Whole-genome sequencing for routine pathogen surveillance in public health: A population snapshot of invasive Staphylococcus aureus in Europe

ESCMID Study Group on Molecular Epidemiological Markers (ESGEM), European Staphylococcal Reference Laboratory Working Group

Research output: Contribution to journalArticle

79 Citations (Scopus)

Abstract

The implementation of routine whole-genome sequencing (WGS) promises to transform our ability to monitor the emergence and spread of bacterial pathogens. Here we combined WGS data from 308 invasive Staphylococcus aureus isolates corresponding to a pan-European population snapshot, with epidemiological and resistance data. Geospatial visualization of the data is made possible by a generic software tool designed for public health purposes that is available at the project URL (http:// www.microreact.org/project/EkUvg9uY?tt=rc). Our analysis demonstrates that high-risk clones can be identified on the basis of population level properties such as clonal relatedness, abundance, and spatial structuring and by inferring virulence and resistance properties on the basis of gene content. We also show that in silico predictions of antibiotic resistance profiles are at least as reliable as phenotypic testing. We argue that this work provides a comprehensive road map illustrating the three vital components for future molecular epidemiological surveillance: (i) large-scale structured surveys, (ii) WGS, and (iii) communityoriented database infrastructure and analysis tools. IMPORTANCE The spread of antibiotic-resistant bacteria is a public health emergency of global concern, threatening medical intervention at every level of health care delivery. Several recent studies have demonstrated the promise of routine wholegenome sequencing (WGS) of bacterial pathogens for epidemiological surveillance, outbreak detection, and infection control. However, as this technology becomes more widely adopted, the key challenges of generating representative national and international data sets and the development of bioinformatic tools to manage and interpret the data become increasingly pertinent. This study provides a road map for the integration of WGS data into routine pathogen surveillance. We emphasize the importance of large-scale routine surveys to provide the population context for more targeted or localized investigation and the development of open-access bioinformatic tools to provide the means to combine and compare independently generated data with publicly available data sets.

Original languageEnglish
Article numbere00444-16
JournalmBio
Volume7
Issue number3
DOIs
Publication statusPublished - May 1 2016

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Public Health Surveillance
Staphylococcus aureus
Genome
Computational Biology
Population
Public Health
Infection Control
Microbial Drug Resistance
Computer Simulation
Health Status
Disease Outbreaks
Virulence
Emergencies
Software
Clone Cells
Databases
Anti-Bacterial Agents
Technology
Bacteria
Delivery of Health Care

ASJC Scopus subject areas

  • Microbiology
  • Virology

Cite this

ESCMID Study Group on Molecular Epidemiological Markers (ESGEM), European Staphylococcal Reference Laboratory Working Group (2016). Whole-genome sequencing for routine pathogen surveillance in public health: A population snapshot of invasive Staphylococcus aureus in Europe. mBio, 7(3), [e00444-16]. https://doi.org/10.1128/mBio.00444-16

Whole-genome sequencing for routine pathogen surveillance in public health : A population snapshot of invasive Staphylococcus aureus in Europe. / ESCMID Study Group on Molecular Epidemiological Markers (ESGEM), European Staphylococcal Reference Laboratory Working Group.

In: mBio, Vol. 7, No. 3, e00444-16, 01.05.2016.

Research output: Contribution to journalArticle

ESCMID Study Group on Molecular Epidemiological Markers (ESGEM), European Staphylococcal Reference Laboratory Working Group 2016, 'Whole-genome sequencing for routine pathogen surveillance in public health: A population snapshot of invasive Staphylococcus aureus in Europe', mBio, vol. 7, no. 3, e00444-16. https://doi.org/10.1128/mBio.00444-16
ESCMID Study Group on Molecular Epidemiological Markers (ESGEM), European Staphylococcal Reference Laboratory Working Group. Whole-genome sequencing for routine pathogen surveillance in public health: A population snapshot of invasive Staphylococcus aureus in Europe. mBio. 2016 May 1;7(3). e00444-16. https://doi.org/10.1128/mBio.00444-16
ESCMID Study Group on Molecular Epidemiological Markers (ESGEM), European Staphylococcal Reference Laboratory Working Group. / Whole-genome sequencing for routine pathogen surveillance in public health : A population snapshot of invasive Staphylococcus aureus in Europe. In: mBio. 2016 ; Vol. 7, No. 3.
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