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

Adrian Egli | Zendy; Dominique Blanc | Zendy; Gilbert Greub | Zendy; Peter M. Keller | Zendy; Vladimir Lazarević | Zendy; Aitana Lebrand | Zendy; Stephen L. Leib | Zendy; Richard A. Neher | Zendy; Vincent Perreten | Zendy; Alban Ramette | Zendy; Jacques Schrenzel | Zendy; Roger Stephan | Zendy; Karolin Wagner | Zendy; Daniel Wuethrich | Zendy; Ioannis Xénarios | Zendy

Open Access

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

Author(s) -

Adrian Egli,

Dominique Blanc,

Gilbert Greub,

Peter M. Keller,

Vladimir Lazarević,

Aitana Lebrand,

Stephen L. Leib,

Richard A. Neher,

Vincent Perreten,

Alban Ramette,

Jacques Schrenzel,

Roger Stephan,

Karolin Wagner,

Daniel Wuethrich,

Ioannis Xénarios

Publication year - 2018

Publication title -

schweizerische medizinische wochenschrift

Language(s) - English

Resource type - Journals

ISSN - 0036-7672

DOI - 10.4414/smw.2018.14693

Subject(s) - workflow , interoperability , transmission (telecommunications) , computational biology , whole genome sequencing , typing , metadata , data quality , genome , data science , medicine , computer science , genetics , biology , world wide web , database , gene , telecommunications , metric (unit) , operations management , economics

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.

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