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; Keller, Peter Michael; Lazarevic, Vladimir; Lebrand, Aitana; Leib, Stephen; Neher, Richard A; Perreten, Vincent; Ramette, Alban Nicolas; Schrenzel, Jacques; Stephan, Roger; Wagner, Karolin; Wuethrich, Daniel; Xenarios, Ioannis (2018). Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform. Swiss medical weekly, 148(w14693), w14693. EMH Media 10.4414/smw.2018.14693

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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.

Item Type:

Journal Article (Review Article)

Division/Institute:

05 Veterinary Medicine > Department of Infectious Diseases and Pathobiology (DIP) > Institute of Veterinary Bacteriology > Molecular Bacterial Epidemiology and Infectiology
05 Veterinary Medicine > Research Foci > Host-Pathogen Interaction
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Research
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Clinical Microbiology
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Mycobacteriology
05 Veterinary Medicine > Department of Infectious Diseases and Pathobiology (DIP) > Institute of Veterinary Bacteriology

UniBE Contributor:

Keller, Peter Michael; Leib, Stephen; Perreten, Vincent and Ramette, Alban Nicolas

Subjects:

600 Technology > 630 Agriculture
500 Science > 570 Life sciences; biology
600 Technology > 610 Medicine & health

ISSN:

1424-3997

Publisher:

EMH Media

Language:

English

Submitter:

Stephen Leib

Date Deposited:

11 Feb 2019 12:14

Last Modified:

24 Oct 2019 00:50

Publisher DOI:

10.4414/smw.2018.14693

PubMed ID:

30552858

BORIS DOI:

10.7892/boris.123341

URI:

https://boris.unibe.ch/id/eprint/123341

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