whole-genome sequencing, molecular surveillance
Short Read Whole Genome Sequencing for Laboratory Based Surveillance of Bordetella pertussis
... Ongoing molecular surveillance of ...short-read whole-genome sequencing data generated from 40 clinical ...pertussis molecular data that can be linked to clinical and ...
8
Whole Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe
... targeted surveillance and containment at the population ...of sequencing entire bacterial genomes in steady decline and the de- velopment of powerful bioinformatic tools gathering pace, whole- ...
15
Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole Genome Sequencing Single Nucleotide Polymorphism Based Analysis for Surveillance and Outbreak Detection
... next-generation sequencing technologies have made it possible to examine whole-genome sequencing (WGS) as a potential molecular subtyping tool for outbreak detec- tion and source trace ...
7
Genomics for Molecular Epidemiology and Detecting Transmission of Carbapenemase Producing Enterobacterales in Victoria, Australia, 2012 to 2016
... genomic surveillance is critical to effectively manage this ...and whole-genome sequencing (WGS) methods and com- pared with epidemiological ...
12
Same Day Diagnostic and Surveillance Data for Tuberculosis via Whole Genome Sequencing of Direct Respiratory Samples
... the molecular determinants of antibiotic resistance (1), we have developed a method of extracting and purifying mycobacterial DNA from primary clinical samples and producing accurate sequence data in a clinically ...
14
Application of Whole Genome Sequencing for Bacterial Strain Typing in Molecular Epidemiology
... Clinical surveillance and investigation of nosocomial out- breaks are primarily dependent on determining whether biogeo- graphically related pairs of strains are clonal and thus on whether they could have ...
8
Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitis outbreak
... on whole genome se- quencing by NGS technology, comparative genomics, and gene function prediction was set up and applied to investi- gate ...standard molecular typing methods based on PFGE, MLST, ...
8
Same day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples
... the molecular determinants of antibiotic resistance (1), we have developed a method of extracting and purifying mycobacterial DNA from primary clinical samples and producing accurate sequence data in a clinically ...
14
Whole genome sequencing for surveillance of antimicrobial resistance in Actinobacillus pleuropneumoniae
... with surveillance of AMR, with calls for a more standardized method to allow direct comparisons between labs (Michael et ...for surveillance of AMR in ...resistance. Genome sequencing not only ...
6
Unbiasing in the Genome Analysis of Iconic Shark Species
... (XP_020377040.1 in NCBI; presented in Figure 3 by Marra et al. (1)) seems to harbor a wrong open reading frame (ORF) possibly due to problems in genome assembly. The error causes a remarkable dissimilarity to ...
5
Whole-Exome/Genome Sequencing and Genomics
... fi ltering; that is, the discarding of those variants judged, by a number of rules, as likely to be nonpathogenic. Even after that, however, it is not un- common to be left with several hun- dred variants that are ...
7
Whole Genome Sequencing of Invasion Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion
... cells. Whole-genome sequencing and transcriptome sequencing (RNA-Seq) uncovered a deletion in the gene encoding the laminin subunit ␣ 2 (Lama2) that eliminated much of domain ...
11
What’s in a Name? Species Wide Whole Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B
... This work underlines the difficulty posed when genomic ap- proaches are not used to subdivide lineages and exemplifies the challenges that face classical typing, reinforcing the need for un- ambiguous molecular ...
9
Clinical Laboratory Response to a Mock Outbreak of Invasive Bacterial Infections: a Preparedness Study
... iar or initially unknown, or the pathogen grew slowly or re- quired biosafety level 3 containment, the pace of our response would have been slowed. Also, the existence of multiple high- quality, well-annotated, closed ...
7
<p>Genomic and Phenotypic Diversity of <em>Listeria monocytogenes</em> Causing Pregnancy-Associated Listeriosis from Zhejiang Province, China, 2016–2018</p>
... In addition to the 13 genomes generated in this work, 82 publicly available L. monocytogenes genomes from China were selected to determine the evolutionary relationship among L. monocytogenes (Table S1). The isolate ...
6
Whole genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes
... short-read whole-genome sequencing data from the Ag1000G Phase 2 data set to find genomic regions with increased read coverage relative to the genomic average, controlling for GC richness and ...
13
Selective Whole Genome Amplification Is a Robust Method That Enables Scalable Whole Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples
... Eighteen whole-blood samples used for additional testing and further sequencing analysis were derived from whole-blood samples collected from patients with symptomatic ...microscopists. ...
15
Draft genome of the Arabidopsis thaliana phyllosphere bacterium, Williamsia sp. ARP1
... the 4509 predicted genes, 4438 (98.42 %) were protein- coding, and 3505 (77.73 %) annotated with putative func- tion. Pseudogenes were not detected. Genes not linked to a function were annotated as hypothetical or ...
11
Circulating Tumour DNA in Muscle-Invasive Bladder Cancer.
... amplicon sequencing (TAm-Seq) using a bladder cancer-specific panel of eight genes to detect mutant DNA in TUR tumour tissue, plasma, urinary cell pellet (UCP), and urinary supernatant ...shallow whole ...
14
A protocol for the identification and validation of novel genetic causes of kidney disease
... generation sequencing bioinfor- matics (RT, CS or delegate), one coopted clinical geneticist (CP, MG, JM or delegate), and one coopted medical spe- cialist in the field to which the potential disease pertains (eg ...
10