@article{egli_improving_2018,
 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.},
 area = {influenza, virus_evolution},
 author = {Egli, Adrian and Blanc, Dominique S. and Greub, Gilbert and Keller, Peter M. and Lazarevic, Vladimir and Lebrand, Aitana and Leib, Stephen and Neher, Richard A. and Perreten, Vincent and Ramette, Alban and Schrenzel, Jacques and Stephan, Roger and Wagner, Karolin and Wuethrich, Daniel and Xenarios, Ioannis},
 date = {2019-01-04},
 doi = {10.4414/smw.2018.14693},
 file = {Full Text:/home/richard/.mozilla/firefox/1i8d13g2.default/zotero/storage/TUY4JRCP/Egli et al. - 2018 - Improving the quality and workflow of bacterial ge.pdf:application/pdf},
 issn = {1424-3997},
 journal = {Swiss Medical Weekly},
 keywords = {Bacteria, Disease Outbreaks, Drug Resistance, Microbial, Genome, Bacterial, Humans, Molecular Epidemiology, Molecular Typing, Population Surveillance, Switzerland, Whole Genome Sequencing, Workflow},
 language = {eng},
 pages = {w14693},
 pmid = {30552858},
 shorttitle = {Improving the quality and workflow of bacterial genome sequencing and analysis},
 title = {Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a {Switzerland}-wide molecular epidemiological surveillance platform},
 volume = {148},
 year = {2018}
}