Search results - 31 results
A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and In Silico Approaches
single nucleotide polymorphism VALIDATION whole genome sequencing Abstract: The use of whole genome sequencing (WGS) for routine typing of bacterial isolates has increased substantially in recent years. ...
Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection.
Polymorphism, Single Nucleotide Real-Time Polymerase Chain Reaction RNA Replicase RNA, Viral Sensitivity and Specificity whole genome sequencing Abstract: The current CO ronaVIrus Disease 2019 (COVID-19) pandemic ...
Use of a Whole Genome Sequencing-based approach for Mycobacterium tuberculosis surveillance in Europe in 2017-2019: an ECDC pilot study.
including both core genome multilocus sequence typing (cgMLST), and single nucleotide polymorphism (SNP)-based calculation of distances on all WGS data that fulfilled minimum quality criteria to ensure data ...
Phylogeography of Human and Animal Strains: Genetic Fingerprinting of Q Fever in Belgium.
reservoirs. To determine the relationship between animal and human strains, Multiple Locus Variable-number Tandem Repeat Analysis (MLVA) (n=146), Single-Nucleotide Polymorphism (SNP) (n=92) and Whole Genome ...
Development of a genoserotyping system for the identification of Salmonella serotypes
Paratyphi B var. Java where only one suitable marker could be retrieved among more than 3 million Single Nucleotide Polymorphism (SNP) positions obtained from a genomic comparison. This valuable SNP marker ...
Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates
multilocus sequence typing and single nucleotide polymorphism analysis). Shiga toxin-producing Escherichia coli (STEC) was selected as a case study. Overall, data quality and inferred phylogenetic ...
Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing
Mutation frequencies and single nucleotide polymorphisms were used for comparisons to address the level of natural intrinsic heterogeneity of influenza A viruses. Clear differences in single nucleotide ...
Data analysis associated with the use of whole genome sequencing for subtyping of pathogenic microorganisms, Salmonella Typhimurium as a case study
identification of a link between the origin of an infection and the human isolate in case of outbreak situations.Here, we have explored the possibilities offered by single nucleotide polymorphism (SNP)-based ...
Optimized MOL-PCR for Characterization of Microbial Pathogens
Oligonucleotide Probes Phycoerythrin polymerase chain reaction Polymorphism, Single Nucleotide Salmonella typhimurium Streptavidin Temperature Abstract: Characterization of microbial pathogens is necessary for ...
A multiplex oligonucleotide ligation-PCR as a complementary tool for subtyping of Salmonella Typhimurium
genomic island 1 (SGI1), allantoinase gene allB, MLVA locus STTR10, antibiotic resistance genes, single nucleotide polymorphisms (SNP s) and phase 2 flagellar gene fljB. The in vitro stability of these ...