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Laboratory capability for molecular detection and confirmation of novel coronavirus in Europe, November 2012287
other target RT- PCR assays with sequence analysis or whole-genome sequence analysis was available in 22/46 responding countries of which 18/30 in EU / EEA countries Service: Virale ziekten Viral ...
DNase SISPA-next generation sequencing confirms Schmallenberg virus in Belgian field samples and identifies genetic variation in Europe.
4.27-4.89 log(10) RNA copies per µL did not allow identification using DN ase SISPA- NGS. This partial sequence information was compared to the whole genome sequence of SBV isolated from bovines in Germany, ...
Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates.
C.J. De Keersmaecker Source: Sci Rep, Volume 10, Issue 1 (2020) Keywords: NGS pathogenic E. coli STEC WGS Abstract: Whole genome sequencing (WGS) has proven to be the ultimate tool for bacterial isolate ...
Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei.
antimicrobials, including the fluoroquinolones. Here we analyse nearly 400 S. sonnei whole genome sequences from both endemic and non-endemic regions to delineate the evolutionary history of the recently emergent ...
Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198.
an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S.enterica serotype Kentucky sequence type 198 isolates ...
Integrative transnational analysis to dissect tuberculosis transmission events along the migratory route from Africa to Europe.
Mycobacterium tuberculosis isolates from these recently arrived migrants were analysed by Mycobacterial Interspersed Repetitive-Unit/Variable-Number of Tandem Repeat (MIRU- VNTR) and subsequent whole genome ...
Whole-genome-based phylogenomic analysis of the Belgian 2016-2017 influenza A(H3N2) outbreak season allows improved surveillance.
technologies enable a shift to whole-genome sequencing (WGS) for influenza surveillance, but this requires laboratory workflow adaptations and advanced bioinformatics workflows. In this study, 253 influenza ...
The AMR-ARRAY: A modular bead array detecting β-lactam, (fluoro) quinolone, colistin, aminoglycoside and macrolide resistance determinants in Gram-negative bacteria.
(856/904) of the assessed resistances. When compared to resistance profiles inferred from whole genome sequencing results, the AMR- ARRAY showed a selectivity and specificity of 99.3% and 100%, respectively. ...
High-resolution melting PCR analysis for rapid genotyping of Burkholderia mallei.
genome sequences of 45 B. mallei isolates identified 3 lineages for this species. In this study, we designed a high-resolution melting (HRM) method for the screening of 15 phylogenetically informative SNP ...
Development and evaluation of a core genome multilocus sequence typing scheme for Paenibacillus larvae, the deadly American foulbrood pathogen of honeybees.
this approach has limited resolution, especially for epidemiological studies. As the cost of whole-genome sequencing has decreased and as it becomes increasingly available to most laboratories, an ...