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Bacterial genome sequencing and analysis: paving the way for a Swiss-wide molecular epidemiological surveillance platform


Egli, Adrian; Blanc, Dominique S; Greub, Gilbert; Keller, Peter M; Lazarevic, Vladimir; Lebrand, Aitana; Leib, Stephen; Neher, Richard A; Perreten, Vincent; Ramette, Alban; Schrenzel, Jaques; Stephan, Roger; Wagner, Karoline; Wüthrich, Daniel; Xenarios, Ioannis (2018). Bacterial genome sequencing and analysis: paving the way for a Swiss-wide molecular epidemiological surveillance platform. Swiss Medical Weekly, 148:w14693.

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 usedf or 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.

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 usedf or 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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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:05 Vetsuisse Faculty > Institute of Food Safety and Hygiene
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
Scopus Subject Areas:Health Sciences > General Medicine
Uncontrolled Keywords:next generation sequencing,whole genomesequencing,molecular epidemiology,typing,quality as-sessment,quality control,ring trial,surveillance database,Swiss pathogen surveillance platform
Language:English
Date:2018
Deposited On:11 Feb 2019 12:09
Last Modified:26 Jan 2022 21:02
Publisher:EMH Swiss Medical Publishers
ISSN:0036-7672
OA Status:Gold
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.4414/smw.2019.14707

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