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

Egli, Adrian; Blanc, Dominique S; Greub, Gilbert Daniel; Keller, Peter M; Lazarevic, Vladimir; Lebrand, Aitana; Leib, Stephen; Neher, Richard A; Perreten, Vincent; Ramette, Alban; Schrenzel, Jacques; Stephan, Roger; Wagner, Karolin; Wuethrich, Daniel; Xenarios, Ioannis

doi:10.4414/smw.2018.14693

Scientific article

Review

Open access

English

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

ContributorsEgli, Adrian; Blanc, Dominique S; Greub, Gilbert Daniel; Keller, Peter M; Lazarevic, Vladimir

; Lebrand, Aitana; Leib, Stephen; Neher, Richard A; Perreten, Vincent; Ramette, Alban; Schrenzel, Jacques; Stephan, Roger; Wagner, Karolin; Wuethrich, Daniel; Xenarios, Ioannis

Published inSwiss Medical Weekly, vol. 148, no. w14693, p. 1-10

Publication date2018

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/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/standards
Workflow

Affiliation

Research group

Analyse génomique et fonctionnelle du staphylocoque doré (604)

Funding

Swiss National Science Foundation - Grant Nr. 407240_177504/1

Citation (ISO format)

EGLI, Adrian et al. Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform. In: Swiss Medical Weekly, 2018, vol. 148, n° w14693, p. 1–10. doi: 10.4414/smw.2018.14693