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Detailed Evaluation of Data Analysis Tools for Subtyping of Bacterial Isolates Based on Whole Genome Sequencing: as a Proof of Concept.

Volume 10 (2019) Abstract: Whole genome sequencing is increasingly recognized as the most informative approach for characterization of bacterial isolates. Success of the routine use of this technology in ...

Comparative Analysis of Whole-Genome Sequence of African Swine Fever Virus Belgium 2018/1.

25, Issue 6 (2019) Abstract: We analyzed the whole-genome sequence of African swine fever virus Belgium 2018/1. The strain fits into the European genotype II (>99.98% identity). The high-coverage ...

Development of a real-time PCR method for the genoserotyping of Salmonella Paratyphi B variant Java.

biochemical tests. Therefore, a quadruplex real-time PCR method, based on the allelic discrimination of molecular markers selected from the scientific literature and from whole genome sequencing data produced ...

Shifting national surveillance of Shigella infections toward geno-serotyping by the development of a tailored Luminex assay and NGS workflow.

respectively. All discrepancies were analyzed with whole-genome sequencing and shown to be related to causative mutations (stop codons, indels, and promoter mutations) in glycosyltransferase genes. This ...

Occurrence and identification of spore-forming bacteria in skim-milk powders

manufacturing environments. Using whole genome sequencing, 16 of 23 isolates identified as  B.  licheniformis  by 16S sequencing were confirmed as  B.  licheniformis, four were identified as  Bacillus ...

Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing

determine the whole genome genetic heterogeneity of the three categories of influenza A viruses that circulated in humans between 2007 and 2012 in France, directly from clinical respiratory specimens. ...

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

susceptibility to first-line antituberculosis drugs has not been clear. METHODS: We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis ...

Application of whole genome data for in silico evaluation of primers and probes routinely employed for the detection of viral species by RT-qPCR using dengue virus as a case study.

targeted nucleic acid regions. Whole genome sequencing allows to characterize and track such changes, which in turn enables to evaluate, optimize, and (re-)design novel and existing RT-qPCR methods. The ...

Preparing cDNA Libraries from Lytic Phage-Infected Cells for Whole Transcriptome Analysis by RNA-Seq.

Bacteriophage RNA-seq Abstract: Whole genome wide analysis of transcription using RNA-Seq methods is a powerful way to elucidate differential expression of gene features in bacteria across different conditions as ...

Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5],12:i:.

Salmonella; Salmonella enterica; Salmonella typhimurium; SNP; subtyping; whole genome sequencing Abstract: Whole genome sequencing represents a promising new technology for subtyping of bacterial pathogens. ...

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