Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform.

Details

Ressource 1Download: smw_148_w14693.pdf (739.77 [Ko])
State: Public
Version: Final published version
Serval ID
serval:BIB_185F2FAA4116
Type
Article: article from journal or magazin.
Publication sub-type
Review (review): journal as complete as possible of one specific subject, written based on exhaustive analyses from published work.
Collection
Publications
Institution
Title
Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform.
Journal
Swiss medical weekly
Author(s)
Egli A., Blanc D.S., Greub G., Keller P.M., Lazarevic V., Lebrand A., Leib S., Neher R.A., Perreten V., Ramette A., Schrenzel J., Stephan R., Wagner K., Wuethrich D., Xenarios I.
ISSN
1424-3997 (Electronic)
ISSN-L
0036-7672
Publication state
Published
Issued date
03/12/2018
Peer-reviewed
Oui
Volume
148
Pages
w14693
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Abstract
Facing multidrug resistant (MDR) bacterial pathogens is one of the most important challenges for our society. The spread of highly virulent and resistant pathogens can be described using molecular typing technologies; in particular, whole genome sequencing (WGS) data can be used for molecular typing purposes with high resolution. WGS data analysis can explain the spatiotemporal patterns of pathogen transmission. However, the transmission between compartments (human, animal, food, environment) is very complex. Interoperable and curated metadata are a key requirement for fully understanding this complexity. In addition, high quality sequence data are a key element between centres using WGS data for diagnostic and epidemiological applications. We aim to describe steps to improve WGS data analysis and to implement a molecular surveillance platform allowing integration of high resolution WGS typing data and epidemiological data.
Keywords
Bacteria/genetics, Bacteria/pathogenicity, Disease Outbreaks, Drug Resistance, Microbial, Genome, Bacterial/genetics, Humans, Molecular Epidemiology/organization & administration, Molecular Typing/methods, Population Surveillance/methods, Switzerland, Whole Genome Sequencing/methods, Whole Genome Sequencing/standards, Workflow
Pubmed
Open Access
Yes
Create date
20/12/2018 11:56
Last modification date
20/08/2019 13:48
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