Streptococcus pneumoniae was achieved by “What’s in my pot”. Capsular typing was correctly assigned with PathogenWatch in all 32 isolates at serogroup level and 24 at serotype level. Whole genome-MLST results obtained by genomic epidemiology and pubmlst were consistent with double locus variant clonal complex obtained by Sanger-MLST in 31 isolates. Conclusion MinION sequencer provides a rapid, cost-effective and promising pathway for performing WGS by a pocked-sized device for epidemiological purposes but improving its sequencing accuracy will make it more appealing to be used in clinical microbiology laboratories.

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