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

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

doi:10.4414/smw.2018.14693

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

Swiss Med Wkly. 2018 Dec 15:148:w14693. doi: 10.4414/smw.2018.14693. eCollection 2018 Dec 3.

Authors

Affiliations

¹ Division of Clinical Microbiology, University Hospital Basel, Switzerland /Applied Microbiology Research, Department of Biomedicine, University of Basel, Switzerland.
² Hospital Preventive Medicine Service, Lausanne University Hospital, Switzerland.
³ Institute for Microbiology, Lausanne University Hospital, Switzerland.
⁴ Institute of Microbiology, University of Zurich, Switzerland.
⁵ Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Switzerland.
⁶ SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
⁷ Institute for Infectious Diseases, University of Bern, Switzerland.
⁸ SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; Biozentrum, University of Basel, Switzerland.
⁹ Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Switzerland.
¹⁰ Institute for Infectious Diseases, University of Bern, Switzerland; Swiss Centre for Antibiotic Resistance (anresis.ch), Institut für Infektionskrankheiten, University of Bern, Switzerland.
¹¹ Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Switzerland; Genomic Research Laboratory, Division of Infectious Diseases, Geneva University Hospitals, Switzerland.
¹² Institute for Food Safety, Vetsuisse Faculty, University of Zurich, Switzerland.
¹³ Division of Clinical Microbiology, University Hospital Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Switzerland.

PMID: 30552858
DOI: 10.4414/smw.2018.14693

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.

MeSH terms

Bacteria / genetics
Bacteria / 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*
Whole Genome Sequencing / standards
Workflow*