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


Egli, A; Blanc, D; Greub, G; Keller, P; Lazarevic, V; Lebrand, A; Leib, S; Neher, R; Perreten, V; Ramette, A; Schrenzel, J; Stephan, R; Wagner, K; Wüthrich, D; Xenarios, I (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 isone of the most important challenges for our society. Thespread of highly virulent and resistant pathogens can bedescribed using molecular typing technologies; in particu-lar, whole genome sequencing (WGS) data can be usedfor molecular typing purposes with high resolution. WGSdata analysis can explain the spatiotemporal patterns ofpathogen transmission. However, the transmission be-tween compartments (human, animal, food, environment)is very complex. Interoperable and curated metadata area key requirement for fully understanding this complexity.In addition, high quality sequence data are a key elementbetween centres using WGS data for diagnostic and epi-demiological applications. We aim to describe steps to im-prove WGS data analysis and to implement a molecularsurveillance platform allowing integration of high resolu-tion WGS typing data and epidemiological data

Abstract

Facing multidrug resistant (MDR) bacterial pathogens isone of the most important challenges for our society. Thespread of highly virulent and resistant pathogens can bedescribed using molecular typing technologies; in particu-lar, whole genome sequencing (WGS) data can be usedfor molecular typing purposes with high resolution. WGSdata analysis can explain the spatiotemporal patterns ofpathogen transmission. However, the transmission be-tween compartments (human, animal, food, environment)is very complex. Interoperable and curated metadata area key requirement for fully understanding this complexity.In addition, high quality sequence data are a key elementbetween centres using WGS data for diagnostic and epi-demiological applications. We aim to describe steps to im-prove WGS data analysis and to implement a molecularsurveillance platform allowing integration of high resolu-tion 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
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:11 Feb 2019 18:09
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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